DOCSLIB.ORG

Cell Cycle-Regulated Oscillator Coordinates Core Histone Gene Transcription Through Histone Acetylation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Cell Cycle-Regulated Oscillator Coordinates Core Histone Gene Transcription Through Histone Acetylation Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation Christoph F. Kurata,1, Jean-Philippe Lambertb, Julia Petschnigga, Helena Friesena, Tony Pawsonb,c, Adam Rosebrocka, Anne-Claude Gingrasb,c, Jeffrey Fillinghamd, and Brenda Andrewsa,c,2 aThe Donnelly Center, University of Toronto, Toronto, ON, Canada M5S 3E1; bLunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; cDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 3E1; and dDepartment of Chemistry and Biology, Ryerson University, Toronto, ON, Canada M5B 2K3 Edited by Jasper Rine, University of California, Berkeley, CA, and approved August 21, 2014 (received for review July 25, 2014) DNA replication occurs during the synthetic (S) phase of the eukary- Although the roster of histone chaperones and chromatin otic cell cycle and features a dramatic induction of histone gene remodelers involved in histone gene regulation is impressive, the expression for concomitant chromatin assembly. Ectopic production cell cycle oscillator responsible for restricting histone gene acti- of core histones outside of S phase is toxic, underscoring the critical vation to S phase has remained elusive. In this context, we de- importance of regulatory pathways that ensure proper expression cided to revisit the functions of two poorly understood proteins of histone genes. Several regulators of histone gene expression in that physically interact and are involved in histone gene regula- the budding yeast Saccharomyces cerevisiae are known, yet the key tion, suppressor of Ty (Spt)10 and Spt21 (15–21). Spt10 is a DNA- oscillator responsible for restricting gene expression to S phase has binding protein that localizes to the upstream-activation sequences remained elusive. Here, we show that suppressor of Ty (Spt)10, a pu- (UAS) of histone genes (22, 23). Spt10 contains a putative HAT tative histone acetyltransferase, and its binding partner Spt21 are key domain similar to that of general control nonderepressible (Gcn) 5 – determinants of S-phase specific histone gene expression. We show that (19, 24), which was reported to be involved in acetylation of H3K56 Spt21 abundance is restricted to S phase in part by anaphase pro- at histone promoters in vivo (14). However, to date, HAT activity of moting complex Cdc20-homologue 1 (APCCdh1) and that it is re- Spt10 has not been demonstrated in vitro. cruited to histone gene promoters in S phase by Spt10. There, Spt21 is a protein of unknown function that physically inter- Spt21-Spt10 enables the recruitment of a cascade of regulators, acts with Spt10 (19). Like Spt10, Spt21 influences histone gene including histone chaperones and the histone-acetyltransferase transcription as spt21Δ mutants display dramatically reduced general control nonderepressible (Gcn) 5, which we hypothesize lead to histone acetylation and consequent transcription activation. levels of HTA2, HTB2, and HHF2 transcripts in logarithmically growing cells (15, 25). Here we show that Spt21 is a cell cycle os- cillator that serves as a master regulator of S-phase–dependent ukaryotic chromosomes are composed of chromatin, which in histone gene expression. We demonstrate that Spt10 is required turn is composed of a fundamental repeated unit of a histone E to establish repression by the recruitment of HIR and HIR- octamer and DNA, the nucleosome. Each histone octamer includes dependent regulators outside of S phase. Furthermore, the ex- two H3-H4 histone dimers flanked on either side by H2A-H2B pression of Spt21 is cell cycle-regulated with levels peaking in dimers. The four replication-dependent (RD) core histones (H2A, S phase, when it is recruited to histone gene promoters by its H2B, H3, and H4) are among the most conserved eukaryotic partner protein Spt10. We use genetic and biochemical experi- proteins, and all characterized eukaryotic genomes carry more than ments to show that the abundance of Spt21 during G1 phase is one gene encoding each core histone protein. Budding yeast con- tains two copies of each RD histone gene, each arranged in Significance opposite orientation to a gene encoding its partner within the nucleosome: HHT1-HHF1 and HHT2-HHF2,thetwogenepairs DNA replication and histone gene transcription are tightly encoding core histones H3 and H4, and HTA1-HTB1 and HTA2- linked and occur during the S phase of the