Review The Code of

Harikrishnareddy Paluvai, Eros Di Giorgio and Claudio Brancolini *

Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine, Italy; [email protected] (H.P.); [email protected] (E.D.G.) * Correspondence: [email protected]

 Received: 2 February 2020; Accepted: 17 February 2020; Published: 18 February 2020 

Abstract: Senescence is the end point of a complex cellular response that proceeds through a set of highly regulated steps. Initially, the permanent -cycle arrest that characterizes senescence is a pro-survival response to irreparable DNA damage. The maintenance of this prolonged condition requires the adaptation of the cells to an unfavorable, demanding and stressful microenvironment. This adaptation is orchestrated through a deep epigenetic resetting. A first wave of epigenetic changes builds a dam on irreparable DNA damage and sustains the pro-survival response and the cell-cycle arrest. Later on, a second wave of epigenetic modifications allows the genomic reorganization to sustain the of pro-inflammatory genes. The balanced epigenetic dynamism of senescent cells influences physiological processes, such as differentiation, embryogenesis and aging, while its alteration leads to , and premature aging. Here we provide an overview of the most relevant histone modifications, which characterize senescence, aging and the activation of a prolonged DNA damage response.

Keywords: DNA damage; OIS; RS; SIPS; SAHF; SASP

1. Introduction Aging is a physiological condition characterized by the functional deficit of tissues and organs due to the accumulation of senescent cells [1]. The key role of senescence in aging is well-established. Clearance of senescent cells in mouse models delays the appearance of age-related tissue and organ disfunctions [2,3]. Senescent cells are characterized by the permanent cell-cycle arrest sustained by the accumulation of cyclin-dependent kinase inhibitors/CDKi), like , and p27, as well as by the release of , chemokines and soluble factors. This modified microenvironment is known as senescence-associated secretory (SASP) [4]. The senescence state is triggered by different stimuli/stressors. These include the shortening of the (replicative senescence), the -induced replication stress, the oncogene-induced senescence (OIS), the accumulation of misfolded protein and/or (stress-induced premature senescence, SIPS) [5]. The impairment of the non-homologous end joining (NHEJ) and (HR) repair mechanisms are common traits of senescent cells [6–9]. Moreover, a widespread epigenetic resetting characterizes senescent cells and sustains cell-cycle arrest and cellular survival, through the activation of (i) CDKi [10,11], (ii) tumor suppressors [12], and (iii) secretion of chemokines and cytokines, as well as the remodeling of the microenvironment [13]. Macroscopically, senescent cells are characterized by the formation of peculiar areas of , named as SAHF (senescence-associated heterochromatin foci), mainly at E2F loci [14]. However, SAHF do not characterize all senescent cells [15] and are not causally linked to the onset of senescence [16]. Other epigenetic features, like the distension of satellites (senescence-associated distension of satellites, SADS) [17], the re-activation of transposable elements, and of endogenous retroviruses (ERV) [18,19], seem to better qualify different types of senescence. Finally, aging appears

Cells 2020, 9, 466; doi:10.3390/cells9020466 www.mdpi.com/journal/cells Cells 2020, 9, 466 2 of 18 to be marked by substantial re-arrangements of the , with the loss of H3 and H4 [20,21]. During senescence the epigenome undergoes temporal and sequential modifications that are mandatory to accomplish different cellular adaptations. Initially, this epigenetic resetting is mainly due to the accumulation of irreparable DNA damage. After this first wave of epigenetic modifications, the epigenome is remodeled and fixed in order to sustain the permanent cell-cycle arrest and to modulate the microenvironment.

2. The Epigenome of Replicative Senescence (RS) The telomeric TTAGGG repeats at ends protect the genome from degradation and distinguish natural ends from double-strand breaks (DSBs) [5,22,23]. Histone and non-histone (Shelterin) proteins sustain the folding of telomeric repeats in high-order structures that acquire a G-quadruplex shape as a consequence of Hoogsteen base pairing between consecutive guanines [24]. The loss of active telomerase complexes in somatic human cells blocks the lengthening of the telomeric ends. As a consequence, for each successful , telomeres get shorter and is restricted. This phenomenon is defined as replicative senescence (RS) [25]. The accumulation of irreparable DNA damage triggered during RS leads to permanent cell-cycle arrest and is considered among the main driving forces of aging [22].

2.1. Histone Variants The progressive accumulation of double-strand breaks (DSBs) at the chromosome ends is coupled with a deep epigenetic resetting that can be observed in pre-senescent cells, even distal from telomeres. This epigenetic repertoire builds up an epigenetic clock that dictates the replicative potential of human cells [26]. Late passage IMR90 and WI38 human fibroblasts are characterized by a reduced expression of core and H4 [21], of the linker histone H1 [27] and of the histone chaperons ASF1A/B and CAF1-p150/p60 [28]. While the decreased levels of H3 and H4 are due to reduced neosynthesis and increased mRNA degradation [21,29], H1 is post-translationally regulated [27]. Moreover, alternative spliced histone mRNAs belonging to the HIST1 cluster are reported to be accumulated in quiescent and RS-arrested human fibroblasts [30]. The epigenome of RS cells is also characterized by the deposition, at certain genomic loci, of the histone variants H3.3 [31], H2A.J [32] and by the release of genomic DNA from H2A.Z [33–35] (Table1). This redistribution results in and promotes the transcription of (i) tumor suppressors [30,31], (ii) inflammatory genes marking the SASP, [32] and iii) the cleavage of H3.3, which mediates the repression of E2F/RB target genes [31]. While in senescence, the HIRA-mediated deposition of H3.3 sustains cell-cycle arrest [31], and in embryonic stem cells ATRX and DAXX recruit H3.3 to repress the transcription of endogenous retroviruses (ERVs) [36]. It is possible that the redistribution of H3.3 between the proliferating and senescent cells, which depends on the detachment from ATRX/DAXX and the complexing to HIRA, is at the basis of the activation of ERVs observed in senescence [37] and aging [38]. The regulated deposition of all these histone variants is necessary [30] and sufficient to sustain cell-cycle arrest [31]. Interestingly, genes encoding these histone variants are frequently mutated in cancer, in confirmation of their tumor-suppressive properties [30,39].

2.2. SAHF an Open Question? The HIRA chaperone complex (HIRA/UBN1/CABIN1) controls both the deposition of H3.3 [30] and SAHF formation [40]. SAHF accumulation of //macroH2A blocks on E2F loci characterizes OIS and cells undergoing oncogene-induced replication stress [15]. However, RS is not uniformly characterized by the formation of SAHF [41]. In fact, focused heterochromatinization of E2F loci maintains cell-cycle arrest, also in cells described as SAHF-negative (e.g., BJ and MEFs) [41,42]. SAHF are defined as DAPI-dense nuclear regions characterized by the presence of a central core of Cells 2020, 9, 466 3 of 18 condensed chromatin, enriched for H3K9me3 and macroH2A. This core is surrounded by a peripheral ring of H3K27me3 [43,44]. SAHF formation requires p16/INK4 and consists of a deep and focused heterochromatin re-organization [45]. This reorganization is HMGA1/ASF1/HIRA-dependent [40,46] and is triggered by the GSK3β-mediated HIRA re-localization at PML bodies [47]. Even though SAHF dismantling, achieved through HMGA1 [46], ASF1 [40] or GSK3β knockdown [48], allows senescence escape, BJ fibroblasts and Hutchinson–Gilford syndrome (HGPS) cells enter senescence with minimal or no signs of SAHF formation. On the opposite, the SAHF formation in HMEC and MCF10A mammary cells in response to H-RAS/G12V over-expression fails to bring the cells to senescence [15]. Whether SAHF formation is only due to the arising of replication stress and could act as a barrier to DNA double-strand breaks spreading [15], or could mark chromatin regions stitched between remodeled LAD domains [45], needs further investigation. It is possible that a better definition of the SAHF, achieved through the improvement of the resolution of confocal nanoscopy and of ChIP-seq histone mapping, will clarify the debated role played by SAHF in senescence.

2.3. Histone Modifications A global decrease in /3 and but increase in H3K9me1 levels in gene bodies characterize RS in human fibroblasts [49,50]. By contrast, the heterochromatin marker H3K27me3 and the euchromatin marker are mostly redistributed with respect to proliferating cells (Table2). This redistribution correlates well with the expression profile of senescent cells [51–53]. A different behavior was reported for the repressive mark H4K20me3 and the activating mark . Although they are enriched in the regulative elements of genes modulated during RS, they do not correlate with changes observed in senescent cells [30,54]. This apparent paradox could stem from the masking effect imposed by the senescence-specific activation of super-enhancers (marked by /) and the activation of neighbor genes involved in SASP and metabolism [55]. A detailed comparison of H3K4me3 and H3K27me3 levels in proliferating and senescent human evidenced large-scale chromatin modifications during RS [56]. In senescent cells the augmented levels of H3K4me3 and H3K27me3 frequently co-localize in areas defined “mesas” that extend for hundreds of kilobases. Larger domains of RS genome (up to 10Mb) and defined “canyons” are characterized by decreased levels of H3K27me3 [56]. H3K4me3 and H3K27me3 mesas colocalize in LMNB1-associated domains and overlap DNA hypomethylation. Instead, canyons are enriched in gene bodies and enhancers and H3K27me3 loss correlates with the up-regulation of senescent transcriptional programs [56].

2.4. Nuclear Lamins The loss of LMNB1 typifies all senescence conditions [57] and triggers a deep re-modelling of lamina-associated domains (LADs) [44,56]. LADs re-modelling contributes to re-organizing not only heterochromatin and SAHF [44], but also euchromatin (eLADs) [58]. Moreover, the knockdown of LMNB1 in proliferating cells promotes the premature senescence and gives rise to a H3K4me3 /H3K27me3 re-organization similarly to what observed in RS, OIS and HGPS [56]. However, LMNB1 re-expression in RIS senescent cells does not overcome the proliferation of arrest and does not repair nuclear membrane blebbing [59]. It is still unknown if the re-expression of LMNB1 in senescent cells is strong enough to re-establish normal LAD domains or if the co-expression of an epigenetic regulator is needed. Similarly, the ectopic expression of lamina-associated polypeptide 2α restores the proliferation of HGPS cells [60], characterized by the expression of the form of LMNA [61,62]. Unfortunately, the impact of LAP2α expression on LAD domains has not been explored yet. The re-localized LAD domains in RS are characterized also by a general DNA hypomethylation that affects LINE and SINE repetitive elements and pericentromeric satellites [17]. This hypomethylation triggers the general distension of the chromatin associated to these genomic regions (senescence-associated distension of satellites or SADS) and their de-repression [17]. The activation of centromeric and Cells 2020, 9, 466 4 of 18 pericentromeric satellite repeats is associated with their exclusion from nucleoli compartments, while all the other nucleoli-associated domains (NADs) are significantly altered in senescent cells [63]. Despite LADs redistribution, 3D chromatin organization of human dermal fibroblasts (HDFs) is only partially altered when proliferating, quiescent and senescent cells are compared. A modest gain of short-range and the loss of long-range intra-chromosome interactions in permanently arrested cells was observed [64]. More evident in quiescent and senescent cells is the switch of topologically associated domains (TADs) from euchromatin areas (Hi-C compartment A) to heterochromatin (Hi-C compartment B) and vice versa. This remodeling reflects the transcriptional status of cell-cycle-associated genes [64]. Most of the heterochromatinization is due to condensin mobilization [65] and PRC2 (EZH2) deposition [66], while MLL1 plays a role in mediating euchromatinization [67,68]. Moreover, RS cells lose the TADs associated to the telomeres [69].

2.5. The CpG Clock In general, DNA methylation during aging progressively involve both hypomethylation and hypermethylation events. Importantly, the methylation status of a limited number of well-defined CpG islands associate well with human aging [26]. The quantification of the methylation rate of these CpG island allows a good prediction of human biological age [26,70–72]. According to these estimations, the methylome of men ages 4% faster than women [70]. Moreover, the methylation clock is accelerated in patients affected by neurodegenerative diseases [73–75], chronic stress and insomnia [76], as well as in two premature aging disorders like Werner’s syndromes and Hutchinson–Gilford Progeria syndrome [76,77], while it is subverted in cancer [78,79]. Aging is characterized by hypomethylation [41] and this correlates with the loss-of-function of stem cells [80]. Similar changes in the methylation prolife also characterize RS [81], and global hypomethylation characterizes both genomic and mitochondrial DNA [82]. CpG hypermethylated regions are associated with H3K27me3, H3K4me3 and H3K4me1, whereas hypomethylation is observed in the constitutive heterochromatin and lamina-associated domains (LADs) [83].

3. The Epigenome of Oncogene-Induced Senescence (OIS) The expression of a certain number of (K-RAS and H-RAS, BRAFV600E, myrAKT1, STAT5, nuclear HDAC4, N1ICD, ERBB2 and β-catenin) [84–92] or ablation of tumor suppressors (PTEN, APC and AXIN) in normal cells triggers a permanent and premature cell-cycle arrest defined as OIS [93,94]. OIS can occur also in the presence of ectopic TERT expression [6]. The most studied model of OIS is the RAS-induced senescence (RIS), obtained by over-expressing oncogenic mutants of RAS in fibroblasts, melanocytes and retinal pigment epithelial cells. The consistency of the RIS model has been validated in mice, after conditional induction of the monoallelic expression of K-RAS/G12V. Mice develop lung adenomas characterized by the accumulation of senescent cells [95]. Similarly, premature senescence blocks the spreading of oncogenic lesions in BRAF/V600E expressing melanocytic nevi [89]. Curiously, RAS fails to induce senescence in immortalized human mammary epithelial cells (HMECs), even after the ectopically expression of p16/INKa [96,97]. This failure has been associated to defects in the TGFβ signaling pathway [97]. It is generally accepted that the premature cell-cycle arrest characterizing OIS is elicited by the accumulation of irreparable DNA damage. In fact, the abrogation of ATM signaling allows senescence escape [6]. It is important to note that the DDR dependence was observed for RAS but its involvement in the case of other oncogenes, such as NOTCH and AKT1, needs further validations [90,98]. As explained above, RIS is characterized by the accumulation of SAHF [14]. However, the oncogenic activation of AKT1 and NOTCH or the knockdown of PTEN trigger OIS without SAHF formation [85,86,98]. In the case of NOTCH, this is due to the repression of HMGA1 [90]. Differently, in the case of AKT1 it was hypothesized a mechanism operating through GSK3β inhibition. In fact GSK3β controls the -dependent HIRA sub-compartmentalization [99]. In this respect, a similar defect in HIRA signaling prevents SAHF formation in senescent murine embryonic and fibroblasts expressing Cells 2020, 9, 466 5 of 18

RAS, but not to the accumulation of nuclear macroH2A.1 [42]. The deposition of the histone variant macroH2A.1 is not only required for SAHF formation. It also sustains a chromatin re-organization that allows the focused histone and the expression of the typical SASP cytokines and chemokines [100]. Moreover, the knock-down of macroH2A.1 in H-RAS/V12 IMR90-expressing cells not only blunts SASP, but also decreases the phosphorylation of γH2AX [100]. A common property of OIS cells is the loss of LMNB1 [57]. This causes a deep re-organization of LAD domains [44], similarly to what was observed during RS [56]. As a consequence, OIS is characterized by the re-localization and re-organization of LAD-associated heterochromatin domains [43,101]. This re-organization is sculptured in the distribution of H3K4me3 and H3K27me3 “mesas” and H3K27me3 “canyons”, as described above for RS cells [56]. Interestingly, the expansion of H3K27me3 “canyons” achieved though EZH2 repression sustains OIS by promoting the expression of cytokines [56] and of CDKi [66,102,103]. Similarly to RS, the histone variant H3.3 [31,104] and its Cathepsin L-mediated cleavage product H3.3cs1 [104] are deposited in RIS cells in the regulative elements of RB/E2F target allowing the permanent removal of H3K4me3 [31] and the increase in H3K9me3 levels [14]. Contemporary, the removal of H2A.Z and the de-methylation of H3K27me3 at tumor suppressor loci sustains cell-cycle arrest [33,66]. The inflammatory response is achieved through the deposition of the histone variant H2A.J [32] and the binding of HMGB2, which excludes these loci from SAHF [41]. HMGB2 also allows the H3K4 trimethylation mediated by the methyltransferase MLL1 [53]. Moreover, SASP loci are localized in newly formed super-enhancers that require the binding of BRD4 to promote their transcription [105,106]. Finally, OIS in human fibroblasts is characterized by the spatial rearrangement of pre-existing heterochromatin that give rise to SAHF [45]. Differently, HGPS cells are refractory to SAHF formation [45,107,108] and to heterochromatin focusing [45], probably because the huge alterations in the lamina compartment of these cells prevents the proper heterochromatin 3D-structure organization [109]. A similar displacement of H3K9me3 from LADs is observed in OIS, but it is followed by an increase in local interactions between H3K9me3 domains and sharp heterochromatinization [45]. Curiously and differently from RS and aging, OIS cells do not display any changes in CpG island methylation levels [110].

Different Types of OIS? While studies are increasingly describing RIS , detailed data about the epigenetic modifications in other types of OIS are unavailable. Additional data are desirable since increasing evidences highlight the key roles played by epigenetic regulators in maintaining OIS and counteracting oncogenic transformation [84,111–116]. For example, in melanomas the activation of H3K9me3 demethylases (LSD1 and JMJD2C) selectively de-represses E2F target genes, allowing senescence escape and tumorigenesis [117]. This result reinforces the idea that a better investigation of the epigenetic mechanism that sustains the early step of tumorigenesis is desperately needed.

