DOCSLIB.ORG

Nascent Chromatin Capture Proteomics Determines Chromatin Dynamics During DNA Replication and Identifies Unknown Fork Components

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Nascent Chromatin Capture Proteomics Determines Chromatin Dynamics During DNA Replication and Identifies Unknown Fork Components RESOURCE Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components Constance Alabert1, Jimi-Carlo Bukowski-Wills2, Sung-Bau Lee1, Georg Kustatscher2, Kyosuke Nakamura1, Flavia de Lima Alves2, Patrice Menard1,4, Jakob Mejlvang1,4, Juri Rappsilber2,3,5 and Anja Groth1,5 To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin–dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance. Mammalian genomes are replicated by the simultaneous progress- packaged into a structure with nucleosomal periodicity and nuclease ion of thousands of replication forks1. In this process, chromatin resistance similar to bulk chromatin5,6. This process is referred to as organization is disrupted ahead of the replication machinery and chromatin maturation6,7. Restoration of nucleosomal density is rapid restored behind, on the two daughter strands2,3. This genome-wide and relies on recycling of old histones combined with addition of disruption of chromatin raises fundamental questions about how DNA new ones8. Old parental histones are thought to maintain their marks, replication is integrated with chromatin dynamics and how specific which are thereby transmitted to the daughter strands. In contrast, new chromatin structures are transmitted through mitotic cell division. histones H3–H4 are acetylated, principally at Lys 5 and 12 of histone These questions underpin how cells maintain epigenetically defined H4 (K5K12diAc; ref. 9). These histone H4 acetylations are removed gene-expression patterns and thus their identity, which is central to shortly after replication, as nascent (immature) chromatin matures development and disease avoidance2–4. into a nuclease-resistant state6,10,11. Chromatin restoration on newly synthesized DNA is a multi- The sliding clamp proliferating cell nuclear antigen (PCNA) plays layered process, including nucleosome assembly and remodelling, a central role in coupling replication with chromatin restoration restoration of DNA methylation and histone marks, deposition of through its ability to recruit the nucleosome assembly factor histone variants and establishment of higher-order chromosomal chromatin assembly factor 1 (CAF-1) the maintenance DNA structures including sister-chromatid cohesion2,3. Correspondingly, a methyltransferase DNMT1, several chromatin remodellers and large number of proteins are involved, for many of which timing and lysine deacetylases and methyl transferases2,3. Still it remains largely action are yet to be elucidated or even their identity to be revealed. unknown when and how most chromatin constituents and modifiers Pioneering work using nucleases to probe chromatin assembly, argues are recruited. As a discovery approach, proteomics has been used for a time window of approximately 15–20 min for new DNA to be to define the composition of purified telomeres12 and of mitotic 1Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark. 2Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK. 3Department of Biotechnology, Technische Universität Berlin, 13353 Berlin, Germany. 4Present addresses: Novo Nordisk Foundation Center for Biosustainability, DK-2970 Hørsholm, Denmark (P.M.); Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway (J.M.). 