eukaryotic cell cycle. HTB2, the two gene pairs encoding H2A and H2B (for recent Histone production outside of S phase is highly toxic, under- reviews see refs. 1 and 2). scoring the importance of regulatory pathways that control Histone gene expression is repressed outside of the synthetic histone gene expression. Although various histone regulators (S) phase by a histone chaperone called the histone regulatory (HIR) have been discovered, the molecular mechanisms responsible complex, which is recruited to a poorly defined DNA sequence, the for the spatial and temporal control of histone gene expression negative regulatory (NEG) region, present upstream of three of the have remained elusive. Here, we describe the discovery of four histone-gene pairs in yeast: HTA1-HTB1, HHT1-HHF1,and Spt21 as a long-elusive cell cycle oscillator responsible for HHT2-HHF2 (3–7). HTA2-HTB2, the fourth histone gene pair, does restricting histone gene transcription to the S phase of the not have a NEG region and is regulated in a HIR-independent eukaryotic cell cycle. We show here that Spt21, together with manner. At HIR-dependent promoters, HIR recruits other histone its partner protein Spt10, regulates histone gene transcrip- chaperones, Asf1 and Rtt106, as well as the chromatin boundary tion by enabling the recruitment of a roster of chromatin- protein Yta7 (8, 9) and the remodel structure of chromatin remodeling proteins. (RSC) ATP-dependent chromatin-remodeling complex (10), which together assemble repressive chromatin, blocking recruitment of Author contributions: C.F.K., J.F., and B.A. designed research; C.F.K., J.-P.L., J.P., and H.F. performed research; T.P., A.R., and A.-C.G. contributed new reagents/analytic tools; C.F.K., RNAPII (11, 12). In S phase, this repressive chromatin is overcome, J.-P.L., J.P., H.F., and A.R. analyzed data; and C.F.K., J.F., and B.A. wrote the paper. allowing recruitment of RNAPII and activation of transcription. The authors declare no conflict of interest. After recruitment of RNAPII, the AAA-ATPase Yta7 is important This article is a PNAS Direct Submission. for efficient transcript elongation by evicting histones H3-H4 (11–13). 1Present address: Cancer Research UK London Research Institute, Clare Hall Laboratories, Other chromatin remodelers also have roles in histone gene South Mimms EN6 3LD, United Kingdom. activation, including the SWI/SNF chromatin-remodeling com- 2To whom correspondence should be addressed. Email: [email protected]. plex, which activates NEG-dependent histone genes (14), and This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. the histone-acetyltransferase (HAT) complex Rtt109-Vps75 (8). 1073/pnas.1414024111/-/DCSupplemental. 14124–14129 | PNAS | September 30, 2014 | vol. 111 | no. 39 www.pnas.org/cgi/doi/10.1073/pnas.1414024111 Downloaded by guest on October 1, 2021 regulated by the anaphase-promoting complex/cyclosome (APC/C) A associated with its activator protein Cdc20-homologue 1 (Cdh1). During S phase, Spt21 accumulates and recruits the Gcn5 HAT to histone gene promoters, where they influence histone gene transcription. Our data reveal an important cell cycle oscillator that links the cell cycle machinery and histone acetylation and explain how the timing of histone acetylation at histone gene B promoters leads to gene activation. C Results Spt10 and Spt21 Recruit HIR and Associated Proteins/Complexes. To explore the mechanism of Spt10-dependent activation of histone gene transcription, we first used affinity purification and mass spectrometry to discover proteins associated with Spt10. Spe- cifically, we used a tandem affinity purification (TAP)-tagged version of Spt10 expressed either at its endogenous locus or from an inducible promoter (GAL1-10) and a modified chromatin immunoprecipitation (mChIP) protocol to identify proteins associated with Spt10 on chromatin (8, 11, 26). We discovered interactions between Spt10 and all HIR subunits (Hir1, Hir2, Hir3, and Hpc2), RSC, as well as most subunits of SWI/SNF (Fig. S1). We did not identify peptides for these Spt10-interacting proteins across several control purifications, and the recovery of peptides for interacting proteins scaled with the amount of Spt10 in our purifications. We performed a similar mChIP analysis with Spt21-TAP and detected SWI/SNF peptides, but only when Spt21 was overexpressed, consistent with its low abundance relative to Spt10 (Fig. S1). We also confirmed the Spt10/Spt21 interaction described previously (Fig. S1)(19). Because we detected all four HIR subunits in our mChIP of Spt10-TAP, we next used chromatin