4. The Epigenome of Stress Induced Premature Senescence (SIPS) SIPS is characterized by the accumulation of ROS (), due to mitochondrial disfunctions, ER stress or the exogenous administration of oxidative compounds [118–120]. Even though SIPS onset is independent from attrition, ROS accumulation can cause telomere disfunction and fusion in primary cells, thus sustaining cell-cycle arrest [120,121]. Accordingly, murine embryonic fibroblasts (MEFs) cultured in normoxia undergo premature senescence due to the accumulation of ROS-induced DNA damage, while the same cells cultured in hypoxia tend to indefinitely proliferate in virtue of the long telomeres [122]. When human cells are exposed to oxidative stress in vitro, they undergo stochastic transcriptional changes which resemble aged tissue. Recently, it has been demonstrated that oxidative stress contributes not only to aging but also to age-related diseases [123]. Moreover, the accumulation of 8-oxo-7,8-dihydro- Cells 2020, 9, 466 6 of 18

20-deoxyguanosine (8-oxodG) has been observed in the liver of aged mice [124]. Global histone of H3K4, K27 and K9 are increased when BEAS-2B cells are exposed to H2O2, and preincubation with ascorbate reverse these changes [125]. These evidences are confirmed also in other contexts [126]. The general heterochromatinization observed after H2O2 treatment is achieved in two steps. Firstly, by reducing acetylation (, , H4K16ac) [125,127] in a HDAC-dependent manner [127,128]. Secondly, by recruiting histone methyltransferases (HMTs) and inducing H3K27me3, H3K9me3 and H4K20me3 [127,129]. Chromatin condensation is an attempt to preserve the DNA from genotoxicity [130]. The downstream pathways that lead to cell-cycle arrest in cells exposed to oxidative stress imply the up-regulation of CDKi, the DDR response and SASP production, similarly to cells undergoing RS [131,132]. In addition, mitochondrial dysfunctions in IMR90 human fibroblasts lead to the ROS–JNK retrograde signaling pathways, which promote SASP and drive cytoplasmic chromatin fragments (CCFs) [133]. Importantly, the epigenetic homeostasis perturbation, achieved through HMTs or HDACs inhibition [129], is reported to expose cells to endogenous ROS production [134] or to trigger and sustain the senescence induced by the treatment with oxidative compounds [135]. In particular, some ROS generators inhibit PRC2 methyltransferases to allow the focused demethylation and transcriptional activation of CDKi [132]. Similarly, the senescence entry of PAK2 knocked-down MEFs cultured in normoxia is delayed because of the decreased deposition of H3.3 on CDKi loci [136]. At the DNA level, SIPS is characterized by a global DNA hypomethylation that only partially overlaps with the one observed during RS [81]. Cells 2020, 9,The 466 alteredCells 2020 expression, 9, 466 Cells and 2020 activation, 9, 466 of epigenetic regulators allows cancer cells7 toof 19 escape 7 of 19 7 of 19 Cells 2020, 9, 466 Cells 2020, 9, 466 Cells 2020, 9, 466 7 of 19 7 of 19 7 of 19 Cells 2020cell-cycle, 9, 466 arrest and to proliferate even in the presence of high levels of oxidative and7 replication of 19 Table 1. Histone Tablevariants 1. Histonethat characterize Tablevariants 1. Histonethatsenescence characterize variants. RS: Replicative thatsenescence characterize senescence;. RS: Replicative senescence OIS: Oncogenesenescence;. RS: Replicative OIS: Oncogenesenescence; OIS: Oncogene Cells 2020stress,Table, 9, 4661. perpetuating HistoneCells 2020 Tablevariants, 9 the, 4661. accumulationHistonethat characterize Tablevariants 1. of Histonethatsenescence DNA characterize damage variants. RS: Replicative fromthatsenescence characterize generation senescence;. RS: Replicative tosenescence generation OIS: Oncogenesenescence;. RS: [137Replicative7]. of In OIS:19 short, Oncogenesenescence;7 of OIS:19 Oncogene Tableinduced 1. Histonesenescence; variantsinduced SIPS: thatsenescence; Stress characterize inducedinduced SIPS: senescencesenescence; prematureStress induced. RS:senescence;SIPS: Replicative prematureStress SASP:induced senescence; senescence; Senescence premature OIS: SASP: Oncogeneassociated senescence; Senescence SASP: associated Senescence associated histoneinduced variantssenescence;induced and ↑SIPS: histone senescence; Stress posttranslational inducedinduced ↑SIPS: senescence; prematureStress↓ modifications induced senescence;SIPS: prematureStress↓ taking SASP:induced placesenescence;→ Senescence duringpremature SASP: senescence associated senescence;→ Senescence are listedSASP: associated Senescence associated inducedsecretory senescence;phenotype;secretory SIPS:↑: Increased phenotype;Stress inducedexpression; ↑: Increased premature ↓: Decreased expression; senescence;↑ expression; ↓: DecreasedSASP: → Senescence: No expression; change;↓ associated NI:→: NotNo change; NI:→ Not Tablesecretoryin Tables 1. Histone1phenotype; and2 .Tablesecretoryvariants ↑ :1. Increased Histonethatphenotype; characterize secretory variantsexpression; ↑: Increased thatsenescencephenotype; ↓characterize: Decreased expression;. RS:↑: IncreasedReplicative senescenceexpression; ↓: Decreased expression; senescence;. RS: → : ReplicativeNo expression; change;↓ OIS:: Decreased Oncogenesenescence; NI:→: NotNo expression; change; OIS: Oncogene NI:→: NotNo change; NI: Not Cells 2020investigated.secretory, 9, 466 phenotype;Cells 2020investigated.secretory, 9↑, 466: Increased phenotype;Cells 2020secretory expression;, 9, 466: Increased phenotype; ↓ : Decreased expression; : Increased expression; : Decreased expression; → : No expression; change;: Decreased NI:: NotNo expression;7 ofchange; 19 NI:: NotNo7 ofchange; 19 NI: Not7 of 19 secretoryinducedinvestigated. senescence;phenotype; inducedinvestigated. SIPS:: Increased senescence; Stress investigated.expression;induced SIPS: prematureStress : Decreased induced senescence; expression;premature SASP: senescence; :Senescence No change; SASP: associated NI: SenescenceNot associated investigated. investigated. investigated. Cells 2020investigated., 9,Table 466 1. Histone↑ variantsCells that 2020 characterize, 9↑, 466 ↓ senescence. RS:↓ Replicative→ senescence; OIS:→ Oncogene7 of 19 7 of 19 secretoryTable 1. Histonephenotype; secretoryTablevariants :1. Increased Histonethatphenotype; characterize Tablevariantsexpression; :1. Increased Histonethatsenescence characterize: Decreased variantsexpression;. RS: Replicative thatsenescenceexpression; characterize: Decreased senescence;. RS:: Replicative No senescenceexpression; change; OIS: Oncogenesenescence;. RS:NI:: ReplicativeNotNo change; OIS: Oncogenesenescence; NI: Not OIS: Oncogene Histonesinvestigated.induced and senescence;Histonesinvestigated.Role and SIPS: during Stress inducedRoleChanges during premature senescence;Changes SASP: SenescenceChanges associated ReferencesChanges secretory References HistonesTableinduced 1. and Histonesenescence; Histones inducedvariants RoleSIPS: and duringthatsenescence; Stress characterizeHistones Tableinducedinduced RoleSIPS: 1. and Changes duringHistonesenescencesenescence; premature Stress variantsinduced. RoleRS:senescence;SIPS: ReplicativeChanges duringthat prematureStress characterize SASP:induced senescence; senescence; SenescenceChanges senescencepremature OIS: SASP: associatedOncogene. RS:senescence;References SenescenceReplicativeChanges SASP: associatedsenescence;References SenescenceChanges OIS: associatedOncogeneReferences HistoneHistonesTable Variantsphenotype; 1. and Histone HistoneHistones variants: IncreasedRole Variants and thatduring expression; characterizeHistones Role and: Changes Decreasedsenescenceduring expression;. RS:Role ReplicativeChanges during: No senescence; change;Changes NI: OIS: Not Oncogene investigated.ReferencesChanges ReferencesChanges References HistoneHistonessecretory Variants and phenotype; HistonesecretoryRole SenescenceVariants↑: Increased during phenotype; Histone secretory expression; SenescenceVariants↑: duringChangesIncreased phenotype; ↓ :RS Decreased expression; ↑: duringduringIncreasedChanges expression; ↓ OIS:RS Decreased expression; →duringduring: ChangesNo expression; change;↓ SIPSOIS: Decreased NI:References→during: NotNo expression; change; SIPS NI:→: NotNo change; NI: Not Histoneinduced Variants senescence; Histone↑ Senescence SIPS:Variants Stress Histone inducedinducedSenescence Variants↓during senescence;premature RS Senescencesenescence;SIPS:duringduring Stress→ OISRS SASP: induced duringSenescenceduringduring premature SIPS OISRS associated senescence;duringduring SIPSOIS SASP: duringSenescence SIPS associated Histone Variants Senescence Senescenceduring RS Senescenceduringduring OISRS duringduringduring SIPS OISRS duringduring SIPSOIS during SIPS Histonesinvestigated.Histones and andHistonesinvestigated.Senescence↑ and investigated.during ↓ RS ↑ during OIS →during ↓SIPS → secretory phenotype;ChromatinRole ↑Role: Increased coduringndensation during Chromatinsecretory expression; RoleChanges Changescoduring phenotype;ndensation ↓: Decreased : IncreasedChangesChanges expression; expression; →: ChangesNo NI change; : Decreased NI:References NotChanges [27]expression;NI References: No[27] change; NI: Not HistoneH1 Variants Histone HistoneChromatinH1 Variants condensation Chromatin condensation Chromatin condensation NI References[27]NI [27]NI [27] investigated.H1 ChromatinH1SenescenceSenescence condensation investigated.Chromatin H1Senescence duringduring condensation RS Chromatin duringduring condensation OISRS duringduringNI SIPSOIS during[27]NI SIPS [27]NI [27] H1Variants ChromatinH1 condensation H1 NI [27] HistonesH1 and Histones and Histones and ChromatinRoleChromatin duringndensation Chromatin RoleIncreasedChanges duringndensation ratio RoleIncreasedChanges during ratio Changes ReferencesChanges ReferencesChanges References Chromatin condensationChromatin Increased condensation ratioChromatin Increased condensationNI ratio IncreasedNI ratio [15,40][27]NI [15,40][27]NI [15,40] HistoneH2AH1 Variants H1 HistoneH2AH1 SenescenceVariants SenescenceVariantsIncreasedduring H2A2/H2A1 RSratio SenescenceIncreasedduringduringH2A2/H2A1 OIS RSratio duringIncreasedduringduringNI SIPS OIS RSratio duringduring[27 ] SIPSOIS during SIPS Histones and ChromatinRolecondensation duringcondensationHistones Chromatin Increased andH2A2/H2A1Changes co ndensation ratio Chromatin RoleH2A2/H2A1Changes duringcondensationNI H2A2/H2A1ChangesNI References[15,40]ChangesNI [15,40]ChangesNI References[15,40] H2A ChromatinH2ARole co duringndensation H2A H2A2/H2A1Changes H2A2/H2A1ChangesNI H2A2/H2A1ChangesNI References[15,40] HistoneH2A Variants ChromatinHistone VariantsIncreasedH2A2/H2A1 ratio H2A ChromatinSenescence ndensation Chromatin Increasedduring ndensation ratioRS SenescenceIncreasedduringNI OISratio duringduringNI SIPS RS during[15,40 OIS] during SIPS H3, H4 ChromatinH3, condensationH4 co ndensationChromatin H2A2 condensation/ H2A1Chromatin condensationNI NI [15,40][21][27]NI [15,40][21][27]NI [21][27] H3,H2AH1 H4 ChromatinH3,H2AH1 H4 co ndensationChromatinH3, H1 H4 H2A2/H2A1 co ndensation Chromatin H2A2/H2A1 condensation [21] [21] [21] H3, H4 ChromatinH3, H4Chromatin co ndensationH3, H4 [21] H3, H4H3, H4 Chromatin condensation Chromatin condensation NI [27][21 ] NI [27] H1 condensation H1Increased ratio Increased ratio Increased ratio H2A.X ChromatinSensorH2A.X of DNAco ndensation damageChromatinSensor of DNAcondensation damageChromatinSensor of DNAcondensationNI damage NI [15,40][21]NI [15,40][21]NI [15,40][21] H3,H2A.XH2A H4 SensorH3,H2A.XH2ASensor H4 of DNA of damage DNASensorH2A.X H2A of H2A2/H2A1 DNA damage Sensor ofH2A2/H2A1 DNA damage H2A2/H2A1 [21] [21] [21] H2A.XH2A.X SensorH2A.X of DNA damage H2A.XIncreased ratio Increased ratio [21][21 ] H2A.X Chromatindamage condensation Increased ratioChromatin condensationNI NI [15,40]NI NI [15,40] H2A H2A H2A2/H2A1 H2A2/H2A1 H2A.J ChromatinSensorH2A.JPromote of DNA condensation SASP damage ChromatinSensor Promote ofH2A2/H2A1 DNAcondensation SASP damage Chromatin Promote condensation SASP [21][32] [21][32] [32][21] H3,H2A.XH2A.J H4H2A.J H3,H2A.XH2A.JPromotePromote H4 SASP SASP H3,H2A.JPromote H4 SASP Promote SASP [32][32 ] [32] [32] H2A.J H2A.JPromote SASP H2A.J [32] H2A.J Chromatin condensation Chromatin condensation [21] [21] H3, H4 Regulation ofH3, H4 H2A.ZH2A.Z SensorH2A.ZRegulationPromote of DNA ofSASP damage CDKi Sensor RegulationPromote of DNA ofSASP damage CDKi Sensor Regulation of DNA of damage CDKi NINI [33,34][32][21][33NI , 34 ] [33,34][32][21]NI [33,34][21] H2A.ZH2A.XH2A.J H2A.ZH2A.XH2A.JRegulation CDKi of CDKi H2A.ZH2A.XRegulation of CDKi Regulation of CDKi NI [33,34]NI [33,34]NI [33,34] H2A.Z H2A.ZRegulation of CDKi H2A.Z NI [33,34] H2A.Z SensorGene of DNA activation, damage Sensor of DNA damage [21] [21] H2A.X Gene activation, silencing,GeneH2A.X activation, silencing, H3.3, H3.3cs1 H3.3,GeneRegulation activation,PromoteH3.3cs1silencing, ofSASP silencing, CDKi Gene Regulation activation,Promote ofSASP silencing, CDKi Gene activation,Promote SASP silencing, NI [31,36,104][33,34][32]NI [31,36,104][33,34][32] [31,36,104][32] H3.3,H2A.ZH2A.J H3.3cs1H3.3, H3.3cs1 H3.3,GenechromosomeH2A.ZH2A.J H3.3cs1activation, segregation silencing,H3.3,GenechromosomeH2A.J H3.3cs1activation, segregation silencing,Gene activation, silencing, [31,36,104][31,36 ,104 ] [31,36,104] [31,36,104] H3.3, H3.3cs1 H3.3,Genechromosome activation, H3.3cs1chromosome segregation silencing, H3.3,chromosome H3.3cs1 segregation chromosome segregation [31,36,104] H3.3, H3.3cs1 chromosomePromote segregation SASP chromosome segregation chromosome Promote segregation SASP [32] [32] H2A.J chromosomeGene activation,segregation segregation silencing,GeneH2A.J activation, silencing, GeneRegulation activation, of silencing, CDKiGene Regulation activation, of silencing, CDKiGene Regulation activation, ofNI silencing, CDKi NI [31,36,104][33,34][21]NI [31,36,104][33,34][21]NI [33,34][21] H3.3,H2A.ZH3.1 H3.3cs1 H3.3,GenechromosomeH2A.ZH3.1 H3.3cs1activation,Gene activation, segregation silencing,GenechromosomeH2A.ZH3.1 activation, segregation silencing,Gene activation, silencing, H3.1 GenechromosomeH3.1 activation, segregation silencing,chromosome H3.1 segregation chromosome segregationNI NI [21]NI [21]NI [21] chromosomeRegulationsilencing, segregation of CDKichromosome segregation chromosomeRegulation segregation ofNI CDKi NINI [33,34][21] NI [33,34] H2A.ZH3.1 H3.1 chromosomeRegulation segregation of CDKi H2A.Z NI NINI [33,34][21 ] Gene activation,chromosome silencing,Gene activation, silencing,Gene activation, silencing, H3.3,H3.1 H3.3cs1 H3.3,H3.1 H3.3cs1 H3.3, H3.3cs1 NI NI [31,36,104][21]NI [31,36,104][21] [31,36,104] Table 2. HistonechromosomeTable post-translation segregation2. Histone segregation chromosome modificationspost-translation segregation (PMTs) chromosomemodifications observed segregation (PMTs)in senescence. observed RS: in Replicativesenescence. RS: Replicative Table 2. HistoneGeneTable post-translation activation, 2. Histone silencing, Table modificationspost-translation 2. Histone (PMTs)Gene modificationspost-translation activation, observed silencing, (PMTs)in modifications senescence. observed RS: (PMTs)in Replicativesenescence. observed RS: in Replicativesenescence. RS: Replicative senescence;Table 2. Histone OIS: oncogenesenescence;Table post-translation 2. Histoneinduced OIS: oncogeneTable modificationspost-translationsenescence; 2. Histoneinduced SIPS: (PMTs) modifications post-translationsenescence;Stress observed induced SIPS: (PMTs)in prematuremodifications