5Correspondence should be addressed to J.R. or A.G. (e-mail: [email protected] or [email protected]) Received 12 October 2012; accepted 15 January 2014; published online 23 February 2014; DOI: 10.1038/ncb2918 NATURE CELL BIOLOGY VOLUME 16 | NUMBER 3 | MARCH 2014 281 © 2014 Macmillan Publishers Limited. All rights reserved. RESOURCE abBiotin–dUTP cRelease from of new DNA thymidine Nascent block Biotin–dUTP chromatin Strong chromatin 3 h 20 min crosslinking Mature 2 h chromatin 5 µm5 µm Sonication into d 2-3 kb fragment Purification on streptavidin beads Collecting mature chromatin 5 µm 5 µm Labelling and collecting nascent chromatin Proteins Histone marks DNA G1 Thymidine block DAPI, biotin–dUTP and PCNA G2 e g PCNA H4 H1 90 DLSHIGDAVVISCAK DNIQGITKPAIR ASGPPVSELITK 75 100 531.61 100 442.59 447.27 100 559.84 z = 3 z = 2 60 z = 3 z = 3 603.84 z = 2 45 528.29 z = 3 30 15 0 0 0 Relative abundance m/z Light Heavy m/z Light Heavy m/z Light Heavy 0 (mature) (nascent) (mature) (nascent) (mature) (nascent) Biotin–dUTP-positive cells (%) Early Mid Late S phase SILAC ratio N/M (log2) = 2.51 SILAC ratio N/M (log2) = 0.00 SILAC ratio N/M (log2) = –0.38 f NCC pulldown h Clamp and Fork stability Okazaki fragment ) 3 CMG DNA polymerases clamp loader complex processing Nascent Mature Control 2 PCNA 2 H4K12ac 1 Histone H4 NF POLE3 NF Histone H1 Histone H3 0 Histone H2B SILAC ratio N/M (log TIPIN RPA1 RPA2 RPA3 FEN1 ELG1 –1 RFC1 RFC2 RFC3 RFC4 RFC5 AND1 DNA2 DCC1 PCNA GINS1 GINS2 GINS3 GINS4 PRIM1 PRIM2 MCM2 MCM3 MCM4 MCM5 MCM6 MCM7 POLE1 POLE1 POLE4 CHTF1 CHTF8 POLA1 POLA2 POLD1 POLD2 POLD3 POLD4 CDC45 MCM10 Nascent Mature CLASPIN TIMELESS DNA LIGASE I Figure 1 Isolation of replication forks and nascent chromatin by NCC with 300 cells counted in total. (f) NCC pulldown analysed by western technology. (a) Outline of the NCC protocol. See Methods for details. (b) blotting. Control: no addition of biotin–dUTP. Uncropped blots are provided Biotin-labelled newly synthesized DNA co-localizes with PCNA in replication in Supplementary Fig. 7. (g) Mass spectra showing the SILAC intensities foci. (c) Experimental design for comparison of nascent and mature for peptides of PCNA, H4 and H1. (h) Nascent chromatin enrichment of chromatin. Cells released from a single thymidine block were labelled with core replication fork components. Enrichments are given as the median, biotin–dUTP in early–mid S phase and collected directly (nascent) or after 2 from three independent experiments, of log2 of the SILAC ratios of nascent h chase without biotin–dUTP (mature). (d) Cell cycle profiles representative (heavy) over mature (light) (N/M). Error bars represent standard error of of experimental design in c.(e) S-phase distribution of cells labelled the mean (s.e.m.), and indicate the precision of ratio measurements for according to the experimental design in c. Cells were scored according to each protein. POLE1 and histone H1 are included as a reference in all their PCNA pattern50. Error bars represent standard deviation (s.d.), n D 4 enrichment plots. chromosomes13. The latter study revealed a surprising complexity insight into the process of building chromatin and maintaining of whole chromosomes and a machine learning approach, multi- epigenetic information. Moreover, our proteomic analysis provides classifier combinatorial proteomics (MCCP) was used to predict a discovery approach to identify proteins recruited to replication functional significance of associated proteins13. Given the power forks and/or nascent chromatin. Applying a MCCP-derived of these tools in defining chromosomes, we applied them to study chromatin-probability list to our data, we predict a role for chromatin replication. 93 uncharacterized proteins at replication forks or in newly We profile DNA replication and chromatin maturation in replicated chromatin behind the fork, and identify FAM111A as human cells by NCC, a biochemical approach to isolate newly a PCNA interaction partner required for DNA replication and synthesized DNA for quantitative proteomic analysis. By determining S-phase entry. the dynamic association of 3,995 proteins with nascent newly synthesized chromatin and mature post-replicative chromatin, RESULTS we reveal three classes of factors: enriched in nascent chromatin; Isolation of replication forks and nascent chromatin by NCC present in both nascent and mature chromatin; and enriched Mammalian replication and chromatin assembly factors are in mature chromatin. This rich data set offers unprecedented commonly recognized by co-localization with newly synthesized 282 NATURE CELL BIOLOGY VOLUME 16 | NUMBER 3 | MARCH 2014 © 2014 Macmillan Publishers Limited. All rights reserved. RESOURCE SILAC ratio N/M (log2) purification of tagged chromatin (Supplementary Methods). Biotin– –10 1 2 dUTP can be introduced by a short hypotonic shift of HeLa S3 spinner POLE1 cultures without affecting S-phase progression or triggering DNA EXO1 MSH6 damage (Supplementary Fig. 1a,b). MSH2 RAD18 To follow DNA synthesis and its assembly into chromatin, MSH3