immunoprecipitation (ChIP) to test whether SPT10 is required for recruitment of HIR (Hir1- TAP), the HIR-dependent regulators RSC (Rsc8-TAP), SWI/SNF (Snf6), Rtt106-TAP, and Asf1-TAP, and the transcriptional acti- vator Yta7 (Yta7-TAP) (8, 11, 13) to the promoter region of Fig. 1. The Spt10/Spt21 complex recruits chromatin-modifying proteins and HTA1-HTB1 (Fig. 1A) (11). Consistent with an important function complexes to the HTA1-HTB1 promoter. (A) Schematic representation of the for the Spt10–HIR interaction on chromatin, we observed a strong HIR-dependent HTA1-HTB1 and HIR-independent HTA2-HTB2 histone gene reduction in the recruitment of both negative regulators of histone promoters. UAS sequences (green circles) found in both regulatory regions gene expression—HIR, Rtt106, Asf1, and RSC–as well as activa- (for a comprehensive review see ref. 2). Primer pairs used for ChIP assays are tors of histone transcription–SWI/SNF and Yta7–to the HTA1- shown with black arrows (8, 10, 11). (B) Spt10 and Spt21 recruit histone HTB1 promoter in an SPT10 deletion strain (Fig.
Load more

Recommended publications
  • Recurrent Herpes Simplex Virus Type 1 (HSV-1) Infection Modulates Neuronal Aging Marks in in Vitro and in Vivo Models
    International Journal of Molecular Sciences Article Recurrent Herpes Simplex Virus Type 1 (HSV-1) Infection Modulates Neuronal Aging Marks in In Vitro and In Vivo Models Giorgia Napoletani 1 , Virginia Protto 1 , Maria Elena Marcocci 1 , Lucia Nencioni 1 , Anna Teresa Palamara 1,2,† and Giovanna De Chiara 3,*,† 1 Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia–Fondazione Cenci Bolognetti, 00185 Rome, Italy; [email protected] (G.N.); [email protected] (V.P.); [email protected] (M.E.M.); [email protected] (L.N.); [email protected] (A.T.P.) 2 Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy 3 Institute of Translational Pharmacology, National Research Council (CNR), 00133 Rome, Italy * Correspondence: [email protected] † Co-last authors. Abstract: Herpes simplex virus 1 (HSV-1) is a widespread neurotropic virus establishing a life-long latent infection in neurons with periodic reactivations. Recent studies linked HSV-1 to neurodegen- erative processes related to age-related disorders such as Alzheimer’s disease. Here, we explored whether recurrent HSV-1 infection might accelerate aging in neurons, focusing on peculiar marks of aged cells, such as the increase in histone H4 lysine (K) 16 acetylation (ac) (H4K16ac); the decrease Citation: Napoletani, G.; Protto, V.; of H3K56ac, and the modified expression of Sin3/HDAC1 and HIRA proteins. By exploiting both Marcocci, M.E.; Nencioni, L.; in vitro and in vivo models of recurrent HSV-1 infection, we found a significant increase in H4K16ac, Palamara, A.T.; De Chiara, G.
    [Show full text]
  • Hst3 Is Turned Over by a Replication Stress-Responsive SCF Phospho
    Hst3 is turned over by a replication stress-responsive SCFCdc4 phospho-degron Ellen R. Edenberga, Ajay A. Vashishtb, Benjamin R. Topacioa, James A. Wohlschlegelb, and David P. Toczyskia,1 aDepartment of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; and bDepartment of Biological Chemistry, University of California, Los Angeles, CA 90095 Edited* by Stephen J. Elledge, Harvard Medical School, Boston, MA, and approved March 10, 2014 (received for review August 13, 2013) Hst3 is the histone deacetylase that removes histone H3K56 several E3 ubiquitin ligases to identify the one responsible for acetylation. H3K56 acetylation is a cell-cycle– and damage-regu- targeting Hst3 for degradation and found that Hst3 is partially lated chromatin marker, and proper regulation of H3K56 acetyla- stabilized at the nonpermissive temperature of temperature- tion is important for replication, genomic stability, chromatin sensitive mutants in CDC53 (the cullin scaffold for all SCF assembly, and the response to and recovery from DNA damage. ligases) and CDC4 (encoding an essential F-box protein) (Fig. Understanding the regulation of enzymes that regulate H3K56 1A). Inactivation of SCFCdc4 also stabilized Hst3 after treatment acetylation is of great interest, because the loss of H3K56 acetyla- B HST3 with hydroxyurea (HU) to induce replication stress (Fig. 1 ). tion leads to genomic instability. is controlled at both the Cdc4 transcriptional and posttranscriptional level. Here, we show that SCF recognizes its substrates through a phospho-degron – Hst3 is targeted for turnover by the ubiquitin ligase SCFCdc4 (20 22). To understand how Hst3 was targeted for turnover both after phosphorylation of a multisite degron.