senescence.Stress observed induced senescence; RS: (PMTs)in premature Replicativesenescence. [31,36,104]SASP:observed senescence; RS: in Replicativesenescence. SASP: RS: Replicative[31,36,104] H3.3,Tablesenescence; H3.3cs1 2. Histone OIS: Genechromosome oncogenesenescence;post-translation activation, induced segregation OIS: silencing,H3.3, Geneoncogenesenescence;modifications senescence; activation,H3.3cs1 induced OIS: silencing, SIPS:(PMTs) Genechromosomeoncogene senescence;Stress activation, observed induced induced segregation silencing,SIPS: in premature senescence.senescence;Stress induced senescence; SIPS:RS: prematureReplicative Stress SASP: induced senescence; premature SASP: senescence; SASP: senescence; OIS: chromosomeoncogenesenescence; inducedsegregation OIS: oncogenesenescence; senescence; ↑ induced OIS: SIPS: oncogene senescence;Stress ↑induced inducedNI SIPS:↓ premature senescence;Stress induced senescence;NI SIPS:↓ premature Stress →SASP: induced[21] senescence;NI premature →SASP:[21] senescence;NI SASP:[21] senescence;SenescenceH3.1 associatedOIS: oncogeneSenescenceH3.1 secretory induced associated phenotype; senescence;H3.1 secretory ↑: Increased SIPS: phenotype; Stress expression; induced↑: Increased ↓ :premature Decreased expression;↑ senescence;expression; ↓: Decreased →SASP:: No expression; ↓ →: No → TableSenescence 2. Histone associatedchromosomeTableSenescence post-translation secretory 2. Histone segregation associated phenotype; chromosomeSenescence modificationspost-translation secretory ↑: segregation Increasedassociated phenotype;(PMTs) chromosomemodifications expression; secretory observed ↑: segregation Increased phenotype; (PMTs)↓in: Decreased senescence. expression; observed ↑: Increasedexpression; RS: ↓in: Decreased Replicativesenescence. expression; →: No expression; RS: ↓: DecreasedReplicative →: No expression; →: No change;Senescence NI: associatedNot investigated.Genechange;Senescence activation, secretory NI: associatedNot silencing, phenotype; investigated.Senescence secretory↑ : Increased associated phenotype;Gene activation,expression; secretory : IncreasedNI silencing, phenotype;↓ : Decreased expression; : Increasedexpression;NI : Decreased expression;→ : [21]No expression;NI : Decreased : No expression;NI : [21]No Senescencesenescence;change;H3.1 NI: associated NotOIS: investigated. oncogenesenescence;change; secretory NI: induced NotOIS: phenotype; investigated. oncogenechange; senescence;H3.1 NI: :induced Increased Not SIPS: investigated. senescence;Stress expression; induced NI SIPS: : prematureDecreased Stress induced expression;senescence;NI premature SASP:: No[21] senescence; SASP: change; NI: Not investigated.chromosomechange; NI: segregation Not investigated.change; NI: Not investigated.chromosome segregation change; NI: Not investigated. ↑ ↑ ↓ ↓ → → SenescenceTable 2. Histone associatedSenescenceTable post-translation secretory 2. Histone associated phenotype; Table modificationspost-translation secretory 2. Histone: Increased phenotype;(PMTs) modificationspost-translation expression; observed : Increased (PMTs)in : modificationsDecreased senescence. expression; observed expression; RS: (PMTs)in: Decreased Replicativesenescence. observed: No expression; RS: in Replicativesenescence. : No RS: Replicative Histonechange;senescence; NI: NotOIS: investigated.Enzymes Histoneoncogenechange;senescence; NI: induced NotOIS: investigated.Enzymes HistoneRoleoncogenesenescence; senescence; during induced OIS: SIPS:Enzymes Roleoncogene Changessenescence;Stress during induced induced SIPS:Changes Rolepremature Changessenescence;Stress during induced senescence; Changes SIPS:Changes premature ChangesStress SASP: References induced senescence;Changes Changes premature SASP: References senescence;Changes SASP:References HistoneTable 2. HistoneEnzymesHistone post-translation Enzymes HistoneRoleTablemodifications during 2. Histone (PMTs)EnzymesRole post-translationChanges duringobserved Changesin Rolemodifications Changessenescence. during Changes RS:(PMTs)Changes ReplicativeChanges observed References Changes Changesin senescence. ReferencesChanges RS: Replicative References HistoneSenescencePMTs associatedEnzymesinvolvedSenescencePMTs secretory associated phenotype;involvedRoleSenescencesenescencePMTs duringsecretory ↑: Increasedassociated phenotype;involvedsenescenceduringChanges expression; secretory RS ↑ : Increased duringphenotype; Changes↓:senescence duringDecreased expression;OIS RS ↑:during Increasedexpression;Changesduring ↓: SIPSduringDecreased expression;OIS →References :RS Noduring expression; during ↓: SIPSDecreased OIS →: Noduring expression; SIPS →: No senescence;PMTs OIS: involvedoncogenePMTs inducedinvolvedsenescence;senescencePMTs senescence; OIS: SIPS: involvedoncogenesenescenceduring Stress RSinduced induced during prematuresenescence duringsenescence; OIS RS during senescence; SIPS:during SIPSduring Stress OIS SASP: RS inducedduring during prematureSIPS OIS duringsenescence; SIPS SASP: PMTschange; NI: Not involvedinvestigated.change; NI: Not investigated.senescencechange; NI: Not investigated.↓during RS ↑during↓ OIS during↑ SIPS HistoneSenescence associatedEnzymesHistone secretory phenotype;EnzymesRoleSenescence during ↑ : Increasedassociated ↓RoleRelocalizedChanges expression; duringsecretory in ↑ Relocalizedphenotype; Changes↓↓: RelocalizedDecreasedChanges in ↑ : inIncreasedexpression;Changes ↑RelocalizedChanges↓ expression; → inReferences: No Changes ↑ ↓: Decreased References expression; →: No KDM4A KDM4B KDM4AHeterochromatin KDM4B KDM4AHeterochromatin↓Relocalized KDM4B in ↑RelocalizedHeterochromatin↓Relocalized in in ↑Relocalized ↓Relocalized in[43,45,128,129] in ↑Relocalized in[43,45,128,129] H3K9me3PMTs H3K9me3involvedPMTs H3K9me3involvedsenescence senescencefocusedRelocalizedduring areaRS in duringfocusedRelocalizedfocusedRelocalizedduring OISarea areain RS during in duringfocusedRelocalized SIPSRelocalized OISarea [43,45,128,129]in during in Relocalized SIPS [43,45,128,129]in [43,45,128,129] H3K9me3change; NI: NotKDM4A H3K9me3investigated. KDM4B KDM4AHeterochromatinH3K9me3change; KDM4B NI: Not KDM4A Heterochromatin↓investigated.Relocalizedfocused KDM4B area in ↑ RelocalizedfocusedHeterochromatinfocused area inarea focused focused area area[43,45,128,129] focused area[43,45,128,129] [43,45,128,129] H3K9me3 KDM4A KDM4B Heterochromatin focused area focusedfocused area area focused focused area[43,45,128,129] area focused area Histone EnzymesHistone EnzymesHistoneRole during Enzymes↓RolefocusedChanges during area ↑focusedChanges↓RoleChanges area during Changes↑ ChangesChanges [43–References ChangesChanges [43–ReferencesChanges References ↓Relocalized in ↓Relocalized↓Relocalized in in ↓Relocalized↓ in[43– ↓ [43– [43– KDM4AKDM6B (JMJD3)KDM4B KDM4AKDM6BHeterochromatin (JMJD3)KDM4B HeterochromatinRelocalized in RelocalizedRelocalized in in Relocalized Relocalized in[43,45,128,129][43– in Relocalized in[43,45,128,129][43– [43– H3K27me3H3K9me3PMTs KDM6BH3K27me3H3K9me3involvedPMTs (JMJD3) KDM6BHeterochromatininvolvedsenescencePMTs (JMJD3) KDM6BHeterochromatininvolved↓senescencefocusedRelocalizedduring (JMJD3) area RS in ↓duringfocusedRelocalizedHeterochromatin↓senescencefocusedRelocalizedduring OISarea areain RS during in ↓duringfocusedRelocalized↓ SIPSRelocalizedduring OISarea 45,102,103,127–in RS during in ↓duringRelocalized SIPS OIS 45,102,103,127–in during SIPS H3K27me3Histone KDM6BH3K27me3Enzymes (JMJD3) KDM6BH3K27me3HeterochromatinHistoneRole (JMJD3) during KDM6BHeterochromatin↓EnzymesRelocalizedfocusedChanges (JMJD3) area in ↓ RelocalizedfocusedChangesHeterochromatinRolefocused areaduring inarea Changes focusedfocusedChanges area [43–45,102,103,127–areaReferences focusedChanges area 45,102,103,127– Changes 45,102,103,127–References H3K27me3 KDM6BH3K27me3 (JMJD3) HeterochromatinH3K27me3 focused area focusedfocused area area focusedfocused area 129]45,102,103,127–area focused area129]45,102,103,127– 45,102,103,127– H3K27me3PMTs involved senescencePMTs involved↓focusedRelocalizedduring area RS in ↑focusedduringRelocalized↓senescenceRelocalized areaOIS in during in ↑Relocalized↓ RelocalizedSIPSduring 45,102,103,127–[43– 129]inRS in ↑duringRelocalized OIS [43–129]in during SIPS 129] KDM4A KDM4B KDM4AHeterochromatin KDM4B KDM4AHeterochromatin↓Relocalized KDM4B in ↓ RelocalizedHeterochromatin↓Relocalized in in ↓ Relocalized in[43,45,128,129]129] [43,45,128,129]129] [43,45,128,129]129] H3K9me3 IncreasedH3K9me3 activity IncreasedHeterochromatinH3K9me3 activity geneHeterochromatin gene 129] IncreasedKDM6B (JMJD3) activity IncreasedHeterochromatinKDM6BHeterochromatin (JMJD3) activity geneIncreased HeterochromatinHeterochromatin focused activity area gene Heterochromatinfocused focused area area gene focused focused area 45,102,103,127–area [54,127] focused area45,102,103,127– [54,127] H3K27me3 H3K27me3 ↓Relocalizedfocused area in ↑Relocalizedfocusedfocused area inarea focused↓ Relocalized area [54,127] in ↑Relocalized in [54,127] [54,127] H4K20me3 KDM4AIncreasedH4K20me3of Suv420h2 KDM4B activity IncreasedHeterochromatinH4K20me3Heterochromatinof Suv420h2repression activity gene KDM4AIncreasedHeterochromatin Relocalizedrepression KDM4B activity in gene HeterochromatinRelocalizedHeterochromatin in gene [43,45,128,129] [43,45,128,129] H4K20me3H3K9me3 IncreasedKDM4AofH4K20me3 Suv420h2 KDM4Bactivity HeterochromatinofHeterochromatinH4K20me3H3K9me3 Suv420h2repression gene of Suv420h2repression repression 129][43,45,128,129][54,127] 129][54,127] [54,127] H4K20me3 of Suv420h2 of Suv420h2repression of↓ RelocalizedfocusedSuv420h2repression area in ↓Relocalizedfocused↓Relocalizedrepression area in in ↓Relocalized ↓Relocalizedfocused [43–areain [54,127] in ↓Relocalizedfocused area [43–in [43– IncreasedKDM6BKMT2/KDM5D/of Suv420h2 (JMJD3) activity IncreasedHeterochromatinKDM6BKMT2/KDM5D/Euchromatin,Heterochromatinrepression (JMJD3) activity gene geneHeterochromatin KDM6B Euchromatin, Heterochromatin (JMJD3) gene gene Heterochromatin H3K27me3 KMT2/KDM5D/H3K27me3 KMT2/KDM5D/Euchromatin,H3K27me3 gene KMT2/KDM5D/ Euchromatin,focusedRelocalized area gene focusedEuchromatin,RelocalizedfocusedRelocalized area area gene focusedRelocalized focused area 45,102,103,127– area [54,127][56,125] focused area45,102,103,127– [54,127][56,125] 45,102,103,127– H4K20me3H3K4me3 KMT2/KDM5D/H4K20me3H3K4me3 KMT2/KDM5D/Euchromatin, geneKMT2/KDM5D/ Euchromatin,↓RelocalizedRelocalized gene in ↓ RelocalizedRelocalizedEuchromatin,Relocalized in gene Relocalized↓ RelocalizedRelocalized[43– [56,125] in ↓RelocalizedRelocalized in [56,125] [43–[56,125] H3K4me3 KMT2/KDM5D/ofH3K4me3 KDM2BSuv420h2 Euchromatin,ofH3K4me3 KDM2BSuv420h2repressionactivation gene KDM2BRelocalizedrepressionRelocalizedactivation in RelocalizedRelocalizedRelocalizedactivation in Relocalized Relocalized129] [56,125] Relocalized 129] [56,125] 129][56,125] H3K4me3 KDM6BH3K4me3 (JMJD3) HeterochromatinH3K4me3 KDM6BRelocalized (JMJD3) RelocalizedHeterochromatin 45,102,103,127–[56,125] 45,102,103,127– H3K27me3H3K4me3 KDM2B H3K27me3KDM2Bactivation KDM2Bfocusedactivation area focusedactivation area focused 45,102,103,127–area focused area (MOF)KDM2B Histone DNA(MOF) repair,activation Histone chromatin DNA repair, chromatin IncreasedKMT2/KDM5D/(MOF) Histone activity DNAIncreasedHeterochromatinKMT2/KDM5D/(MOF)Euchromatin, repair, Histone activity chromatin gene geneDNAIncreasedHeterochromatin (MOF)Euchromatin, repair, Histone activity chromatin gene geneDNAHeterochromatin repair, chromatin gene 129][125,127] [125,127] 129] H4K16ac (MOF)H4K16ac Histone DNA(MOF) repair, Histone chromatin DNA(MOF) Relocalizedrepair, Histone chromatin DNARelocalized Relocalizedrepair, chromatin Relocalized [125,127][56,125][54,127] [125,127][56,125][54,127] [125,127][54,127] H4K20me3H3K4me3H4K16ac acetyltransferaseH4K20me3ofH3K4me3H4K16ac KDM2BSuv420h2 acetyltransferaseH4K20me3ofH4K16ac KDM2BSuv420h2compactionrepressionactivation of Suv420h2compactionrepressionactivation repression [125,127] [125,127] [125,127] H4K16ac Increasedacetyltransferase(MOF)H4K16ac Histone activity DNAHeterochromatinacetyltransferaseH4K16ac repair,compaction chromatin geneIncreasedacetyltransferase compaction activity Heterochromatincompaction gene Increasedacetyltransferase activity Heterochromatinacetyltransferasecompaction geneacetyltransferase compaction compaction [125,127][54,127] [54,127] H4K20me3H4K16ac acetyltransferase H4K20me3compaction [54,127] KMT2/KDM5D/(MOF)ofHAT/p300 Suv420h2 Histone DNAKMT2/KDM5D/(MOF)Euchromatin,HAT/p300Euchromatin, repair,repression Histone chromatin gene DNAKMT2/KDM5D/ Euchromatin,of Euchromatin, Suv420h2repair, chromatin gene Euchromatin, repression gene [55,125,127] [55,125,127] H3K9ac HAT/p300H3K9ac HAT/p300Euchromatin, HAT/p300Euchromatin,Relocalized RelocalizedEuchromatin,Relocalized Relocalized Relocalized [55,125,127][125,127][56,125] Relocalized [55,125,127][125,127][56,125] [55,125,127][56,125] H3K4me3H4K16acH3K9ac acetyltransferaseH3K4me3H4K16acHAT/p300H3K9acKDM2B acetyltransferaseH3K4me3HAT/p300H3K9acKDM2BEuchromatin,compactionactivation HAT/p300KDM2BEuchromatin,compactionactivation Euchromatin,activation [55,125,127] [55,125,127] [55,125,127] H3K9ac KMT2/KDM5D/HAT/p300H3K9ac Euchromatin,Euchromatin,H3K9ac gene KMT2/KDM5D/ Euchromatin, gene [55,125,127] H3K4me3H3K9ac H3K4me3 Relocalized Relocalized Relocalized[56,125] Relocalized [56,125] (MOF)HAT/p300KDM2B Histone DNA(MOF)HAT/p300Euchromatin repair,activation Histone chromatin DNA(MOF) KDM2BEuchromatin repair, HistoneNI chromatin DNA repair,activationNI NI chromatin NI [125,127] [125,127] H4K8ac HAT/p300H4K8ac HAT/p300Euchromatin,Euchromatin HAT/p300Euchromatin,EuchromatinNI EuchromatinNI NI NI NI [55,125,127][125,127] NI [55,125,127][125,127] [125,127] H4K16acH3K9acH4K8ac acetyltransferaseHAT/p300H4K16acH3K9acH4K8ac acetyltransferaseHAT/p300H4K16acH4K8acEuchromatincompaction acetyltransferaseHAT/p300EuchromatincompactionNI EuchromatincompactionNI NI NI NI [125,127] NI [125,127] [125,127] H4K8ac (MOF)HAT/p300H4K8ac Histone DNAEuchromatinH4K8ac repair, chromatin (MOF) HistoneNI DNA repair,NI chromatin [125,127] H4K16acH4K8ac H4K16ac [125,127] [125,127] H4K16ac acetyltransferase compaction acetyltransferase compaction H4K8acH3K9ac HAT/p300H4K8acH3K9ac HAT/p300Euchromatin,H3K9acEuchromatin HAT/p300Euchromatin,EuchromatinNI Euchromatin,NI NI NI [55,125,127][125,127] [55,125,127][125,127] [55,125,127] 5. The Epigenome5. The at DSBs Epigenome and5. during The at DSBs Epigenome DDR: and Early during at Epigenetic DSBs DDR: and Early Eventsduring Epigenetic inDDR: the SenescentEarly Events Epigenetic in Response the Senescent Events in Response the Senescent Response 5. The Epigenome5. The atHAT/p300 DSBs Epigenome and5. during The atEuchromatin, DSBs Epigenome DDR: and Early during atHAT/p300 Epigenetic DSBs DDR: and Early EventsduringEuchromatin, Epigenetic inDDR: the SenescentEarly Events Epigenetic in Response the[55,125,127] Senescent Events in Response the Senescent Response[55,125,127] 5. TheH3K9ac Epigenome atHAT/p300 DSBs and duringH3K9acEuchromatin, DDR: Early Epigenetic Events in the Senescent Response[55,125,127] HAT/p300 HAT/p300Euchromatin HAT/p300EuchromatinNI EuchromatinNI NI NI NI [125,127] NI [125,127] [125,127] 5. TheH4K8ac Epigenome 5. The atH4K8ac DSBs Epigenome and during atH4K8ac DSBs DDR: and Early during Epigenetic DDR: Early Events Epigenetic in the Senescent Events in Response the Senescent Response HAT/p300 Euchromatin HAT/p300NI EuchromatinNI NI [125,127] NI [125,127] H4K8ac H4K8ac