Load more

Recommended publications
  • Synthetic Lethality Between DNA Polymerase Epsilon and RTEL1 in Metazoan DNA Replication
    Article Synthetic Lethality between DNA Polymerase Epsilon and RTEL1 in Metazoan DNA Replication Graphical Abstract Authors Roberto Bellelli, Jillian Youds, Valerie Borel, Jennifer Svendsen, Visnja Pavicic-Kaltenbrunner, Simon J. Boulton Correspondence [email protected] In Brief Bellelli et al. report that RTEL1 deficiency is synthetic lethal with the loss of pole-4 in C. elegans/hypomorphy of Pol epsilon. An analysis of replication dynamics in Rtel1À/À Pole4À/À mouse cells revealed a combination of dysfunctional fork progression and defective origin activation, which cooperatively drive incomplete genomic replication and genetic instability. Highlights d rtel-1 is synthetic lethal with the loss of DNA polymerase epsilon in C. elegans d rtel-1; pole-4 double mutants accumulate Rad51 and RPA foci and fail to replicate d Impaired DNA replication and genome instability in Rtel1 Pole4 knockout mouse cells d Rtel1 Pole4 double knockout mouse cells exhibit fork asymmetry and defective origin activation Bellelli et al., 2020, Cell Reports 31, 107675 May 26, 2020 ª 2020 The Author(s). https://doi.org/10.1016/j.celrep.2020.107675 ll ll OPEN ACCESS Article Synthetic Lethality between DNA Polymerase Epsilon and RTEL1 in Metazoan DNA Replication Roberto Bellelli,1,2,3 Jillian Youds,1,2 Valerie Borel,1 Jennifer Svendsen,1 Visnja Pavicic-Kaltenbrunner,1 and Simon J. Boulton1,4,* 1The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK 2These authors contributed equally 3Present address: Center for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, Barbican, EC1M 6BE London, UK 4Lead Contact *Correspondence: [email protected] https://doi.org/10.1016/j.celrep.2020.107675 SUMMARY Genome stability requires coordination of DNA replication origin activation and replication fork progression.
    [Show full text]
  • Transcriptome-Wide Profiling of Multiple RNA Modifications Simultaneously at Single-Base Resolution,” by Vahid Khoddami, Archana Yerra, Timothy L
    Correction BIOCHEMISTRY, CHEMISTRY Correction for “Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution,” by Vahid Khoddami, Archana Yerra, Timothy L. Mosbruger, Aaron M. Fleming, Cynthia J. Burrows, and Bradley R. Cairns, which was first published March 14, 2019; 10.1073/pnas.1817334116 (Proc Natl Acad Sci USA 116:6784–6789). The authors note that the following statement should be added to the Acknowledgments: “This work was also supported by Grant R01 GM093099 from the NIH/National Institute of General Medical Sciences (to C.J.B.).” Published under the PNAS license. Published online April 22, 2019. www.pnas.org/cgi/doi/10.1073/pnas.1905628116 9136 | PNAS | April 30, 2019 | vol. 116 | no. 18 www.pnas.org Downloaded by guest on October 2, 2021 Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution Vahid Khoddamia,b,c,1,2, Archana Yerrab,c,1, Timothy L. Mosbrugerd, Aaron M. Fleminge, Cynthia J. Burrowse,3, and Bradley R. Cairnsb,c,3 aDepartment of Cell Biology, Harvard Medical School, Boston, MA 02115; bHoward Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; cDepartment of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; dBioinformatics Shared Resource, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112; and eDepartment of Chemistry, University of Utah, Salt Lake City, UT 84112 Contributed by Cynthia J. Burrows, January 25, 2019 (sent for review October 9, 2018; reviewed by Juan D. Alfonzo, Thomas Carell, and Peter C.