    [Show full text]
  • Watanabe S, Resch M, Lilyestrom W, Clark N
    NIH Public Access Author Manuscript Biochim Biophys Acta. Author manuscript; available in PMC 2010 November 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Biochim Biophys Acta. 2010 ; 1799(5-6): 480±486. doi:10.1016/j.bbagrm.2010.01.009. Structural characterization of H3K56Q nucleosomes and nucleosomal arrays Shinya Watanabe1,*, Michael Resch2,*, Wayne Lilyestrom2, Nicholas Clark2, Jeffrey C. Hansen2, Craig Peterson1, and Karolin Luger2,3 1 Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation St.; Worcester, Massachusetts 01605 2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870 3 Howard Hughes Medical Institute Abstract The posttranslational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome free regions. Here we show by x-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans (‘oligomerization’) are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome free regions accessible to the DNA replication and repair machinery.
    [Show full text]
  • Transcription Shapes Genome-Wide Histone Acetylation Patterns
    ARTICLE https://doi.org/10.1038/s41467-020-20543-z OPEN Transcription shapes genome-wide histone acetylation patterns Benjamin J. E. Martin 1, Julie Brind’Amour 2, Anastasia Kuzmin1, Kristoffer N. Jensen2, Zhen Cheng Liu1, ✉ Matthew Lorincz 2 & LeAnn J. Howe 1 Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between histone acetylation and transcription is causal or consequential has not been addressed. 1234567890():,; Using immunoblot and chromatin immunoprecipitation-sequencing in S. cerevisiae, here we show that the majority of histone acetylation is dependent on transcription. This dependency is partially explained by the requirement of RNA polymerase II (RNAPII) for the interaction of H4 histone acetyltransferases (HATs) with gene bodies. Our data also confirms the targeting of HATs by transcription activators, but interestingly, promoter-bound HATs are unable to acetylate histones in the absence of transcription. Indeed, HAT occupancy alone poorly predicts histone acetylation genome-wide, suggesting that HAT activity is regulated post- recruitment. Consistent with this, we show that histone acetylation increases at nucleosomes predicted to stall RNAPII, supporting the hypothesis that this modification is dependent on nucleosome disruption during transcription. Collectively, these data show that histone acetylation is a consequence of RNAPII promoting both the recruitment and activity of histone acetyltransferases. 1 Department of Biochemistry and Molecular Biology, Life Sciences Institute, Molecular
    [Show full text]
  • Histone Deacetylase Inhibitors Globally
    Histone Deacetylase Inhibitors Globally Enhance H3/H4 Tail Acetylation SUBJECT AREAS: BIOCHEMISTRY Without Affecting H3 Lysine 56 CELL BIOLOGY MOLECULAR BIOLOGY Acetylation PROTEOMICS Paul Drogaris1,4*, Vale´rie Villeneuve1,5*, Christelle Pomie`s1, Eun-Hye Lee1,Ve´ronique Bourdeau2, E´ric Bonneil1, Gerardo Ferbeyre2, Alain Verreault1,3 & Pierre Thibault1,4 Received 25 October 2011 1Institute for Research in Immunology and Cancer (IRIC), Universite´ de Montre´al (QC), Canada, 2Department of Biochemistry, Accepted Universite´ de Montre´al (QC), Canada, 3Department of Pathology and Cell Biology, Universite´ de Montre´al (QC), Canada, 4Department 20 December 2011 of Chemistry, Universite´ de Montre´al (QC), Canada, 5Department of Molecular Biology, Universite´ de Montre´al (QC), Canada. Published 12 January 2012 Histone deacetylase inhibitors (HDACi) represent a promising avenue for cancer therapy. We applied mass spectrometry (MS) to determine the impact of clinically relevant HDACi on global levels of histone acetylation. Intact histone profiling revealed that the HDACi SAHA and MS-275 globally increased histone Correspondence and H3 and H4 acetylation in both normal diploid fibroblasts and transformed human cells. Histone H3 lysine requests for materials 56 acetylation (H3K56ac) recently elicited much interest and controversy due to its potential as a diagnostic and prognostic marker for a broad diversity of cancers. Using quantitative MS, we demonstrate that should be addressed to H3K56ac is much less abundant than previously reported in human cells. Unexpectedly, in contrast to P.T. (pierre.thibault@ H3/H4 N-terminal tail acetylation, H3K56ac did not increase in response to inhibitors of each class of umontreal.ca) or A.V. HDACs. In addition, we demonstrate that antibodies raised against H3K56ac peptides cross-react against (alain.verreault@ H3 N-terminal tail acetylation sites that carry sequence similarity to residues flanking H3K56.