5. The Epigenome5. The at DSBs Epigenome and5. during The at DSBs Epigenome DDR: and Early during at Epigenetic DSBs DDR: and Early Eventsduring Epigenetic inDDR: the SenescentEarly Events Epigenetic in Response the Senescent Events in Response the Senescent Response 5. The Epigenome at DSBs and5. during The Epigenome DDR: Early at Epigenetic DSBs and Eventsduring inDDR: the SenescentEarly Epigenetic Response Events in the Senescent Response

Cells 2020, 9, 466 7 of 19

Table 1. Histone variants that characterize senescence. RS: Replicative senescence; OIS: Oncogene induced senescence; SIPS: Stress induced premature senescence; SASP: Senescence associated secretory phenotype; ↑: Increased expression; ↓: Decreased expression; →: No change; NI: Not Cells 2020, 9, 466 7 of 19 Cells 2020, 9, 466 Cells 2020, 9, 466 Cells 2020investigated., 9, 466 7 of 19 7 of 19 7 of 19

Table 1. Histone variants that characterize senescence. RS: Replicative senescence; OIS: Oncogene Table 1. HistoneTable variants 1. Histone thatHistones characterizeTable variants 1.and Histone that senescence characterize variantsRole. RS: duringthat senescenceReplicative characterize . RS:senescence;Changes senescenceReplicative OIS:. RS:senescence; Oncogene ReplicativeChanges OIS: senescence; OncogeneChanges OIS: OncogeneReferences induced senescence; SIPS: Stress induced premature senescence; SASP: Senescence associated induced senescence;induced SIPS: senescence; HistoneStressinduced inducedVariants SIPS: senescence; Stresspremature induced SenescenceSIPS: senescence; Stresspremature induced SASP: senescence;during prematureSenescence RS SASP: senescence;associatedduring Senescence OIS SASP: associated duringSenescence SIPS associated ↑ secretory↑ phenotype;↓ ↑: Increased↓ expression;→ ↓: Decreased→ expression; →: No change; NI: Not Cells 2020, 9,secretory 466 phenotype;secretory : Increasedphenotype;secretory expression; : Increasedphenotype; : Decreasedexpression; : Increased expression; : Decreasedexpression; : expression; No: Decreasedchange; NI:: expression;No Not 7change; of 18 NI:: No Not change; NI: Not Cells 2020investigated., 9, 466 Chromatin condensation NI [27]7 of 19 Cells 2020investigated., 9, 466 Cells 2020investigated., 9, 466 Cells 2020investigated.,H1 9, 466 7 of 19 7 of 19 7 of 19

HistonesTable 1.and Histone variants that characterizeIncreased senescence ratio . RS: Replicative senescence; OIS: Oncogene TableHistonesTable 2. Histone 1.and Histone post-translationHistonesTable variantsRole 1.and Histone duringthatHistones modificationscharacterizeTable variantsRole 1.and Histone duringthatChanges senescence (PMTs)characterize Chromatin variants Role observed. RS: coduringthatChanges ndensationsenescenceReplicativeChanges characterize in senescence. . RS:senescence;Changes senescenceReplicativeChangesChanges RS: OIS: . Replicative RS:senescence; Oncogene ReplicativeChangesReferencesChangesNI OIS: senescence; OncogeneReferencesChangesNI OIS: OncogeneReferences[15,40] HistoneinducedH2A Variants senescence; SIPS: Stress inducedH2A2/H2A1 premature senescence; SASP: Senescence associated senescence;Histoneinduced Variants OIS: senescence; oncogene Histoneinduced Variants SIPS: induced senescence; HistoneStressinduced senescence; inducedVariants SIPS: senescence; Stress SIPS:premature Stressinduced SenescenceSIPS: senescence; induced Stresspremature induced premature SASP: senescence;during prematureSenescence senescence; RS SASP: senescence;associatedduring SASP:Senescence OIS SASP: associated duringSenescence SIPS associated Senescence Senescenceduring RS Senescence↑ duringduring RS OIS duringduringduring↓ RS OIS SIPS duringduring OIS SIPS →during SIPS ↑ secretory↑ phenotype;↓ ↑: Increased↓ expression;→ ↓: Decreased→ expression; →: No change; NI: Not Senescencesecretory associated phenotype;secretory secretory : Increasedphenotype; phenotype;secretory expression; : :Increasedphenotype; Increased Chromatin: Decreasedexpression; expression;: Increased condensation expression; : : Decreasedexpression; Decreased : expression; No expression;: Decreasedchange; NI:: :expression;No NoNot change; NI:: No Not change; NI: Not[21] Cells 2020, 9, 466 Cells 2020, 9, 466 investigated.H3, H4↑ Chromatin condensation↓ → 7 of 19 NI7 of 19 [27] change;investigated. NI:H1 Not investigated. investigated.ChromatinH1 condensation investigated.ChromatinH1 condensation Chromatin condensation NI [27] NI [27]NI [27] HistoneTable 1. EnzymesHistoneTable variants 1. HistoneRole that duringcharacterize variants thatChanges senescence characterizeSensor .of RS: DNAChanges senescenceReplicative damage . RS:senescence;IncreasedChanges Replicative ratio OIS: senescence; Oncogene OIS: Oncogene [21] HistonesH2A.X and Increased Chromatin ratioRole Increased coduringndensation ratio IncreasedChanges ratio ReferencesChangesNI ChangesNI References[15,40] PMTsHistonesinducedH2A and Involvedsenescence; HistonesinducedChromatinH2A Role SIPS:and senescence; coSenescenceduring ndensationStressHistonesChromatin H2A induced Role SIPS:and coduringduring Changes ndensationStressprematureChromatin RS induced Role senescence; duringcoChanges ndensationChangesprematureNI OIS SASP: senescence;duringH2A2/H2A1Changes ChangesSenescenceChangesNI SIPSNI SASP: associated ChangesReferencesSenescenceChanges[15,40]NINI associatedReferencesChanges[15,40]NI References[15,40] Histone VariantsH2A2/H2A1 SenescenceH2A2/H2A1 duringH2A2/H2A1 RS during OIS during SIPS Histonesecretory Variants phenotype; Histonesecretory VariantsSenescence ↑: Increasedphenotype; Histone Variantsexpression;Senescence ↑: IncreasedduringRelocalized ↓ :RS Decreasedexpression; duringRelocalizedduring expression; ↓ :RS OISDecreased →duringduring: expression;No OISchange; SIPS →NI:during: No Not change; SIPS NI: Not SenescencePromote SASP during RS [43during,45,128 OIS, during SIPS [32] H2A.J ↓ Chromatin↑ condensation [21] H3K9me3investigated.KDM4A KDM4Binvestigated.ChromatinHeterochromatin Cellscondensation 2020ChromatinH3,, 9, 466H4 coinndensation focused Chromatin coinndensation focused [21] [21] [21]7 of 19 H3, H4 H3, H4 H3, H4 Chromatin condensation 129] NI [27] Chromatin condensationChromatinH1 condensationarea area NI [27]NI [27] H1 H1 H1 Chromatin condensation NI [27] RelocalizedRegulationRelocalized of CDKi NI [33,34] TableH2A.Z 1. Histone variantsSensor of DNAthat damage characterize senescence . RS:[43 Replicative–45,102 , senescence; OIS: Oncogene[21] Sensor of DNA damageH2A.XSensor of ↓DNA damage Sensor of ↓DNA damage [21] [21] [21] H3K27me3HistonesH2A.XKDM6B and (JMJD3)HistonesH2A.XRole and Heterochromatin duringH2A.X Role duringinChanges focusedChromatin coinChangesndensation focusedChanges IncreasedChangesChanges ratio ReferencesChangesNI ReferencesNI [15,40] Chromatin condensationinducedChromatinH2A senescence;Increased condensation ratio SIPS: Increased StressNI ratio induced Increased prematureNI ratioNI senescence;103,127[15,40]–129NI ] SASP: Senescence[15,40] associated HistoneH2A Variants HistoneH2A VariantsSenescence H2ASenescence duringareaChromatin RS coduringduringndensationarea RS OIS H2A2/H2A1duringduring OIS SIPS duringNI SIPS NI [15,40] Cells 2020, 9, 466 H2A2/H2A1Gene activation,↑ H2A2/H2A1 silencing, H2A2/H2A1 ↓ → [31,36,104]7 of 19 HeterochromatinH3.3,secretory H3.3cs1 phenotype; Promote: Increased SASP expression; : Decreased expression; : No change; NI: Not[32] Increased activityPromote SASP H2A.JPromote SASP chromosome Promote segregation SASP [32] [32] [32] H2A.J H2A.J investigated.H2A.J Chromatin condensation [21] H4K20me3 ChromatinChromatin cocondensationndensationgeneChromatinH3,Chromatin H4 cocondensationndensation NI [54,127[21][27]NI] [21][27] H3,H1 H4 of Suv420h2H3,H1 H4 TableH3, H41. Histone Chromatinvariants cothatndensation characterize senescence . RS: Replicative senescence; OIS: Oncogene[21] repression Gene activation, silencing, NI NI [21] H3.1 Regulation of CDKi NI [33,34] RegulationEuchromatin, of CDKiinducedH2A.Z Regulation senescence; of CDKi chromosome Regulation SIPS: segregationStress of CDKi induced premature NI senescence;[33,34] NI SASP: Senescence[33,34]NI associated[33,34] H2A.Z H2A.Z HistonesH2A.Z and Increased SensorratioRole of IncreasedDNAduring damage ratio Changes Changes Changes References[21] H3K4me3 H2A.XH2AKMT2 /KDM5DH2A.XChromatinSensorH2A/KDM2B of DNA condensation genedamagesecretoryH2A.XChromatinSensor of phenotype;DNA Relocalizedcondensation damage Sensor ↑ :of Increased DNARelocalized damage NI expression; ↓NI: NI Decreased [56 expression;,125[15,40][21] NI] →: No[15,40][21] change; NI: Not[21] HistoneH2A.X Variants H2A2/H2A1 SenescenceH2A2/H2A1 during RS during OIS during SIPS activation Gene activation, silencing, [31,36,104] Gene activation,H3.3, silencing,investigated.TableGene H3.3cs1 activation, 2. Histone silencing, Gene post-translation activation, silencing, modifications (PMTs) observed[31,36,104] in senescence.[31,36,104] RS: Replicative[31,36,104] H3.3, H3.3cs1 H3.3, H3.3cs1DNA H3.3, repair, H3.3cs1 chromosomePromote segregation SASP [32] (MOF) HistonechromosomeChromatinPromote co segregationndensation SASPchromosome ChromatinH2A.JPromote co segregationndensation SASP chromosome Promote segregation SASP [32][21] [32][21] [32] H4K16ac H3,H2A.J H4 H3,H2A.J H4 chromatinsenescence;H2A.JH1 OIS: Chromatinoncogene co inducedndensation senescence; SIPS: Stress[125 induced,127 ] premature senescence;NI SASP:[27] acetyltransferase Gene activation, silencing, ↑ NI ↓ NI → [21] Gene activation,compactionHistones silencing,SenescenceGeneH3.1 activation, and associated silencing, Gene Roleactivation, secretory during silencing, phenotype;NI Changes: Increased NINI expression;ChangesNI[21]NI : DecreasedChanges[21] expression;NI References : [21]No H3.1 H3.1 H3.1 chromosomeRegulation segregation of CDKi NI [33,34] chromosomeSensorRegulation of DNA segregationHistone of damage CDKichromosomeH2A.ZSensor RegulationVariants of DNA segregation of damage CDKi chromosome segregation Increased ratioNI [33,34][21]NI [33,34][21] H3K9ac H2A.ZH2A.XHAT /p300H2A.ZH2A.X Euchromatin,change;H2A.Z NI: Not investigated.ChromatinRegulationSenescence condensation of CDKi during RS [55during,125NI,127 OIS] duringNI SIPS [15,40][33,34] H2A H2A2/H2A1 Gene activation, silencing, Table 2. HistoneChromatin post-translation ndensation modifications (PMTs) observed in senescence. RS: Replicative[31,36,104] H4K8acTable 2. HATHistone/p300TableGene post-translation activation, Promote2. HistoneEuchromatin SASP silencing,TableGene post-translationmodifications activation, Promote 2. Histone SASP silencing,NI Gene post-translation(PMTs)modifications activation, coobserved silencing,NI (PMTs)modifications in senescence. observed (PMTs) RS:in senescence.Replicative observed[125[31,36,104],127[32] ] RS: in senescence.Replicative[31,36,104][32]NI RS: Replicative[27] H3.3,H2A.J H3.3cs1 H3.3,H2A.J H3.3cs1 H3.3,HistoneH1 H3.3cs1 EnzymesChromatinchromosome co ndensationsegregationRole during Changes Changes Changes [31,36,104]References[21] chromosome segregationH3.3,senescence;chromosomeH3, H3.3cs1 H4 segregationOIS: chromosomeoncogene inducedsegregation senescence; SIPS: Stress induced premature senescence; SASP: senescence; OIS:senescence; oncogene inducedOIS:senescence;PMTs oncogene senescence; inducedOIS:involved SIPS:oncogene senescence; Stress induced induced SIPS:senescence senescence; prematureStress induced SIPS: senescence;during prematureStress RSinduced SASP: senescence;during premature OIS SASP: during senescence; SIPS SASP: Gene activation, silencing, ↑ ↓ → Gene activation, silencing,SenescenceGene activation, associated↑ silencing,Chromatin secretory co↑ndensation phenotype;↓ Increased ↑: Increased ratio↓ expression;→ NINI ↓: Decreased→ expression;NINI →[15,40]: [21]No Senescence associatedSenescenceRegulation secretory associated of CDKi Senescencephenotype;H2AH3.1 Regulation secretory associated of: Increased CDKi phenotype; Gene activation, secretory expression; : silencing,Increased phenotype; NI : Decreased expression; : Increased NI expression;NI : Decreased expression; :[33,34]NI [21]No expression;NI : Decreased :[33,34] [21]No expression;NI : [21]No 5. The EpigenomeH2A.ZH3.1 at DSBsH2A.ZH3.1 and duringchange;H3.1 DDR: NI: Early Not investigated.chromosome EpigeneticSensor of DNA segregation damage Events in theH2A2/H2A1 Senescent ↓ Relocalized Response in ↑Relocalized in [21] change; NI: Not change;investigated.chromosome NI: Not segregation change;investigated.chromosomeH2A.X NI: Not segregation KDM4A investigated.chromosome KDM4B segregation Heterochromatin [43,45,128,129] H3K9me3 focused area focused area Double-strand DNAGene breaks activation, cause silencing, massiveGene activation, epigenetic silencing,Chromatin changes. ndensation Immediately, at the damaged sites, H3, H4 co [31,36,104] [31,36,104] [21] H3.3, H3.3cs1 H3.3,chromosome H3.3cs1 segregation Tablechromosome 2. Histone segregation post-translationPromote SASP modifications (PMTs)↓ observed ↓ in senescence. RS: Replicative[43–[32] the DNAHistone unwrapsTable 2. Histone fromHistoneTableEnzymes thepost-translation histones2. Histone HistoneTableEnzymes and H2A.J post-translationRolemodifications the2. during Histone chromatin Enzymes post-translation(PMTs)RolemodificationsChanges undergoesduring observed (PMTs)Rolemodifications Changes ainChanges de-structuration, duringsenescence. observed (PMTs)Changes ChangesRelocalizedRS:inChanges senescence.Replicative observed thus inReferences losingChangesRelocalized Changes RS:in senescence.Replicative in ReferencesChanges RS: Replicative References senescence; OIS:KDM6B oncogene (JMJD3) induced Heterochromatin senescence; SIPS: Stress induced premature senescence; SASP: senescence; OIS:senescence; oncogene inducedOIS:H3K27me3senescence;PMTs oncogene senescence; inducedOIS: involvedSIPS:oncogene senescence; Stress induced induced SIPS:senescence senescence; prematureStress induced SIPS: senescence;focusedduring prematureStress area RSinduced SASP: senescence;duringfocused premature areaOIS SASP: during senescence; SIPS SASP:45,102,103,127– compactnessPMTs [138 ]. ThisPMTsinvolved responseGene activation, is achievedsilencing,PMTsinvolvedGenesenescence activation, mainly silencing,involved Sensor throughsenescenceduring of DNA theRS damage chaperone-mediatedNI senescenceduring during OIS↑ RS duringNINI during during SIPS nucleosomesOIS RS during[21] NIduring ↓ SIPS OIS during[21] SIPS → [21] H3.1 H3.1 SenescenceH2A.X associated↑ Regulation secretory↑ of CDKi phenotype; ↓ : Increased ↓ expression;→ : Decreased→ expression;NI 129][33,34]: No Senescence associatedSenescencechromosome secretory associated segregation Senescencephenotype;H2A.Zchromosome secretory associated segregation: Increased phenotype; secretory expression; : Increased phenotype; : Decreased expression; ↑: Increased expression;↓ : Decreased expression; : No expression;↑ ↓ : Decreased : No expression; →: No disassembly [139]. Functionally, it allows the recruitment↓ of proteins↑ ↓ involved in↑ ↓ DDR.Relocalized Structurally in ↑Relocalized in change; NI: NotIncreasedKDM4A investigated. RelocalizedKDM4B activity Heterochromatin inHeterochromatin RelocalizedRelocalized ingene in RelocalizedRelocalized in in Relocalized in [43,45,128,129] change; NI: NotKDM4A change;investigated. KDM4B NI: Not KDM4AH3K9me3 change;investigated.Heterochromatin KDM4B NI: Not KDM4A investigated. Heterochromatin KDM4B Heterochromatin focused area[43,45,128,129] focused area [43,45,128,129] [43,45,128,129][54,127] it causesH3K9me3 significant topologicalH3K9me3 alterationsH4K20me3H3K9me3 in the DNA fiber.focusedPromote These area SASP modificationsfocusedfocused area area focused arefocused limited area area byfocused the area [32] H2A.J ofGene Suv420h2 activation, silencing,repression [31,36,104] subsequentTable heterochromatinization 2. HistoneTable post-translation 2. HistoneH3.3, upstream post-translation H3.3cs1modifications and downstreamchromosome (PMTs)modifications observed segregation from (PMTs) the in damagesenescence. observed site,↓ RS:in which senescence.Replicative restrains↓ RS: Replicative [43– Histone KMT2/KDM5D/Enzymes↓ Euchromatin,↓Role↓ during gene ↓ ↓RelocalizedChanges [43–in ↓RelocalizedChanges in[43– Changes [43–References Histonesenescence; OIS:Histonesenescence;Enzymes oncogene inducedOIS:Enzymes oncogeneRole senescence; during inducedKDM6B SIPS:Role senescence;Relocalized(JMJD3)Changes Stress during induced in SIPS:Heterochromatin RelocalizedChangesRelocalized Changes prematureStress inducedin in senescence;ChangesRelocalizedChangesRelocalizedRelocalized premature inSASP: in References senescence;ChangesRelocalizedRelocalized inSASP: References [56,125] relaxation [140]. KDM6B (JMJD3) KDM6BH3K27me3H3K4me3HistoneHeterochromatin (JMJD3) KDM6BEnzymes HeterochromatinRegulation (JMJD3) of CDKi HeterochromatinRole during focusedChanges area focusedChanges area NIChanges References[33,34]45,102,103,127– H3K27me3 H3K27me3 H3K27me3PMTsH2A.Z involvedGeneKDM2B focusedactivation, area silencing, senescencefocusedactivationfocused area area focusedfocusedduring area area RS 45,102,103,127– duringfocused areaOIS 45,102,103,127–during SIPS 45,102,103,127– SenescencePMTs associatedSenescencePMTsinvolved secretory associated PMTsinvolvedphenotype;senescence secretory ↑: Increased involvedphenotype;senescenceduring expression; ↑ RS: Increased senescenceduring ↓during: Decreased expression; OIS RS during expression;during ↓during: Decreased SIPS OIS RS → :NIduring No expression; during SIPS OIS → :during NoNI SIPS 129][21] The phosphorylation by PIKK kinasesH3.1 (ATM, ATRchromosome and DNA-PK) segregation of ser 139 of H2AX (γH2AX)129] is the 129] 129] (MOF) Histone DNA repair, chromatin ↓ ↑ change; NI: Not change;investigated. NI: Not investigated.Increased Gene↓ activation, activity silencing,Heterochromatin↑ ↓ gene↑ Relocalized in Relocalized in [125,127] widespread histone modificationIncreased activity that IncreasedH4K16acHeterochromatin extends activity for megabases IncreasedKDM4A geneHeterochromatin RelocalizedKDM4B activity around geneHeterochromatin inHeterochromatin a Relocalized DSBs.RelocalizedγH2AX ingene in Relocalized↓Relocalized acts as a in platformin ↑Relocalized in [31,36,104][43,45,128,129][54,127] KDM4A KDM4B KDM4AH3.3,H4K20me3H3K9me3Heterochromatin H3.3cs1 KDM4B KDM4Aacetyltransferase Heterochromatin KDM4B Heterochromatincompaction focused area[43,45,128,129] [54,127]focused area [43,45,128,129][54,127] [43,45,128,129][54,127] H4K20me3H3K9me3 H4K20me3H3K9me3 H4K20me3H3K9me3 ofchromosome Suv420h2focused segregationarea focusedrepressionfocused area area focused area for the recruitment of MDC1of Suv420h2 and 53BP1.ofTable Suv420h2repression This2. Histone recruitment of Suv420h2post-translationrepression is sustained modificationsrepression by the accumulation(PMTs)focused observed area atfocused in the senescence. area RS: Replicative Histone HistoneEnzymes EnzymesRole during KMT2/KDM5D/ HAT/p300GeneRole activation,Changes during silencing, Euchromatin,Euchromatin,Changes Changes gene Changes↓Changes References↓Changes References [43–[55,125,127] damaged site of DDR RNAsKMT2/KDM5D/ [141]. TheKMT2/KDM5D/H3K9acsenescence; generalEuchromatin, relaxation OIS: geneKMT2/KDM5D/ Euchromatin,oncogene ↓ of the induced chromatin geneEuchromatin, ↓ ↓senescence; is achieved gene SIPS: ↓ ↓Relocalized throughRelocalized Stress induced di[43–in NIff ↓ erentRelocalizedRelocalized premature in[43– senescence;NI SASP:[43–[21][56,125] H3K4me3H3.1 KDM6B Relocalized(JMJD3)Relocalized in Heterochromatin RelocalizedRelocalizedRelocalizedRelocalized in in RelocalizedRelocalizedRelocalizedRelocalized in in [56,125]RelocalizedRelocalized in [56,125] [56,125] H3K4me3PMTs KDM6BH3K4me3PMTsinvolved (JMJD3) KDM6BH3K27me3H3K4me3involvedHeterochromatinsenescence (JMJD3) KDM6B chromosomeHeterochromatinKDM2Bsenescence (JMJD3)during segregation RS Heterochromatinduringactivationduring OIS RS during duringfocused SIPS OIS area during focused SIPS area 45,102,103,127– mechanisms,H3K27me3 which includeH3K27me3KDM2B (i) the RNF8H3K27me3SenescenceKDM2B/Ubc13activation / HUWE1 associated KDM2Bactivation ubiquitylationfocused secretory area phenotype; focusedactivationfocused of Histone area ↑ area : Increased H1focused [142 expression; area,143 ],45,102,103,127– (ii) ↓ the: Decreased45,102,103,127– expression; →45,102,103,127–: No focused area focused area 129] change; NI: Not(MOF) investigated.HAT/p300↓ HistoneRelocalized DNA in ↑Euchromatin Relocalizedrepair,↓Relocalized chromatin in in ↑ RelocalizedNI in129] NI 129] 129][125,127] RNF168 mediated K63-ubiquitylationKDM4A(MOF) Histone KDM4B KDM4A(MOF)DNAH4K8ac ofHeterochromatin H2Arepair, Histone KDM4B /B chromatin and (MOF)DNA H2AXHeterochromatin repair, Histone [ 144chromatin ],DNA and repair, (iii) thechromatin PARylation-dependent, [43,45,128,129] [43,45,128,129] [125,127] H3K9me3 H3K9me3 H4K16acTable 2. HistoneIncreasedacetyltransferase post-translation activity Heterochromatin modificationscompaction gene (PMTs) observed[125,127] in senescence. [125,127] RS: Replicative[125,127] proteasomalH4K16ac degradation IncreasedacetyltransferaseH4K16ac of H1.2 activity [145 IncreasedacetyltransferaseH4K16acHeterochromatin]. compaction activity Increasedacetyltransferase geneHeterochromatin compactionfocused activity area geneHeterochromatin compactionfocusedfocused area area gene focused area [54,127] H4K20me3 H4K20me3 H4K20me3 of Suv420h2 repression [54,127] [54,127] [54,127] of Suv420h2 H4K20me3ofsenescence; Suv420h2repression OIS: of oncogene Suv420h2repression induced repressionsenescence; SIPS: Stress induced premature senescence; SASP: In addition to these huge chromatinHistone remodeling, EnzymesHAT/p300↓ localRelocalized histone in ↓RoleEuchromatin,Relocalized↓ modificationsRelocalized during↑ in in ↓Relocalized surroundingChanges in [43– Changes↓ the [43–Changes →References[55,125,127] KDM6BHAT/p300 (JMJD3) 5. TheKDM6BSenescenceH3K9acHAT/p300 HeterochromatinEpigenomeEuchromatin, (JMJD3) associated KMT2/KDM5D/ atHAT/p300 Heterochromatin DSBsEuchromatin, secretory and during phenotype;Euchromatin, Euchromatin, DDR: gene: EarlyIncreased Epigenetic expression; [55,125,127]Events : Decreased in the [55,125,127]Senescent expression; Response : [55,125,127]No DSBs takeH3K27me3H3K9ac place in cells KMT2/KDM5D/H3K27me3H3K9ac undergoing KMT2/KDM5D/ NHEJH3K9acPMTsEuchromatin, or HR, geneKMT2/KDM5D/ thusinvolvedEuchromatin, sculpturingfocused areageneEuchromatin, ansenescencefocusedfocused epigenetic area areagene patternfocusedduringRelocalized area specificRS 45,102,103,127–duringRelocalized for OIS 45,102,103,127–during SIPS [56,125] H3K4me3 H3K4me3 H3K4me3change; NI: Not investigated.KDM2BRelocalized RelocalizedactivationRelocalized RelocalizedRelocalized [56,125]Relocalized [56,125] [56,125] KDM2B H3K4me3KDM2Bactivation KDM2Bactivation activation 129] 129] each of the two repair mechanisms [138]. The activationHAT/p300 of NHEJ is supportedEuchromatin by a↓ generalNI chromatin↑ NI [125,127] HAT/p300 H4K8acHAT/p300Euchromatin KDM4A(MOF) HAT/p300Euchromatin HistoneKDM4B NI DNA HeterochromatinEuchromatin repair,NINI chromatin Relocalized NINI in [125,127]Relocalized NI in [125,127] [125,127] H4K8ac Increased(MOF)H4K8ac Histone activity IncreasedH3K9me3(MOF)DNAHeterochromatinH4K8ac repair, Histone activity chromatin DNA geneHeterochromatin repair, chromatin gene [43,45,128,129][125,127] expansion around the DSBs, by the depositionH4K16ac of the(MOF) histone Histone variants DNA H3.3 repair, [ 146 chromatin ] and H2AZfocused [ 147area] and[125,127][54,127]focused by area [125,127][54,127] H4K20me3H4K16ac H4K20me3H4K16ac H4K16acHistone acetyltransferaseEnzymes Rolecompaction during Changes Changes Changes References[125,127] the monoubiquitylationacetyltransferaseof Suv420h2 H2BK120. acetyltransferase Thisof Suv420h2compactionrepression monoubiquitylation acetyltransferase compactionrepression promotes compaction the appearance of H3K4me3 PMTs involved senescence ↓Relocalizedduring RS in ↓duringRelocalized OIS in during SIPS [43– KMT2/KDM5D/ KMT2/KDM5D/Euchromatin, geneHAT/p300Euchromatin, gene Euchromatin, [55,125,127] and the binding of the SWI/SNF remodeling5. The Epigenome complex.KDM6B at DSBs Moreover, (JMJD3)Relocalized and during the Heterochromatin TIE2-mediatedRelocalizedRelocalized DDR: Early Relocalized Epigenetic phosphorylation Events[56,125] in the Senescent [56,125] Response 5. TheH3K4me3H3K9ac Epigenome 5. TheH3K4me3 H3K9acatHAT/p300 EpigenomeDSBs and 5. TheH3K27me3 during H3K9acatHAT/p300 EpigenomeDSBsEuchromatin, DDR: and Earlyduring atHAT/p300 DSBsEuchromatin, Epigenetic DDR: and Earlyduring EventsEuchromatin, Epigenetic DDR: in the Early SenescentEvents Epigeneticfocused in area theResponse [55,125,127]SenescentEventsfocused in area theResponse [55,125,127]Senescent Response45,102,103,127–[55,125,127] KDM2B H3K9acKDM2Bactivation activation ↓Relocalized in ↑Relocalized in of H4Y51 [148], as well as the RNF20H3K9me3/40-mediated KDM4A H2BK120ub KDM4B Heterochromatin [149] and the RNF168-mediated 129][43,45,128,129] (MOF) Histone (MOF)DNA repair, Histone chromatin DNAHAT/p300 repair, chromatinEuchromatin focusedNI area focusedNI area H2AK15ub [144] act asHAT/p300 platforms toHAT/p300 recruitEuchromatin DDRIncreased proteins,Euchromatin activityNI like Heterochromatin ABL1NI NI [ 148 gene], Ku70 NI/ 80 [149[125,127]] and [125,127] [125,127] H4K16ac H4K16ac H4K8ac HAT/p300 Euchromatin NI [125,127]NI [125,127] [125,127][54,127] H4K8ac acetyltransferaseH4K8ac H4K20me3acetyltransferaseH4K8accompaction compaction 53BP1 [150,151]. The latter modification and theof successful Suv420h2 recruitmentrepression of 53BP1,↓Relocalized which controlsin ↓Relocalized in [43– H3K27me3 KDM6B (JMJD3) Heterochromatin 45,102,103,127– end re-sectioning, dictateHAT/p300 the choice ofHAT/p300 theEuchromatin, NHEJ KMT2/KDM5D/ pathwayEuchromatin,in spite Euchromatin, of HR [gene152 ,153focused]. H4K20me2 area [55,125,127]focused is area [55,125,127] H3K9ac H3K9ac 5. TheH3K4me3 Epigenome at DSBs and during DDR: Early EpigeneticRelocalized EventsRelocalized in the Senescent Response129][56,125] another5. The anti-resection Epigenome5. The modification at EpigenomeDSBs and5. The that during at Epigenome reinforceDSBs DDR: and 53BP1 Earlyduring atKDM2B DSBs bindingEpigenetic DDR: and Earlyduring to theEvents activationEpigenetic chromatin DDR: in the Early SenescentEvents [154 Epigenetic]. However,in theResponse SenescentEvents the in theResponse Senescent Response Increased activity Heterochromatin gene [54,127] co-presence of H2AK15UbHAT/p300 and H4K20me2 H4K20me3HAT/p300Euchromatin in the proximity(MOF) Euchromatin HistoneNI of theDNA DSBs repair,NI bu NIchromatin ff ers NHEJ NI processing [125,127] by [125,127] H4K8ac H4K8ac H4K16ac of Suv420h2 repression [125,127] recruiting the HAT Tip60/KAT5, which triggers H2AK15acacetyltransferase and 53BP1compaction displacement. An activity that KMT2/KDM5D/ Euchromatin, gene H3K4me3 Relocalized Relocalized [56,125] 5. The Epigenome5. The at EpigenomeDSBs and during H3K9acat DSBs DDR: and EarlyduringHAT/p300KDM2B Epigenetic DDR: Early EventsEuchromatin,activation Epigenetic in the SenescentEvents in theResponse Senescent Response [55,125,127] (MOF) Histone DNA repair, chromatin H4K16ac [125,127] H4K8ac acetyltransferaseHAT/p300 Euchromatincompaction NI NI [125,127]