    [Show full text]
  • 1 POL30 Alleles in Saccharomyces Cerevisiae Reveal Complexities Of
    bioRxiv preprint doi: https://doi.org/10.1101/679829; this version posted June 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. POL30 alleles in Saccharomyces cerevisiae reveal complexities of the cell cycle and ploidy on heterochromatin assembly Molly Brothers and Jasper Rine Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 1 bioRxiv preprint doi: https://doi.org/10.1101/679829; this version posted June 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Running title: POL30 effect on heterochromatin assembly Keywords: PCNA, transcriptional silencing, recombination, nucleosome assembly, intragenic complementation Corresponding Author: Jasper Rine University of California, Berkeley, 16 Barker Hall #3220; (510) 642-7047; [email protected] 2 bioRxiv preprint doi: https://doi.org/10.1101/679829; this version posted June 22, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. ABSTRACT In Saccharomyces cerevisiae, transcriptional silencing at HML and HMR maintains mating-type identity. The repressive chromatin structure at these loci is replicated every cell cycle and must be re-established quickly to prevent transcription of the genes at these loci.
    [Show full text]
  • Chromosome Duplication in Saccharomyces Cerevisiae
    | YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Chromosome Duplication in Saccharomyces cerevisiae Stephen P. Bell*,1 and Karim Labib†,1 *Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and yMedical Research Council Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, DD1 5EH, United Kingdom ORCID ID: 0000-0002-2876-610X (S.P.B.) ABSTRACT The accurate and complete replication of genomic DNA is essential for all life. In eukaryotic cells, the assembly of the multi-enzyme replisomes that perform replication is divided into stages that occur at distinct phases of the cell cycle. Replicative DNA helicases are loaded around origins of DNA replication exclusively during G1 phase. The loaded helicases are then activated during S phase and associate with the replicative DNA polymerases and other accessory proteins. The function of the resulting replisomes is monitored by checkpoint proteins that protect arrested replisomes and inhibit new initiation when replication is inhibited. The replisome also coordinates nucleosome disassembly, assembly, and the establishment of sister chromatid cohesion. Finally, when two replisomes converge they are disassembled. Studies in Saccharomyces cerevisiae have led the way in our understanding of these processes. Here, we review our increasingly molecular understanding of these events and their regulation. KEYWORDS DNA replication; cell cycle; chromatin; chromosome duplication; genome stability;
    [Show full text]
  • Family a and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions
    biology Review Family A and B DNA Polymerases in Cancer: Opportunities for Therapeutic Interventions Vinit Shanbhag 1,2, Shrikesh Sachdev 2,3, Jacqueline A. Flores 2,3, Mukund J. Modak 4 and Kamalendra Singh 2,3,4,5,* 1 Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; [email protected] 2 The Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA; [email protected] (S.S.); [email protected] (J.A.F.) 3 Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA 4 Department of Microbiology, Biochemistry and Molecular Genetics 225 Warren Street, NJ 07103, USA; [email protected] 5 Department of Laboratory Medicine, Karolinska Institutet, Stockholm 141 86, Sweden * Correspondence: [email protected]; Tel.: +1-573-882-9024 Received: 13 November 2017; Accepted: 29 December 2017; Published: 2 January 2018 Abstract: DNA polymerases are essential for genome replication, DNA repair and translesion DNA synthesis (TLS). Broadly, these enzymes belong to two groups: replicative and non-replicative DNA polymerases. A considerable body of data suggests that both groups of DNA polymerases are associated with cancer. Many mutations in cancer cells are either the result of error-prone DNA synthesis by non-replicative polymerases, or the inability of replicative DNA polymerases to proofread mismatched nucleotides due to mutations in 30-50 exonuclease activity. Moreover, non-replicative, TLS-capable DNA polymerases can negatively impact cancer treatment by synthesizing DNA past lesions generated from treatments such as cisplatin, oxaliplatin, etoposide, bleomycin, and radiotherapy. Hence, the inhibition of DNA polymerases in tumor cells has the potential to enhance treatment outcomes.