    [Show full text]
  • The Prenucleosome, a Stable Conformational Isomer of the Nucleosome
    Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press The prenucleosome, a stable conformational isomer of the nucleosome Jia Fei,1 Sharon E. Torigoe,1 Christopher R. Brown,2 Mai T. Khuong,1 George A. Kassavetis,1 Hinrich Boeger,2 and James T. Kadonaga1 1Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA; 2Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with 80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable confor- mational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.
    [Show full text]
  • H3k56ac Polyclonal Antibody
    H3K56ac polyclonal antibody Cat. No. C15410213 Specificity: Human: positive Type: Polyclonal ChIP-grade/ChIP-seq grade Other species: not tested Source: Rabbit Purity: Affinity purified polyclonal antibody in PBS containing Lot #: A2068P 0.05% azide and 0.05% ProClin 300. Size: 50 µg/ 84 µl Storage: Store at -20°C; for long storage, store at -80°C. Concentration: 0.6 µg/µl Avoid multiple freeze-thaw cycles. Precautions: This product is for research use only. Not for use in diagnostic or therapeutic procedures. Description: Polyclonal antibody raised in rabbit against the region of histone H3 containing the acetylated lysine 56 (H3K56ac), using a KLH-conjugated synthetic peptide. Applications Suggested dilution Results ChIP * 5 µg per ChIP Fig 1, 2 ELISA 1:500 Fig 3 Dot blotting 1:20,000 Fig 4 * Please note that the optimal antibody amount per IP should be determined by the end-user. We recommend testing 1-5 µg per IP. Target description Histones are the main constituents of the protein part of chromosomes of eukaryotic cells. They are rich in the amino acids arginine and lysine and have been greatly conserved during evolution. Histones pack the DNA into tight masses of chromatin. Two core histones of each class H2A, H2B, H3 and H4 assemble and are wrapped by 146 base pairs of DNA to form one octameric nucleosome. Histone tails undergo numerous post-translational modifications, which either directly or indirectly alter chromatin structure to facilitate transcriptional activation or repression or other nuclear processes. In addition to the genetic code, combinations of the different histone modifications reveal the so-called “histone code”.
    [Show full text]
  • A Dual Role of H4K16 Acetylation in the Establishment of Yeast Silent Chromatin
    The EMBO Journal (2011) 30, 2610–2621 | & 2011 European Molecular Biology Organization | All Rights Reserved 0261-4189/11 www.embojournal.org TTHEH E EEMBOMBO JJOURNALOURN AL A dual role of H4K16 acetylation in the establishment of yeast silent chromatin Mariano Oppikofer1, Stephanie Kueng1, Sir3 and Sir4 proteins as the core components of silent Fabrizio Martino2, Szabolcs Soeroes3, chromatin at telomeres and silent mating type loci (Rine Susan M Hancock2, Jason W Chin2, and Herskowitz, 1987; reviewed in Rusche et al (2003)). Wolfgang Fischle3 and Susan M Gasser1,* Two-hybrid and protein binding studies suggested that they form a complex, with Sir4 being a scaffold protein that 1 Friedrich Miescher Institute for Biomedical Research, Basel, bridges between Sir2 and Sir3 (Moazed et al, 1997; Strahl- Switzerland; 2Medical Research Council Laboratory of Molecular Biology, Cambridge, UK and 3Max Planck Institute for Biophysical Bolsinger et al, 1997; Rudner et al, 2005; Cubizolles et al, Chemistry, Go¨ttingen, Germany 2006). Although initial attempts to purify the Sir proteins from yeast yielded only an Sir2-4 heterodimer (Ghidelli et al, Discrete regions of the eukaryotic genome assume herita- 2001; Hoppe et al, 2002), a stable Sir2-Sir3-Sir4 heterotrimer ble chromatin structure that is refractory to transcription. with 1:1:1 stoichiometry (hereafter SIR complex) was purified In budding yeast, silent chromatin is characterized by the from insect cells (Cubizolles et al, 2006). A fourth Sir protein, binding of the Silent Information Regulatory (Sir) proteins Sir1, is important for the establishment of silencing at the to unmodified nucleosomes. Using an in vitro reconstitu- silent mating type loci, but is not required for repression at tion assay, which allows us to load Sir proteins onto arrays telomeres (Pillus and Rine, 1989; Aparicio et al, 1991).