H3K9ac HAT/p300 Euchromatin, [55,125,127] 5. The Epigenome at DSBs and during DDR: Early Epigenetic Events in the Senescent Response H4K8ac HAT/p300 Euchromatin NI NI [125,127]

5. The Epigenome at DSBs and during DDR: Early Epigenetic Events in the Senescent Response

Cells 2020, 9, 466 8 of 18 favors the establishing of HR [155]. 53BP1 displacement seems to occur during S/G2 transition, as in G1 cells 53BP1 stably occupying the HR sites [156]. The general loss of occupancy achieved in proximity to DSBs is counterbalanced by the distal accumulation of [156]. This PTM can be used as a scaffold for the binding of HDACs, thus ensuring the transcriptional silencing of genomic loci affected by DSBs [157,158]. A different epigenetic environment is associated to the activation of the HR pathway [158]. In this context, macroH2A is found to be more abundant than H2AZ, the acetylation of H2BK120 overcomes ubiquitylation in a SAGA complex-dependent manner [159] and γH2AX is more spread [156]. As explained above, Tip60/KAT5 acetylates H2AK15, thus displacing 53BP1 [155]. Tip60/KAT5 also maintains the acetylation of H4K16, which is required for keeping an open chromatin status [160] at the damaged site. An opposite epigenetic mark, H3K9me2, is required for the BARD1/HP1γ mediated retention of BRCA1 [161] and to allow the loading of the pro-resection factor CtIP [162]. In active genes affected by DSBs, the loss in and of H4 acetylation levels [156], as well as the recruitment of macroH2A [163] and of repressive protein complexes (HP1,KAP1,SUV39H1,PRDM2,HDACs), seems to compensate for the general loss of histones that characterizes the damaged sites [164]. The spatio-temporal regulation of chromatin remodeling at DSBs is achieved and sustained also by the deposition of other histone variants, like the HIRA-assisted H3.3 and the CAF-1-mediated H3.3 [23]. In summary, from the literature emerges a bleeding/vasoconstriction model in which the chromatin expands and becomes flexible at the damaged sites to accommodate the repair complexes, but heterochromatinization and the creation of a transcriptional repressive environment is required later on to allow the repair before restarting the transcription. The successful prediction of DSBs by looking at the histone positioning and PTMs [165], the emerging roles played by epigenetic regulators in DDR as well as the impact of epigenetic drugs on DDR [166] confirm that the epigenetic status of the chromatin not only identifies sites of genome fragility, but it is also causally linked to the successful repair [23].

6. An Anti-Apoptotic Response Sustains the Survival of Damaged Cells Exposed to Irreparable DNA Damage Senescent cells display an increased resistance to pro-apoptotic stimuli that is achieved through the up-regulation of the pro-survival gene Bcl2 and Bcl-XL and the down-regulation of the pro-apoptotic genes Bid and Bax [127]. The TP53-dependent up-regulation of the CDKi p21 plays a key role in sustaining the survival of damaged cells [167], while DNMT3a and HDAC1 are recruited on the p21 to switch off its expression during [168]. The increase in p21 promotes the cell-cycle arrest allowing the activation of DDR; cellular proliferation is subsequently permanently locked through the activation of INK4 CDKi (mainly p16 and p15) [169]. Many of the anti-apoptotic functions of p21 are achieved through the modulation of TFs (p300, STAT, JUN and TP53) [170] and are sustained by an epigenetic reprogramming [127]. In senescent cells, high levels of H4K20me3 and low levels of H4K16ac keep down the transcription of pro-apoptotic genes, while the increased acetylation of H4K16 characterizes pro-survival loci [127]. The heterochromatinization that surrounds and borders DSBs enhances these pro-survival responses and any relaxation of these structures, obtained for example through HDAC inhibition, triggers apoptosis [6]. Finally, the mTORC1 and PGC-1β dependent metabolic reprogramming [171] observed in senescent cells and in different models of aging [5] ensures energy supply. Since the epigenetic regulators require cofactors that are produced in a large majority in mitochondria [172,173], any mitochondrial dysfunction can affect both the transcriptional and the metabolic fitness of the cells and lead to senescence even in absence of DNA damage (MiDAS, mitochondrial dysfunction-associated senescence) [171]. Severe and acute stresses induce cell death, while prolonged and mild insults lead to cellular senescence and survival, probably because the cells have the time and a not completely compromised ability to mount the epigenetic, transcriptional and metabolic responses that characterize them [174]. Cells 2020, 9, 466 9 of 18

7. Final Considerations: The Link between Senescence, Aging, Epigenetics and DDR The accumulation of DSBs is a general hallmark of senescence and aging [6]. The main endogenous sources of DSBs are telomere attrition and replicative stress. Replication stress is commonly observed in RS, OIS and aging. In all these conditions cells slow down DNA synthesis and replication fork progression. However, the reduced replication fork speed activates dormant origin to preserve replication timing during replication stress [175]. This adaptive response allows the maintenance of an unaltered replication timing also in cells entering senescence [176]. On the other side it exposes common fragile sites (CFSs), which are genomic loci more prone to breakage after DNA polymerase inhibition, and the accumulation of genomic alterations. CFS alterations are typically observed in pre-neoplastic lesions [177]. Similarly, cells exposed to genotoxic agents (e.g., chemotherapeutic agents, pollutants and toxins) or to oxidative stress activate the DDR that frequently leads to cell-cycle arrest. Whatever the origin, the accumulation of irreparable DNA damage gives rise to a univocal response characterized by the activation of tumor suppressors and CDKi and by the release of pro-inflammatory cytokines [5]. Global histone loss, as well as the focused deposition of histone variants (H2AX, H2AZ, H2AJ, H3.3 and macroH2A) and the redistribution of H3K4me3, H3K27me3 and H3K36me3 characterize both DDR, DSBs and senescence. The chromatin remodeling observed in different senescence models seems to represent a temporal and spatial evolution of what is observed after a short-time treatment of the cells with DNA damaging agents. Although it is clear that an altered epigenome can expose cells to DSBs [134] and that epigenetic regulators control the fate of damaged cells [15,55,66,115,178–180], investigations on the epigenetic inheritance in daughter cells coming from DNA-damaged cells are still in their infancy [177]. Cancer cells appear as forgetful cells that have lost the epigenetic memory of a healthy genome. Aging seems to be predisposed to this memory loss. One of the major challenges of the future regarding the treatment of aging and cancer, will be the identification of the framework of epigenetic changes that can restore this memory.

Author Contributions: H.P., writing—original draft preparation; E.D.G., writing—original draft preparation; C.B., conceptualization, writing—original draft preparation, writing—review and editing, visualization, supervision, project administration, and funding acquisition. All authors have read and agreed to the published version of the manuscript. Funding: This study was supported by PRIN 2017JL8SRX “Class IIa HDACs as therapeutic targets in human diseases: new roles and new selective inhibitors” and Interreg Italia-Osterreich rITAT1054 EPIC to C.B. Conflicts of Interest: The authors declare no conflict of interest.


1. Van Deursen, J.M. The role of senescent cells in . 2014, 509, 439–446. [CrossRef][PubMed] 2. Baker, D.J.; Wijshake, T.; Tchkonia, T.; LeBrasseur, N.K.; Childs, B.G.; van de Sluis, B.; Kirkland, J.L.; van Deursen, J.M. Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders. Nature 2011, 479, 232–236. [CrossRef][PubMed] 3. Baker, D.J.; Childs, B.G.; Durik, M.; Wijers, M.E.; Sieben, C.J.; Zhong, J.A.; Saltness, R.; Jeganathan, K.B.; Verzosa, G.C.; Pezeshki, A.; et al. Naturally occurring p16Ink4a-positive cells shorten healthy lifespan. Nature 2016, 530, 184–189. [CrossRef] 4. He, S.; Sharpless, N.E. Senescence in Health and Disease. Cell 2017, 169, 1000–1011. [CrossRef][PubMed] 5. Kuilman, T.; Michaloglou, C.; Mooi, W.J.; Peeper, D.S. The essence of senescence. Genes Dev. 2010, 24, 2463–2479. [CrossRef][PubMed] 6. Di Micco, R.; Fumagalli, M.; Cicalese, A.; Piccinin, S.; Gasparini, P.; Luise, C.; Schurra, C.; Garre’, M.; Giovanni Nuciforo, P.; Bensimon, A.; et al. Oncogene-induced senescence is a DNA damage response triggered by DNA hyper-replication. Nature 2006, 444, 638–642. [CrossRef] 7. D’Adda Di Fagagna, F. Living on a break: Cellular senescence as a DNA-damage response. Nat. Rev. Cancer 2008, 8, 512–522. [CrossRef] Cells 2020, 9, 466 10 of 18

8. Seluanov, A.; Mittelman, D.; Pereira-Smith, O.M.; Wilson, J.H.; Gorbunova, V. DNA end joining be comes less efficient and more error-prone during cellular senescence. Proc. Natl. Acad. Sci. USA 2004, 101, 7624–7629. [CrossRef] 9. Pal, S.; Postnikoff, S.D.; Chavez, M.; Tyler, J.K. Impaired cohesion and homologous recombination during replicative aging in budding yeast. Sci. Adv. 2018, 4.[CrossRef] 10. Zhang, W.; Hu, D.; Ji, W.; Yang, L.; Yang, J.; Yuan, J.; Xuan, A.; Zou, F.; Zhuang, Z. Histone modifications contribute to cellular replicative and hydrogen peroxide-induced premature senescence in human embryonic lung fibroblasts. Free Radic. Res. 2014, 48, 550–559. [CrossRef] 11. Bracken, A.P.; Kleine-kohlbrecher, D.; Dietrich, N.; Pasini, D.; Gargiulo, G.; Beekman, C.; Minucci, S.; Porse, B.T.; Marine, J.; Hansen, K.H.; et al. The Polycomb group proteins bind throughout the. Genes Dev. 2007, 21, 525–530. [CrossRef][PubMed] 12. Kaneda, A.; Fujita, T.; Anai, M.; Yamamoto, S.; Nagae, G.; Morikawa, M.; Tsuji, S.; Oshima, M.; Miyazono, K.; Aburatani, H. Activation of Bmp2-Smad1 Signal and Its Regulation by Coordinated Alteration of H3K27 Trimethylation in Ras-Induced Senescence. PLoS Genet. 2011, 7, e1002359. [CrossRef][PubMed] 13. Coppé, J.P.; Patil, C.K.; Rodier, F.; Krtolica, A.; Beauséjour, C.M.; Parrinello, S.; Hodgson, J.G.; Chin, K.; Desprez, P.Y.; Campisi, J. A human-like senescence-associated secretory phenotype is conserved in mouse cells dependent on physiological oxygen. PLoS ONE 2010, 5, e9188. [CrossRef][PubMed] 14. Narita, M.; Nũnez, S.; Heard, E.; Narita, M.; Lin, A.W.; Hearn, S.A.; Spector, D.L.; Hannon, G.J.; Lowe, S.W. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 2003, 113, 703–716. [CrossRef] 15. Di Micco, R.; Sulli, G.; Dobreva, M.; Liontos, M.; Botrugno, O.A.; Gargiulo, G.; Dal Zuffo, R.; Matti, V.; D’Ario, G.; Montani, E.; et al. Interplay between oncogene-induced DNA damage response and heterochromatin in senescence and cancer. Nat. Cell Biol. 2011, 13, 292–302. [CrossRef] 16. Kosar, M.; Bartkova, J.; Hubackova, S.; Hodny, Z.; Lukas, J.; Bartek, J. Senescence-associated heterochromatin foci are dispensable for cellular senescence, occur in a cell type- And insult-dependent manner, and follow expression of p16ink4a. 2011, 10, 457–468. [CrossRef] 17. Cruickshanks, H.A.; McBryan, T.; Nelson, D.M.; VanderKraats, N.D.; Shah, P.P.; van Tuyn, J.; Singh Rai, T.; Brock, C.; Donahue, G.; Dunican, D.S.; et al. Senescent cells harbour features of the cancer epigenome. Nat. Cell Biol. 2013, 15, 1495–1506. [CrossRef] 18. De Cecco, M.; Criscione, S.W.; Peckham, E.J.; Hillenmeyer, S.; Hamm, E.A.; Manivannan, J.; Peterson, A.L.; Kreiling, J.A.; Neretti, N.; Sedivy, J.M. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 2013, 12, 247–256. [CrossRef] 19. Chiappinelli, K.B.; Strissel, P.L.; Desrichard, A.; Li, H.; Henke, C.; Akman, B.; Hein, A.; Rote, N.S.; Cope, L.M.; Snyder, A.; et al. Inhibiting DNA Methylation Causes an Interferon Response in Cancer via dsRNA Including Endogenous Retroviruses. Cell 2015, 162, 974–986. [CrossRef] 20. Feser, J.; Truong, D.; Das, C.; Carson, J.J.; Kieft, J.; Harkness, T.; Tyler, J.K. Elevated Histone Expression Promotes Life Span Extension. Mol. Cell 2010, 39, 724–735. [CrossRef] 21. O’Sullivan, R.J.; Kubicek, S.; Schreiber, S.L.; Karlseder, J. Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat. Struct. Mol. Biol. 2010, 17, 1218–1225. [CrossRef] [PubMed] 22. Günes, C.; Rudolph, K.L. The Role of Telomeres in Stem Cells and Cancer. Cell 2013, 152, 390–393. [CrossRef] [PubMed] 23. Dabin, J.; Fortuny, A.; Polo, S.E. Europe PMC Funders Group Epigenome maintenance in response to DNA damage. 2017, 62, 712–727. 24. Moye, A.L.; Porter, K.C.; Cohen, S.B.; Phan, T.; Zyner, K.G.; Sasaki, N.; Lovrecz, G.O.; Beck, J.L.; Bryan, T.M. Telomeric G-quadruplexes are a substrate and site of localization for human telomerase. Nat. Commun. 2015, 6, 7643. [CrossRef][PubMed] 25. Ishikawa, F. Portrait of replication stress viewed from telomeres. Cancer Sci. 2013, 104, 790–794. [CrossRef] 26. Wagner, W. The link between epigenetic clocks for aging and senescence. Front. Genet. 2019, 10, 1–6. [CrossRef] 27. Funayama, R.; Saito, M.; Tanobe, H.; Ishikawa, F. Loss of linker histone H1 in cellular senescence. J. Cell Biol. 2006, 175, 869–880. [CrossRef] Cells 2020, 9, 466 11 of 18

28. Volk, A.; Crispino, J.D. The role of the chromatin assembly complex (CAF-1) and its p60 subunit (CHAF1b) in homeostasis and disease. Biochim. Biophys. Acta - Gene Regul. Mech. 2015, 1849, 979–986. [CrossRef] 29. Kaygun, H.; Marzluff, W.F. Translation Termination Is Involved in Histone mRNA Degradation when DNA Replication Is Inhibited. Mol. Cell. Biol. 2005, 25, 6879–6888. [CrossRef] 30. Rai, T.S.; Cole, J.J.; Nelson, D.M.; Dikovskaya, D.; Faller, W.J.; Vizioli, M.G.; Hewitt, R.N.; Anannya, O.; McBryan, T.; Manoharan, I.; et al. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev. 2014, 28, 2712–2725. [CrossRef] 31. Duarte, L.F.; Young, A.R.J.; Wang, Z.; Wu, H.-A.; Panda, T.; Kou, Y.; Kapoor, A.; Hasson, D.; Mills, N.R.; Ma’ayan, A.; et al. Histone H3.3 and its proteolytically processed form drive a cellular senescence programme. Nat. Commun. 2014, 5, 5210. [CrossRef] 32. Contrepois, K.; Coudereau, C.; Benayoun, B.A.; Schuler, N.; Roux, P.-F.; Bischof, O.; Courbeyrette, R.; Carvalho, C.; Thuret, J.-Y.; Ma, Z.; et al. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression. Nat. Commun. 2017, 8, 14995. [CrossRef][PubMed] 33. Gévry, N.; Ho, M.C.; Laflamme, L.; Livingston, D.M.; Gaudreau, L. p21 transcription is regulated by differential localization of histone H2A.Z. Genes Dev. 2007, 21, 1869–1881. [CrossRef][PubMed] 34. Svotelis, A.; Gévry, N.; Gaudreau, L. Regulation of gene expression and cellular proliferation by histone H2A.Z. Biochem. Cell Biol. 2009, 87, 179–188. [CrossRef] 35. Lazorthes, S.; Vallot, C.; Briois, S.; Aguirrebengoa, M.; Thuret, J.Y.; Laurent, G.S.; Rougeulle, C.; Kapranov, P.; Mann, C.; Trouche, D.; et al. A vlincRNA participates in senescence maintenance by relieving H2AZ-mediated repression at the INK4 locus. Nat. Commun. 2015, 6.[CrossRef][PubMed] 36. Elsässer, S.J.; Noh, K.-M.; Diaz, N.; Allis, D.; Banaszynski, L.A. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells. Nature 2015, 522, 240–244. [CrossRef][PubMed] 37. Colombo, A.R.; Elias, H.K.; Ramsingh, G. Senescence induction universally activates transposable element expression. Cell Cycle 2018, 17, 1846–1857. [CrossRef][PubMed] 38. Cardelli, M. The epigenetic alterations of endogenous retroelements in aging. Mech. Ageing Dev. 2018, 174, 30–46. [CrossRef] 39. Rivera-Casas, C.; Gonzalez-Romero, R.; Cheema, M.S.; Ausió, J.; Eirín-López, J.M. The characterization of macroH2A beyond supports an ancestral origin and conserved role for histone variants in chromatin. Epigenetics 2016, 11, 415–425. [CrossRef] 40. Zhang, R.; Poustovoitov, M.V.; Ye, X.; Santos, H.A.; Chen, W.; Daganzo, S.M.; Erzberger, J.P.; Serebriiskii, I.G.; Canutescu, A.A.; Dunbrack, R.L.; et al. Formation of macroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev. Cell 2005, 8, 19–30. [CrossRef] 41. Cole, J.J.; Robertson, N.A.; Rather, M.I.; Thomson, J.P.; McBryan, T.; Sproul, D.; Wang, T.; Brock, C.; Clark, W.; Ideker, T.; et al. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 2017, 18, 58. [CrossRef] 42. Kennedy, A.L.; McBryan, T.; Enders, G.H.; Johnson, F.B.; Zhang, R.; Adams, P.D. Senescent mouse cells fail to overtly regulate the HIRA histone chaperone and do not form robust Senescence Associated Heterochromatin Foci. Cell Div. 2010, 5, 1–11. [CrossRef][PubMed] 43. Chandra, T.; Kirschner, K.; Thuret, J.; Pope, B.D.; Ryba, T.; Newman, S.; Ahmed, K.; Samarajiwa, S.A.; Salama, R.; Carroll, T.; et al. Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation. Mol. Cell 2012, 47, 203–214. [CrossRef][PubMed] 44. Sadaie, M.; Salama, R.; Carroll, T.; Tomimatsu, K.; Chandra, T.; Young, A.R.J.; Narita, M.; Pérez-Mancera, P.A.; Bennett, D.C.; Chong, H.; et al. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic doma.pdf. Genes Dev. 2013, 27, 1800–1808. [CrossRef][PubMed] 45. Chandra, T.; Narita, M. High-order chromatin structure and the epigenome in SAHFs. Nucleus 2013, 4, 23–28. [CrossRef][PubMed] 46. Narita, M. Cellular senescence and chromatin organisation. Br. J. Cancer 2007, 96, 686–691. [CrossRef] [PubMed] 47. Ye, X.; Zerlanko, B.; Zhang, R.; Somaiah, N.; Lipinski, M.; Salomoni, P.; Adams, P.D. Definition of pRB- and TP53-Dependent and -Independent Steps in HIRA/ASF1a-Mediated Formation of Senescence-Associated Heterochromatin Foci. Mol. Cell. Biol. 2007, 27, 2452–2465. [CrossRef][PubMed] Cells 2020, 9, 466 12 of 18

48. Liu, S.; Fang, X.; Hall, H.; Yu, S.; Smith, D.; Lu, Z.; Fang, D.; Liu, J.; Stephens, L.C.; Woodgett, J.R.; et al. Homozygous deletion of glycogen synthase kinase 3β bypasses senescence allowing Ras transformation of primary murine fibroblasts. Proc. Natl. Acad. Sci. USA 2008, 105, 5248–5253. [CrossRef] 49. Jørgensen, S.; Schotta, G.; Sørensen, C.S. 20 methylation: Key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 2013, 41, 2797–2806. [CrossRef] 50. Sidler, C.; Kovalchuk, O.; Kovalchuk, I. Epigenetic Regulation of Cellular Senescence and Aging. Front. Genet. 2017, 8.[CrossRef] 51. Zhang, W.; Li, J.; Suzuki, K.; Qu, J.; Wang, P.; Zhou, J.; Liu, X.; Ren, R.; Xu, X.; Ocampo, A.; et al. A model unveils heterochromatin alterations as a driver of human aging. Science 2015, 348, 1160–1163. [CrossRef] 52. Benayoun, B.A.; Pollina, E.A.; Brunet, A. Epigenetic regulation of ageing: Linking environmental inputs to genomic stability. Nat. Rev. Mol. Cell Biol. 2015, 16, 593–610. [CrossRef][PubMed] 53. Capell, B.C.; Drake, A.M.; Zhu, J.; Shah, P.P.; Dou, Z.; Dorsey, J.; Simola, D.F.; Donahue, G.; Sammons, M.; Rai, T.S.; et al. Mll1 is essential for the senescenceassociated secretory phenotype. Genes Dev. 2016, 30, 321–336. [CrossRef][PubMed] 54. Nelson, D.M.; Jaber-Hijazi, F.; Cole, J.J.; Robertson, N.A.; Pawlikowski, J.S.; Norris, K.T.; Criscione, S.W.; Pchelintsev, N.A.; Piscitello, D.; Stong, N.; et al. Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability. Genome Biol. 2016, 17, 1–20. [CrossRef][PubMed] 55. Sen, P.; Lan, Y.; Li, C.Y.; Sidoli, S.; Donahue, G.; Dou, Z.; Frederick, B.; Chen, Q.; Luense, L.J.; Garcia, B.A.; et al. Histone Acetyltransferase p300 Induces De Novo Super-Enhancers to Drive Cellular Senescence. Mol. Cell 2019, 73, 684–698.e8. [CrossRef][PubMed] 56. Shah, P.P.; Donahue, G.; Otte, G.L.; Capell, B.C.; Nelson, D.M.; Cao, K.; Aggarwala, V.; Cruickshanks, H.A.; Rai, T.S.; McBryan, T.; et al. Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape. Genes Dev. 2013, 27, 1787–1799. [CrossRef] 57. Freund, A.; Laberge, R.-M.; Demaria, M.; Campisi, J. Lamin B1 loss is a senescence-associated . Mol. Biol. Cell 2012, 23, 2066–2075. [CrossRef] 58. Pascual-Reguant, L.; Blanco, E.; Galan, S.; Le Dily, F.; Cuartero, Y.; Serra-Bardenys, G.; Di Carlo, V.; Iturbide, A.; Cebrià-Costa, J.P.; Nonell, L.; et al. Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains. Nat. Commun. 2018, 9, 3420. [CrossRef] 59. Dou, Z.; Xu, C.; Donahue, G.; Shimi, T.; Pan, J.A.; Zhu, J.; Ivanov, A.; Capell, B.C.; Drake, A.M.; Shah, P.P.; et al. mediates degradation of nuclear lamina. Nature 2015, 527, 105–109. [CrossRef] 60. Vidak, S.; Kubben, N.; Dechat, T.; Foisner, R. Proliferation of progeria cells is enhanced by lamina-associated polypeptide 2α (LAP2α) through expression of proteins. Genes Dev. 2015, 29, 2022–2036. [CrossRef] 61. Kubben, N.; Adriaens, M.; Meuleman, W.; Voncken, J.W.; Van Steensel, B.; Misteli, T. Mapping of lamin A- and progerin-interacting genome regions. Chromosoma 2012, 121, 447–464. [CrossRef] 62. Kudlow, B.A.; Kennedy, B.K.; Monnat, R.J. Werner and Hutchinson-Gilford progeria syndromes: Mechanistic basis of human progeroid diseases. Nat. Rev. Mol. Cell Biol. 2007, 8, 394–404. [CrossRef][PubMed] 63. Dillinger, S.; Straub, T.; Nemeth, A. Nucleolus association of chromosomal domains is largely maintained in cellular senescence despite massive nuclear reorganisation. PLoS ONE 2017, 12, e0178821. [CrossRef] [PubMed] 64. Criscione, S.W.; Teo, Y.V.; Neretti, N. The Chromatin Landscape of Cellular Senescence. Trends Genet. 2016, 32, 751–761. [CrossRef][PubMed] 65. Iwasaki, O.; Tanizawa, H.; Kim, K.-D.; Kossenkov, A.; Nacarelli, T.; Tashiro, S.; Majumdar, S.; Showe, L.C.; Zhang, R.; Noma, K. Involvement of condensin in cellular senescence through gene regulation and compartmental reorganization. Nat. Commun. 2019, 10, 5688. [CrossRef] 66. Ito, T.; Teo, Y.V.; Evans, S.A.; Neretti, N.; Sedivy, J.M. Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage- and -Dependent Pathways. Cell Rep. 2018, 22, 3480–3492. [CrossRef] 67. Katada, S.; Sassone-Corsi, P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nat. Struct. Mol. Biol. 2010, 17, 1414–1421. [CrossRef] Cells 2020, 9, 466 13 of 18