    [Show full text]
  • Comparative Analysis of Commonly Used Peak Calling Programs for Chip
    Comparative analysis of commonly used peak calling programs for ChIP- Seq analysis Hyeongrin Jeon1, Hyunji Lee1, Byunghee Kang1, Insoon Jang1, Original article Tae-Young Roh1,2,3* 1Department of Life Sciences, Pohang University of Science and Technology (POSTECH), eISSN 2234-0742 Pohang 37673, Korea 2 Genomics Inform 2020;18(4):e42 Division of Integrative Biosciences and Biotechnology, Pohang University of Science and https://doi.org/10.5808/GI.2020.18.4.e42 Technology (POSTECH), Pohang 37673, Korea 3SysGenLab Inc., Pohang 37613, Korea Received: October 6, 2020 Chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP- Revised: October 26, 2020 Seq) is a powerful technology to profile the location of proteins of interest on a whole-ge- Accepted: November 22, 2020 nome scale. To identify the enrichment location of proteins, many programs and algorithms have been proposed. However, none of the commonly used peak calling programs could *Corresponding author: accurately explain the binding features of target proteins detected by ChIP-Seq. Here, pub- E-mail: [email protected] licly available data on 12 histone modifications, including H3K4ac/me1/me2/me3, H3K9ac/ me3, H3K27ac/me3, H3K36me3, H3K56ac, and H3K79me1/me2, generated from a human embryonic stem cell line (H1), were profiled with five peak callers (CisGenome, MACS1, MACS2, PeakSeq, and SISSRs). The performance of the peak calling programs was com- pared in terms of reproducibility between replicates, examination of enriched regions to variable sequencing depths, the specificity-to-noise signal, and sensitivity of peak predic- tion. There were no major differences among peak callers when analyzing point source his- tone modifications. The peak calling results from histone modifications with low fidelity, such as H3K4ac, H3K56ac, and H3K79me1/me2, showed low performance in all parame- ters, which indicates that their peak positions might not be located accurately.
    [Show full text]
  • Deacetylation of Histone H3 Lysine 56 by the Sirtuins HST3 and HST4 Is
    Genetics: Early Online, published on March 18, 2015 as 10.1534/genetics.115.175919 Interplay between histone H3 lysine 56 deacetylation and chromatin modifiers in response to DNA damage Antoine Simoneau1*, Neda Delgoshaie2,*, Ivana Celic3, Junbiao Dai3,4, Nebiyu Abshiru2,9 Santiago Costantino1,7, Pierre Thibault2,9, Jef D. Boeke3,8, Alain Verreault2,5, and Hugo Wurtele1,6** Running title: Chromatin modifiers of hst3∆ hst4∆ phenotypes 1 Centre de recherche de l’Hôpital Maisonneuve-Rosemont, 5415 boulevard de l’Assomption, Montréal, H1T 2M4, Canada 2 Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Succursale Centre-Ville, Montreal, H3C 3J7, Canada 3 High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, USA 4 School of Life Sciences, Tsinghua University, Beijing, China 5 Département de Pathologie et Biologie Cellulaire, Université de Montréal, Canada 6 Département de Médecine, Université de Montréal, Canada 7 Département d'ophtalmologie, Université de Montréal, Canada 8 Institute for Systems Genetics and Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA 9 Département de Chimie, Université de Montréal, Canada. * These authors contributed equally to this work. ** Corresponding author: [email protected] 1 Copyright 2015. ABSTRACT In Saccharomyces cerevisiae, histone H3 lysine 56 acetylation (H3K56Ac) is present in newly synthesized histones deposited throughout the genome during DNA replication. The sirtuins Hst3 and Hst4 deacetylate H3K56 after S-phase, and virtually all histone H3 molecules are K56-acetylated throughout the cell cycle in hst3∆ hst4∆ mutants. Failure to deacetylate H3K56 causes thermosensitivity, spontaneous DNA damage, and sensitivity to replicative stress via molecular mechanisms that remain unclear.