68. Wang, Y.; Hou, N.; Cheng, X.; Zhang, J.; Tan, X.; Zhang, C.; Tang, Y.; Teng, Y.; Yang, X. Ezh2 Acts as a Tumor Suppressor in Kras-driven Lung Adenocarcinoma. Int. J. Biol. Sci. 2017, 13, 652–659. [CrossRef] 69. Robin, J.D.; Ludlow, A.T.; Batten, K.; Magdinier, F.; Stadler, G.; Wagner, K.R.; Shay, J.W.; Wright, W.E. Telomere position effect: Regulation of gene expression with progressive telomere shortening over long distances. Genes Dev. 2014, 28, 2464–2476. [CrossRef] 70. Hannum, G.; Guinney, J.; Zhao, L.; Zhang, L.; Hughes, G.; Sadda, S.; Klotzle, B.; Bibikova, M.; Fan, J.-B.; Gao, Y.; et al. Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates. Mol. Cell 2013, 49, 359–367. [CrossRef] 71. Petkovich, D.A.; Podolskiy,D.I.; Lobanov,A.V.; Lee, S.-G.; Miller, R.A.; Gladyshev,V.N. Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions. Cell Metab. 2017, 25, 954–960.e6. [CrossRef] 72. Wang, T.; Tsui, B.; Kreisberg, J.F.; Robertson, N.A.; Gross, A.M.; Yu, M.K.; Carter, H.; Brown-Borg, H.M.; Adams, P.D.; Ideker, T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol. 2017, 18, 1–11. [CrossRef][PubMed] 73. Levine, M.E.; Lu, A.T.; Bennett, D.A.; Horvath, S. Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer’s disease related cognitive functioning. Aging (Albany. NY). 2015, 7, 1198–1211. [CrossRef][PubMed] 74. Horvath, S.; Gurven, M.; Levine, M.E.; Trumble, B.C.; Kaplan, H.; Allayee, H.; Ritz, B.R.; Chen, B.; Lu, A.T.; Rickabaugh, T.M.; et al. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol. 2016, 17, 171. [CrossRef][PubMed] 75. Raina, R.; Sen, D. Can crosstalk between DOR and PARP reduce oxidative stress mediated neurodegeneration? Neurochem. Int. 2018, 112, 206–218. [CrossRef][PubMed] 76. Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 2013, 14, R115. [CrossRef] [PubMed] 77. Heyn, H.; Moran, S.; Hernando-Herraez, I.; Sayols, S.; Gomez, A.; Sandoval, J.; Monk, D.; Hata, K.; Marques-Bonet, T.; Wang, L.; et al. DNA methylation contributes to natural human variation. Genome Res. 2013, 23, 1363–1372. [CrossRef] 78. Baylin, S.B.; Jones, P.A.A decade of exploring the cancer epigenome—Biological and translational implications. Nat. Rev. Cancer 2011, 11, 726–734. [CrossRef] 79. Mays-Hoopes, L.L. DNA methylation in senescence, aging and cancer. Oncoscience 2019, 44, 291. 80. Neri, F.; Rapelli, S.; Krepelova, A.; Incarnato, D.; Parlato, C.; Basile, G.; Maldotti, M.; Anselmi, F.; Oliviero, S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017, 543, 72–77. [CrossRef] 81. Zhang, W.; Ji, W.; Yang, J.; Yang, L.; Chen, W.; Zhuang, Z. Comparison of global DNA methylation profiles in replicative versus premature senescence. Life Sci. 2008, 83, 475–480. [CrossRef] 82. Yu, D.; Du, Z.; Pian, L.; Li, T.; Wen, X.; Li, W.; Kim, S.J.; Xiao, J.; Cohen, P.; Cui, J.; et al. Mitochondrial DNA hypomethylation is a biomarker associated with induced senescence in human fetal heart mesenchymal stem cells. Stem Cells Int. 2017, 2017, 14–16. [CrossRef][PubMed] 83. Hänzelmann, S.; Beier, F.; Gusmao, E.G.; Koch, C.M.; Hummel, S.; Charapitsa, I.; Joussen, S.; Benes, V.; Brümmendorf, T.H.; Reid, G.; et al. Replicative senescence is associated with nuclear reorganization and with methylation at specific binding sites. Clin. Epigenetics 2015, 7, 1–19. [CrossRef] [PubMed] 84. Paluvai, H.; Di Giorgio, E.; Brancolini, C. Unscheduled HDAC4 repressive activity in human fibroblasts triggers TTP53-dependent senescence and favors cell transformation. Mol. Oncol. 2018, 12, 2165–2181. [CrossRef][PubMed] 85. Astle, M.V.; Hannan, K.M.; Ng, P.Y.; Lee, R.S.; George, A.J.; Hsu, A.K.; Haupt, Y.; Hannan, R.D.; Pearson, R.B. AKT induces senescence in human cells via mTORC1 and TP53 in the absence of DNA damage: Implications for targeting mTOR during malignancy. Oncogene 2012, 31, 1949–1962. [CrossRef][PubMed] 86. Teo, Y.V.; Rattanavirotkul, N.; Olova, N.; Salzano, A.; Quintanilla, A.; Tarrats, N.; Kiourtis, C.; Müller, M.; Green, A.R.; Adams, P.D.; et al. NOTCH Signaling Mediates Secondary Senescence. Cell Rep. 2019, 27, 997–1007.e5. [CrossRef] 87. Mallette, F.A.; Moiseeva, O.; Calabrese, V.; Mao, B.; Gaumont-Leclerc, M.F.; Ferbeyre, G. Transcriptome analysis and tumor suppressor requirements of STAT5-induced senescence. Ann. N. Y. Acad. Sci. 2010, 1197, 142–151. [CrossRef] Cells 2020, 9, 466 14 of 18

88. Serrano, M.; Lin, A.W.; McCurrach, M.E.; Beach, D.; Lowe, S.W. Oncogenic ras Provokes Premature Cell Senescence Associated with Accumulation of TP53 and p16INK4a. Cell 1997, 88, 593–602. [CrossRef] 89. Michaloglou, C.; Vredeveld, L.C.W.; Soengas, M.S.; Denoyelle, C.; Kuilman, T.; Van Der Horst, C.M.A.M.; Majoor, D.M.; Shay, J.W.; Mooi, W.J.; Peeper, D.S. BRAFE600-associated senescence-like cell cycle arrest of human naevi. Nature 2005, 436, 720–724. [CrossRef] 90. Parry, A.J.; Hoare, M.; Bihary, D.; Hänsel-Hertsch, R.; Smith, S.; Tomimatsu, K.; Mannion, E.; Smith, A.; D’Santos, P.; Russell, I.A.; et al. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. Nat. Commun. 2018, 9, 1–15. [CrossRef] 91. Trost, T.M.; Lausch, E.U.; Fees, S.A.; Schmitt, S.; Enklaar, T.; Reutzel, D.; Brixel, L.R.; Schmidtke, P.; Maringer, M.; Schiffer, I.B.; et al. Premature senescence is a primary fail-safe mechanism of ERBB2-driven tumorigenesis in breast carcinoma cells. Cancer Res. 2005, 65, 840–849. 92. Gu, Z.; Tan, W.; Feng, G.; Meng, Y.; Shen, B.; Liu, H.; Cheng, C. Wnt/β-catenin signaling mediates the senescence of bone marrow-mesenchymal stem cells from systemic lupus erythematosus patients through the TP53/p21 pathway. Mol. Cell. Biochem. 2014, 387, 27–37. [CrossRef] 93. Lee, J.J.; Kim, B.C.; Park, M.J.; Lee, Y.S.; Kim, Y.N.; Lee, B.L.; Lee, J.S. PTEN status switches cell fate between premature senescence and apoptosis in glioma exposed to ionizing radiation. Cell Death Differ. 2011, 18, 666–677. [CrossRef][PubMed] 94. Verschuren, E.W.; Ban, K.H.; Masek, M.A.; Lehman, N.L.; Jackson, P.K. Loss of Emi1-Dependent Anaphase-Promoting Complex/Cyclosome Inhibition Deregulates E2F Target Expression and Elicits DNA Damage-Induced Senescence. Mol. Cell. Biol. 2007, 27, 7955–7965. [CrossRef][PubMed] 95. Collado, M.; Gil, J.; Efeyan, A.; Guerra, C.; Schuhmacher, A.J.; Barradas, M.; Benguría, A.; Zaballos, A.; Flores, J.M.; Barbacid, M.; et al. Tumour biology: Senescence in premalignant tumours. Nature 2005, 436, 642. [CrossRef][PubMed] 96. Olsen, C.L.; Gardie, B.; Yaswen, P.; Stampfer, M.R. Raf-1-induced growth arrest in human mammary epithelial cells is p16-independent and is overcome in immortal cells during conversion. Oncogene 2002, 21, 6328–6339. [CrossRef][PubMed] 97. Cipriano, R.; Kan, C.E.; Graham, J.; Danielpour, D.; Stampfer, M.; Jackson, M.W. TGF-β signaling engages an ATM-CHK2-TP53-independent RAS-induced senescence and prevents malignant transformation in human mammary epithelial cells. Proc. Natl. Acad. Sci. USA 2011, 108, 8668–8673. [CrossRef] 98. Kennedy, A.L.; Morton, J.P.; Manoharan, I.; Nelson, D.M.; Jamieson, N.B.; Pawlikowski, J.S.; McBryan, T.; Doyle, B.; McKay, C.; Oien, K.A.; et al. Activation of the PIK3CA/AKT Pathway Suppresses Senescence Induced by an Activated RAS Oncogene to Promote Tumorigenesis. Mol. Cell 2011, 42, 36–49. [CrossRef] 99. Ye, X.; Zerlanko, B.; Kennedy, A.; Banumathy, G.; Zhang, R.; Adams, P.D. Downregulation of Wnt Signaling Is a Trigger for Formation of Facultative Heterochromatin and Onset of Cell Senescence in Primary Human Cells. Mol. Cell 2007, 27, 183–196. [CrossRef] 100. Chen, H.; Ruiz, P.D.; McKimpson, W.M.; Novikov, L.; Kitsis, R.N.; Gamble, M.J. MacroH2A1 and ATM Play Opposing Roles in Paracrine Senescence and the Senescence-Associated Secretory Phenotype. Mol. Cell 2015, 59, 719–731. [CrossRef] 101. Lenain, C.; De Graaf, C.A.; Pagie, L.; Visser, N.L.; De Haas, M.; De Vries, S.S.; Peric-Hupkes, D.; Van Steensel, B.; Peeper, D.S. Massive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence. Genome Res. 2017, 27, 1634–1644. [CrossRef] 102. Agger, K.; Cloos, P.A.C.; Rudkjaer, L.; Williams, K.; Andersen, G.; Christensen, J.; Helin, K. The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence. Genes Dev. 2009, 23, 1171–1176. [CrossRef][PubMed] 103. Barradas, M.; Anderton, E.; Acosta, J.C.; De Li, S.; Banito, A.; Rodriguez-Niedenführ, M.; Maertens, G.; Banck, M.; Zhou, M.M.; Walsh, M.J.; et al. Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS. Genes Dev. 2009, 23, 1177–1182. [CrossRef][PubMed] 104. Corpet, A.; Olbrich, T.; Gwerder, M.; Fink, D.; Stucki, M. Dynamics of histone H3.3 deposition in proliferating and senescent cells reveals a DAXX-dependent targeting to PML-NBs important for pericentromeric heterochromatin organization. Cell Cycle 2014, 13, 249–267. [CrossRef][PubMed] 105. Tasdemir, N.; Banito, A.; Roe, J.-S.; Alonso-Curbelo, D.; Camiolo, M.; Tschaharganeh, D.F.; Huang, C.; Aksoy, O.; Bolden, J.E.; Chen, C.-C.; et al. BRD4 Connects Enhancer Remodeling to Senescence Immune Surveillance. Cancer Discov. 2016, 6, 612–629. [CrossRef] Cells 2020, 9, 466 15 of 18

106. Watanabe, S.; Kawamoto, S.; Ohtani, N.; Hara, E. Impact of senescence-associated secretory phenotype and its potential as a therapeutic target for senescence-associated diseases. Cancer Sci. 2017, 108, 563–569. [CrossRef] 107. Swanson, E.C.; Manning, B.; Zhang, H.; Lawrence, J.B. Higher-order unfolding of satellite heterochromatin is a consistent and early event in cell senescence. J. Cell Biol. 2013, 203, 929–942. [CrossRef] 108. Shumaker, D.K.; Dechat, T.; Kohlmaier, A.; Adam, S.A.; Bozovsky, M.R.; Erdos, M.R.; Eriksson, M.; Goldman, A.E.; Khuon, S.; Collins, F.S.; et al. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc. Natl. Acad. Sci. USA 2006, 103, 8703–8708. [CrossRef] 109. McCord, R.P.; Nazario-Toole, A.; Zhang, H.; Chines, P.S.; Zhan, Y.; Erdos, M.R.; Collins, F.S.; Dekker, J.; Cao, K. Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013, 23, 260–269. [CrossRef] 110. Xie, W.; Kagiampakis, I.; Pan, L.; Zhang, Y.W.; Murphy, L.; Tao, Y.; Kong, X.; Kang, B.; Xia, L.; Carvalho, F.L.F.; et al. DNA Methylation Patterns Separate Senescence from Transformation Potential and Indicate Cancer Risk. Cancer Cell 2018, 33, 309–321.e5. [CrossRef] 111. Braig, M.; Lee, S.; Loddenkemper, C.; Rudolph, C.; Peters, A.H.F.M.; Schlegelberger, B.; Stein, H.; Dörken, B.; Jenuwein, T.; Schmitt, C.A. Oncogene-induced senescence as an initial barrier in lymphoma development. Nature 2005, 436, 660–665. [CrossRef] 112. Di Giorgio, E.; Franforte, E.; Cefalù, S.; Rossi, S.; Dei Tos, A.P.; Brenca, M.; Polano, M.; Maestro, R.; Paluvai, H.; Picco, R.; et al. The co-existence of transcriptional activator and transcriptional MEF2 complexes influences tumor aggressiveness. PLoS Genet. 2017, 13, e1006752. [CrossRef][PubMed] 113. Wilting, R.H.; Dannenberg, J.H. Epigenetic mechanisms in tumorigenesis, tumor cell heterogeneity and drug resistance. Drug Resist. Updat. 2012, 15, 21–38. [CrossRef][PubMed] 114. Di Giorgio, E.; Paluvai, H.; Picco, R.; Brancolini, C. Genetic programs driving oncogenic transformation: Lessons from in vitro models. Int. J. Mol. Sci. 2019, 20.[CrossRef][PubMed] 115. Di Giorgio, E.; Dalla, E.; Franforte, E.; Paluvai, H.; Minisini, M.; Trevisanut, M.; Picco, R.; Brancolini, C. Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells. Nucleic Acids Res. 2020, 48, 646–664. [CrossRef][PubMed] 116. Cutano, V.; Di Giorgio, E.; Minisini, M.; Picco, R.; Dalla, E.; Brancolini, C. HDAC7-mediated control of tumour microenvironment maintains proliferative and stemness competence of human mammary epithelial cells. Mol. Oncol. 2019, 13, 1651–1668. [CrossRef] 117. Yu, Y.; Schleich, K.; Yue, B.; Ji, S.; Lohneis, P.; Kemper, K.; Silvis, M.R.; Qutob, N.; van Rooijen, E.; Werner-Klein, M.; et al. Targeting the Senescence-Overriding Cooperative Activity of Structurally Unrelated H3K9 Demethylases in Melanoma. Cancer Cell 2018, 33, 322–336.e8. [CrossRef] 118. Frippiat, C.; Chen, Q.M.; Zdanov, S.; Magalhaes, J.P.; Remacle, J.; Toussaint, O. Subcytotoxic H2O2 Stress Triggers a Release of Transforming -β1, Which Induces of Cellular Senescence of Human Diploid Fibroblasts. J. Biol. Chem. 2001, 276, 2531–2537. [CrossRef] 119. Duan, J.; Duan, J.; Zhang, Z.; Tong, T. Irreversible cellular senescence induced by prolonged exposure to H 2O2 involves DNA-damage-and-repair genes and telomere shortening. Int. J. Biochem. Cell Biol. 2005, 37, 1407–1420. [CrossRef] 120. Coluzzi, E.; Leone, S.; Sgura, A. Oxidative Stress Induces Telomere Dysfunction and Senescence by Replication Fork Arrest. Cells 2019, 8, 19. [CrossRef] 121. Fumagalli, M.; Rossiello, F.; Mondello, C.; D’Adda Di Fagagna, F. Stable cellular senescence is associated with persistent DDR activation. PLoS ONE 2014, 9, 44–46. [CrossRef] 122. Parrinello, S.; Samper, E.; Krtolica, A.; Goldstein, J.; Melov, S.; Campisi, J. Oxygen sensitivity severely limits the replicative lifespan of murine fibroblasts. Nat. Cell Biol. 2003, 5, 741–747. [CrossRef][PubMed] 123. Liu, Z.; Zhou, T.; Ziegler, A.C.; Dimitrion, P.; Zuo, L. Oxidative Stress in Neurodegenerative Diseases: From Molecular Mechanisms to Clinical Applications. Oxid. Med. Cell. Longev. 2017, 2017, 2525967. [CrossRef] [PubMed] 124. Mikkelsen, L.; Bialkowski, K.; Risom, L.; Løhr, M.; Loft, S.; Møller, P. Aging and defense against generation of