    [Show full text]
  • Short Communication Mysterious Role of H3k56ac in Embryonic Stem Cells
    Short Communication Mysterious Role of H3K56ac in Embryonic Stem Cells (H3K56ac / p300/CBP / pluripotency / chromatin) S. STEJSKAL, L. TESAŘOVá, I. KOUTNá Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic Abstract. Posttranslational modifications of histones consequence of increased conformation entropy in α-N belong to epigenetic mechanisms that regulate gene helix (Xu et al., 2005). The nucleosome remodelling ac- expression by chromatin structure changes. General- tivity is first modestly in hands (SWI/SNF or RSC) and ly, histone acetylation reduces its positive charge and then even dramatically enhanced (INO80) after recruit- consequently weakens the stability of the nucleo- ment of chromatin remodellers on the chromatin com- some. Acetylation of lysine 56 on histone H3 is impli- posed of H3K56ac nucleosomes (Neumann et al., 2009; cated in the processes associated with loosened chro- Watanabe et al., 2013). Artificially prepared chromatin matin structure. H3K56ac is a mark for histones containing H3K56ac histones showed no evidence of with high nucleosome turnover in the nuclear pro- affecting the nucleosome stability. On the contrary, cesses such as gene transcription, DNA replication H3K56ac noticeably increased nucleosome breathing, and reparation in yeasts. During evolution, the main the state of nucleosome with partially unwrapping DNA H3K56ac regulatory pathway was lost and the level (Neumann et al., 2009). H3K56ac incorporated into nu- of H3K56ac remained very low in mammalian cells. cleosomes facilitates partial DNA unwrapping from the Moreover, the function of this modification still re- histone octamer and uncovers DNA regulatory binding mains unclear. In this minireview, we summarize the sites for other proteins (Neumann et al., 2009).
    [Show full text]
  • Repair Chromatin Restoration of H3k56ac Through Recruitment of Histone Chaperon CAF-1
    www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 61), pp: 104525-104542 Research Paper Human CRL4DDB2 ubiquitin ligase preferentially regulates post- repair chromatin restoration of H3K56Ac through recruitment of histone chaperon CAF-1 Qianzheng Zhu1, Shengcai Wei1, Nidhi Sharma1, Gulzar Wani1, Jinshan He1 and Altaf A. Wani1,2,3 1Department of Radiology, The Ohio State University, Columbus, 43210, OH 2Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, 43210, OH 3James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, 43210, OH Correspondence to: Qianzheng Zhu, email: [email protected] Altaf A. Wani, email: [email protected] Keywords: acetylated histone H3 lysine 56 (H3K56Ac), chromatin assembly, damaged DNA binding protein 2 (DDB2), CRL4DDB2 ubiquitin ligase, CUL4A and CAF-1 Received: August 23, 2017 Accepted: September 30, 2017 Published: October 17, 2017 Copyright: Zhu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Acetylated histone H3 lysine 56 (H3K56Ac) diminishes in response to DNA damage but is restored following DNA repair. Here, we report that CRL4DDB2 ubiquitin ligase preferentially regulates post-repair chromatin restoration of H3K56Ac through recruitment of histone chaperon CAF-1. We show that H3K56Ac accumulates at DNA damage sites. The restoration of H3K56Ac but not H3K27Ac, H3K18Ac and H3K14Ac depends on CAF-1 function, whereas all these acetylations are mediated by CBP/p300. The CRL4DDB2 components, DDB1, DDB2 and CUL4A, are also required for maintaining the H3K56Ac and H3K9Ac level in chromatin, and for restoring H3K56Ac following induction of DNA photolesions and strand breaks.
    [Show full text]