8-oxo-7,8-dihydro-20-deoxyguanosine in DNA. Free Radic. Biol. Med. 2009, 47, 608–615. [CrossRef][PubMed] 125. Niu, Y.; DesMarais, T.L.; Tong, Z.; Yao, Y.; Costa, M. Oxidative stress alters global histone modification and DNA methylation. Free Radic. Biol. Med. 2015, 82, 22–28. [CrossRef] Cells 2020, 9, 466 16 of 18

126. Nishida, N.; Kudo, M.; Nagasaka, T.; Ikai, I.; Goel, A. Characteristic patterns of altered DNA methylation predict emergence of human hepatocellular carcinoma. Hepatology 2012, 56, 994–1003. [CrossRef] 127. Sanders, Y.Y.; Liu, H.; Zhang, X.; Hecker, L.; Bernard, K.; Desai, L.; Liu, G.; Thannickal, V.J. Histone modifications in senescence-associated resistance to apoptosis by oxidative stress. Redox Biol. 2013, 1, 8–16. [CrossRef] 128. Chen, F.; Li, X.; Aquadro, E.; Haigh, S.; Zhou, J.; Stepp, D.W.; Weintraub, N.L.; Barman, S.A.; Fulton, D.J.R. Inhibition of reduces transcription of NADPH oxidases and ROS production and ameliorates pulmonary arterial hypertension. Free Radic. Biol. Med. 2016, 99, 167–178. [CrossRef] 129. Bosch-Presegué, L.; Raurell-Vila, H.; Marazuela-Duque, A.; Kane-Goldsmith, N.; Valle, A.; Oliver, J.; Serrano, L.; Vaquero, A. Stabilization of Suv39H1 by SirT1 Is Part of Oxidative Stress Response and Ensures Genome Protection. Mol. Cell 2011, 42, 210–223. [CrossRef] 130. Raurell-Vila, H.; Bosch-Presegue, L.; Gonzalez, J.; Kane-Goldsmith, N.; Casal, C.; Brown, J.P.; Marazuela-Duque, A.; Singh, P.B.; Serrano, L.; Vaquero, A. An HP1 isoform-specific feedback mechanism regulates Suv39h1 activity under stress conditions. Epigenetics 2017, 12, 166–175. [CrossRef] 131. Bielak-Zmijewska, A.; Mosieniak, G.; Sikora, E. Is DNA damage indispensable for stress-induced senescence? Mech. Ageing Dev. 2018, 170, 13–21. [CrossRef] 132. Ryu, Y.S.; Kang, K.A.; Piao, M.J.; Ahn, M.J.; Yi, J.M.; Bossis, G.; Hyun, Y.M.; Park, C.O.; Hyun, J.W. Particulate matter-induced senescence of skin keratinocytes involves oxidative stress-dependent epigenetic modifications. Exp. Mol. Med. 2019, 51.[CrossRef][PubMed] 133. Vizioli, M.G.; Liu, T.; Miller, K.N.; Robertson, N.A.; Gilroy, K.; Lagnado, A.B.; Perez-garcia, A.; Kiourtis, C.; Dasgupta, N.; Lei, X.; et al. Mitochondria-to-nucleus retrograde signaling drives formation of cytoplasmic chromatin and inflammation in senescence. Genes Dev. 2020, 1–18. [CrossRef][PubMed] 134. Itahana, K.; Zou, Y.; Itahana, Y.; Martinez, J.-L.; Beausejour, C.; Jacobs, J.J.L.; Van Lohuizen, M.; Band, V.; Campisi, J.; Dimri, G.P. Control of the replicative life span of human fibroblasts by p16 and the polycomb protein Bmi-1. Mol. Cell. Biol. 2003, 23, 389–401. [CrossRef][PubMed] 135. Zheng, H.; Huang, Q.; Huang, S.; Yang, X.; Zhu, T.; Wang, W.; Wang, H.; He, S.; Ji, L.; Wang, Y.; et al. Senescence inducer shikonin ROS-dependently suppressed lung cancer progression. Front. Pharmacol. 2018, 9, 1–15. [CrossRef] 136. Lee, J.S.; Mo, Y.; Gan, H.; Burgess, R.J.; Baker, D.J.; van Deursen, J.M.; Zhang, Z. Pak2 kinase promotes cellular senescence and organismal aging. Proc. Natl. Acad. Sci. USA 2019, 116, 13311–13319. [CrossRef] 137. Cheng, Y.; He, C.; Wang, M.; Ma, X.; Mo, F.; Yang, S.; Han, J.; Wei, X. Targeting epigenetic regulators for cancer therapy: Mechanisms and advances in clinical trials. Signal Transduct. Target. Ther. 2019, 4, 62. [CrossRef] 138. Dantuma, N.P.; Attikum, H. Spatiotemporal regulation of posttranslational modifications in the DNA damage response. EMBO J. 2016, 35, 6–23. [CrossRef] 139. Goldstein, M.; Derheimer, F.A.; Tait-Mulder, J.; Kastan, M.B. Nucleolin mediates nucleosome disruption critical for DNA double-strand break repair. Proc. Natl. Acad. Sci. USA 2013, 110, 16874–16879. [CrossRef] 140. Hinde, E.; Kong, X.; Yokomori, K.; Gratton, E. Chromatin dynamics during DNA repair revealed by pair correlation analysis of molecular flow in the nucleus. Biophys. J. 2014, 107, 55–65. [CrossRef] 141. Francia, S.; Michelini, F.; Saxena, A.; Tang, D.; de Hoon, M.; Anelli, V.; Mione, M.; Carninci, P.; d’Adda di Fagagna, F. Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 2012, 488, 231–235. [CrossRef] 142. Thorslund, T.; Ripplinger, A.; Hoffmann, S.; Wild, T.; Uckelmann, M.; Villumsen, B.; Narita, T.; Sixma, T.K.; Choudhary, C.; Bekker-Jensen, S.; et al. Histone H1 couples initiation and amplification of signalling after DNA damage. Nature 2015, 527, 389–393. [CrossRef][PubMed] 143. Mandemaker, I.K.; Van Cuijk, L.; Janssens, R.C.; Lans, H.; Bezstarosti, K.; Hoeijmakers, J.H.; Demmers, J.A.; Vermeulen, W.; Marteijn, J.A. DNA damage-induced histone H1 ubiquitylation is mediated by HUWE1 and stimulates the RNF8-RNF168 pathway. Sci. Rep. 2017, 7, 1–11. [CrossRef][PubMed] 144. Mattiroli, F.; Vissers, J.H.A.; Van Dijk, W.J.; Ikpa, P.; Citterio, E.; Vermeulen, W.; Marteijn, J.A.; Sixma, T.K. RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. Cell 2012, 150, 1182–1195. [CrossRef][PubMed] 145. Li, Y.; Li, Z.; Dong, L.; Tang, M.; Zhang, P.; Zhang, C.; Cao, Z.; Zhu, Q.; Chen, Y.; Wang, H.; et al. Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage. Nucleic Acids Res. 2018, 46, 7716–7730. [CrossRef][PubMed] Cells 2020, 9, 466 17 of 18

146. Luijsterburg, M.S.; de Krijger, I.; Wiegant, W.W.; Shah, R.G.; Smeenk, G.; de Groot, A.J.L.; Pines, A.; Vertegaal, A.C.O.; Jacobs, J.J.L.; Shah, G.M.; et al. PARP1 Links CHD2-Mediated Chromatin Expansion and H3.3 Deposition to DNA Repair by Non-homologous End-Joining. Mol. Cell 2016, 61, 547–562. [CrossRef] 147. Xu, Y.; Ayrapetov, M.K.; Xu, C.; Gursoy-Yuzugullu, O.; Hu, Y.; Price, B.D. Histone H2A.Z Controls a Critical Chromatin Remodeling Step Required for DNA Double-Strand Break Repair. Mol. Cell 2012, 48, 723–733. [CrossRef] 148. Hossain, M.B.; Shifat, R.; Johnson, D.G.; Bedford, M.T.; Gabrusiewicz, K.R.; Cortes-Santiago, N.; Luo, X.; Lu, Z.; Ezhilarasan, R.; Sulman, E.P.; et al. TIE2-mediated tyrosine phosphorylation of H4 regulates DNA damage response by recruiting ABL1. Sci. Adv. 2016, 2, e1501290. [CrossRef] 149. Moyal, L.; Lerenthal, Y.; Gana-Weisz, M.; Mass, G.; So, S.; Wang, S.Y.; Eppink, B.; Chung, Y.M.; Shalev, G.; Shema, E.; et al. Requirement of ATM-Dependent Monoubiquitylation of for Timely Repair of DNA Double-Strand Breaks. Mol. Cell 2011, 41, 529–542. [CrossRef] 150. Fradet-Turcotte, A.; Canny, M.D.; Escribano-Díaz, C.; Orthwein, A.; Leung, C.C.Y.; Huang, H.; Landry, M.-C.; Kitevski-LeBlanc, J.; Noordermeer, S.M.; Sicheri, F.; et al. 53BP1 is a reader of the DNA-damage-induced H2A Lys 15 ubiquitin mark. Nature 2013, 499, 50–54. [CrossRef] 151. Wilson, M.D.; Benlekbir, S.; Fradet-Turcotte, A.; Sherker, A.; Julien, J.P.; McEwan, A.; Noordermeer, S.M.; Sicheri, F.; Rubinstein, J.L.; Durocher, D. The structural basis of modified nucleosome recognition by 53BP1. Nature 2016, 536, 100–103. [CrossRef] 152. Chapman, J.R.; Taylor, M.R.G.; Boulton, S.J. Playing the End Game: DNA Double-Strand Break Repair Pathway Choice. Mol. Cell 2012, 47, 497–510. [CrossRef] 153. Uckelmann, M.; Sixma, T.K. Histone ubiquitination in the DNA damage response. DNA Repair (Amst). 2017, 56, 92–101. [CrossRef][PubMed] 154. Botuyan, M.V.; Lee, J.; Ward, I.M.; Kim, J.-E.; Thompson, J.R.; Chen, J.; Mer, G. Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair. Cell 2006, 127, 1361–1373. [CrossRef][PubMed] 155. Tang, J.; Cho, N.W.; Cui, G.; Manion, E.M.; Shanbhag, N.M.; Botuyan, M.V.; Mer, G.; Greenberg, R.A. Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination. Nat. Struct. Mol. Biol. 2013, 20, 317–325. [CrossRef][PubMed] 156. Clouaire, T.; Rocher, V.; Lashgari, A.; Arnould, C.; Aguirrebengoa, M.; Biernacka, A.; Skrzypczak, M.; Aymard, F.; Fongang, B.; Dojer, N.; et al. Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures. Mol. Cell 2018, 72, 250–262.e6. [CrossRef] 157. Carrozza, M.J.; Li, B.; Florens, L.; Suganuma, T.; Swanson, S.K.; Lee, K.K.; Shia, W.J.; Anderson, S.; Yates, J.; Washburn, M.P.; et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005, 123, 581–592. [CrossRef] 158. Clouaire, T.; Legube, G. A Snapshot on the Cis Chromatin Response to DNA Double-Strand Breaks. Trends Genet. 2019, 35, 330–345. [CrossRef] 159. Morgan, M.T.; Haj-Yahya, M.; Ringel, A.E.; Bandi, P.; Brik, A.; Wolberger, C. Structural basis for histone H2B deubiquitination by the SAGA DUB module. Science 2016, 351, 725–728. [CrossRef] 160. Horikoshi, N.; Sharma, D.; Leonard, F.; Pandita, R.K.; Charaka, V.K.; Hambarde, S.; Horikoshi, N.T.; Gaur Khaitan, P.; Chakraborty, S.; Cote, J.; et al. Pre-existing H4K16ac levels in euchromatin drive DNA repair by homologous recombination in S-phase. Commun. Biol. 2019, 2, 1–12. [CrossRef] 161. Wu, W.; Nishikawa, H.; Fukuda, T.; Vittal, V.; Asano, M.; Miyoshi, Y.; Klevit, R.E.; Ohta, T. Interaction of BARD1 and HP1 Is Required for BRCA1 Retention at Sites of DNA Damage. Cancer Res. 2015, 75, 1311–1321. [CrossRef] 162. Khurana, S.; Kruhlak, M.J.; Kim, J.; Tran, A.D.; Liu, J.; Nyswaner, K.; Shi, L.; Jailwala, P.; Sung, M.-H.; Hakim, O.; et al. A Macrohistone Variant Links Dynamic Chromatin Compaction to BRCA1-Dependent Genome Maintenance. Cell Rep. 2014, 8, 1049–1062. [CrossRef][PubMed] 163. Burgess, R.C.; Burman, B.; Kruhlak, M.J.; Misteli, T. Activation of DNA Damage Response Signaling by Condensed Chromatin. Cell Rep. 2014, 9, 1703–1717. [CrossRef][PubMed] 164. Hauer, M.H.; Seeber, A.; Singh, V.; Thierry,R.; Sack, R.; Amitai, A.; Kryzhanovska, M.; Eglinger, J.; Holcman, D.; Owen-Hughes, T.; et al. Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates. Nat. Struct. Mol. Biol. 2017, 24, 99–107. [CrossRef][PubMed] Cells 2020, 9, 466 18 of 18

165. Mourad, R.; Ginalski, K.; Legube, G.; Cuvier, O. Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution. Genome Biol. 2018, 19, 1–14. [CrossRef] 166. Krumm, A.; Barckhausen, C.; Kucuk, P.; Tomaszowski, K.H.; Loquai, C.; Fahrer, J.; Kramer, O.H.; Kaina, B.; Roos, W.P. Enhanced histone deacetylase activity in malignant melanoma provokes RAD51 and FANCD2-triggered drug resistance. Cancer Res. 2016, 76, 3067–3077. [CrossRef] 167. Childs, B.G.; Baker, D.J.; Kirkland, J.L.; Campisi, J.; van Deursen, J.M. Senescence and apoptosis: Dueling or complementary cell fates? EMBO Rep. 2014, 15, 1139–1153. [CrossRef] 168. Zhang, Y.; Gao, Y.; Zhang, G.; Huang, S.; Dong, Z.; Kong, C.; Su, D.; Du, J.; Zhu, S.; Liang, Q.; et al. DNMT3a plays a role in switches between doxorubicin-induced senescence and apoptosis of colorectal cancer cells. Int. J. Cancer 2011, 128, 551–561. [CrossRef] 169. Takeuchi, S.; Takahashi, A.; Motoi, N.; Yoshimoto, S.; Tajima, T.; Yamakoshi, K.; Hirao, A.; Yanagi, S.; Fukami, K.; Ishikawa, Y.; et al. Intrinsic cooperation between p16INK4aand p21 Waf1/Cip1in the onset of cellular senescence and tumor suppression in vivo. Cancer Res. 2010, 70, 9381–9390. [CrossRef] 170. Karimian, A.; Ahmadi, Y.; Yousefi, B. Multiple functions of p21 in cell cycle, apoptosis and transcriptional regulation after DNA damage. DNA Repair (Amst). 2016, 42, 63–71. [CrossRef] 171. Correia-Melo, C.; Marques, F.D.; Anderson, R.; Hewitt, G.; Hewitt, R.; Cole, J.; Carroll, B.M.; Miwa, S.; Birch, J.; Merz, A.; et al. Mitochondria are required for pro-ageing features of the senescent phenotype. EMBO J. 2016, 35, 724–742. [CrossRef] 172. Ren, R.; Ocampo, A.; Liu, G.-H.; Izpisua Belmonte, J.C. Regulation of Stem Cell Aging by Metabolism and Epigenetics. Cell Metab. 2017, 26, 460–474. [CrossRef][PubMed] 173. Ciotti, S.; Iuliano, L.; Cefalù, S.; Comelli, M.; Mavelli, I.; Di Giorgio, E.; Brancolini, C. GSK3β is a key regulator of the ROS-dependent necrotic death induced by the quinone DMNQ. Cell Death Dis. 2020, 11, 2. [CrossRef] [PubMed] 174. Rivera-Mulia, J.C.; Schwerer, H.; Besnard, E.; Desprat, R.; Trevilla-Garcia, C.; Sima, J.; Bensadoun, P.; Zouaoui, A.; Gilbert, D.M.; Lemaitre, J.M. Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 2018, 17, 1667–1681. [CrossRef][PubMed] 175. Rivera-mulia, J.C.; Dimond, A.; Vera, D.; Trevilla-garcia, C.; Sasaki, T.; Dupont, C.; Gribnau, J.; Fraser, P.; Gilbert, D.M.; Gilbert, D.M.; et al. Allele-specific control of replication timing and genome organization during development DNA replication timing, hybrid mouse ES cells, Hi-C., SNPs in vitro. bioRxiv 2018, 800–811. 176. Tsantoulis, P.K.; Kotsinas, A.; Sfikakis, P.P.; Evangelou, K.; Sideridou, M.; Levy, B.; Mo, L.; Kittas, C.; Wu, X.R.; Papavassiliou, A.G.; et al. Oncogene-induced replication stress preferentially targets common fragile sites in preneoplastic lesions. A genome-wide study. Oncogene 2008, 27, 3256–3264. [CrossRef][PubMed] 177. Thorsson, V.; Gibbs, D.L.; Brown, S.D.; Wolf, D.; Bortone, D.S.; Ou Yang, T.-H.; Porta-Pardo, E.; Gao, G.F.; Plaisier, C.L.; Eddy, J.A.; et al. The Immune Landscape of Cancer. Immunity 2018, 48, 812–830.e14. [CrossRef] 178. Arora, M.; Moser, J.; Phadke, H.; Basha, A.A.; Spencer, S.L. Endogenous Replication Stress in Mother Cells Leads to Quiescence of Daughter Cells. Cell Rep. 2017, 19, 1351–1364. [CrossRef] 179. Di Giorgio, E.; Hancock, W.W.; Brancolini, C. MEF2 and the tumorigenic process, hic sunt leones. Biochim Biophys Acta Rev Cancer 2018, 1870, 261–273. [CrossRef] 180. Peruzzo, P.; Comelli, M.; Di Giorgio, E.; Franforte, E.; Mavelli, I.; Brancolini, C. Transformation by different oncogenes relies on specific metabolic adaptations. Cell Cycle 2016, 15, 2656–2668. [CrossRef]

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).