    [Show full text]
  • Microrna Modulate Alveolar Epithelial Response to Cyclic Stretch
    University of Pennsylvania ScholarlyCommons Departmental Papers (BE) Department of Bioengineering 2012 MicroRNA Modulate Alveolar Epithelial Response to Cyclic Stretch Nadir Yehya University of Pennsylvania, [email protected] Adi Yerrapureddy University of Pennsylvania John Tobias University of Pennsylvania, [email protected] Susan S. Margulies University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/be_papers Part of the Biomedical Engineering and Bioengineering Commons Recommended Citation Yehya, N., Yerrapureddy, A., Tobias, J., & Margulies, S. S. (2012). MicroRNA Modulate Alveolar Epithelial Response to Cyclic Stretch. BMC Genomics, 13 (154), http://dx.doi.org/10.1186/1471-2164-13-154 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/be_papers/205 For more information, please contact [email protected]. MicroRNA Modulate Alveolar Epithelial Response to Cyclic Stretch Abstract Background MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression implicated in multiple cellular processes. Cyclic stretch of alveoli is characteristic of mechanical ventilation, and is postulated to be partly responsible for the lung injury and inflammation in entilatv or-induced lung injury. We propose that miRNAs may regulate some of the stretch response, and therefore hypothesized that miRNAs would be differentially expressed between cyclically stretched and unstretched rat alveolar epithelial cells (RAECs). Results RAECs were isolated and cultured to express type I epithelial characteristics. They were then equibiaxially stretched to 25% change in surface area at 15 cycles/minute for 1 hour or 6 hours, or served as unstretched controls, and miRNAs were extracted. Expression profiling of the miRNAs with at least 1.5-fold change over controls revealed 42 miRNAs were regulated (34 up and 8 down) with stretch.
    [Show full text]
  • DNA Polymerases at the Eukaryotic Replication Fork Thirty Years After: Connection to Cancer
    cancers Review DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer Youri I. Pavlov 1,2,* , Anna S. Zhuk 3 and Elena I. Stepchenkova 2,4 1 Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA 2 Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia; [email protected] 3 International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia; [email protected] 4 Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia * Correspondence: [email protected] Received: 30 September 2020; Accepted: 13 November 2020; Published: 24 November 2020 Simple Summary: The etiology of cancer is linked to the occurrence of mutations during the reduplication of genetic material. Mutations leading to low replication fidelity are the culprits of many hereditary and sporadic cancers. The archetype of the current model of replication fork was proposed 30 years ago. In the sequel to our 2010 review with the words “years after” in the title inspired by A. Dumas’s novels, we go over new developments in the DNA replication field and analyze how they help elucidate the effects of the genetic variants of DNA polymerases on cancer. Abstract: Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization.
    [Show full text]
  • Cshperspect-REP-A015727 Table3 1..10
    Table 3. Nomenclature for proteins and protein complexes in different organisms Mammals Budding yeast Fission yeast Flies Plants Archaea Bacteria Prereplication complex assembly H. sapiens S. cerevisiae S. pombe D. melanogaster A. thaliana S. solfataricus E. coli Hs Sc Sp Dm At Sso Eco ORC ORC ORC ORC ORC [Orc1/Cdc6]-1, 2, 3 DnaA Orc1/p97 Orc1/p104 Orc1/Orp1/p81 Orc1/p103 Orc1a, Orc1b Orc2/p82 Orc2/p71 Orc2/Orp2/p61 Orc2/p69 Orc2 Orc3/p66 Orc3/p72 Orc3/Orp3/p80 Orc3/Lat/p82 Orc3 Orc4/p50 Orc4/p61 Orc4/Orp4/p109 Orc4/p52 Orc4 Orc5L/p50 Orc5/p55 Orc5/Orp5/p52 Orc5/p52 Orc5 Orc6/p28 Orc6/p50 Orc6/Orp6/p31 Orc6/p29 Orc6 Cdc6 Cdc6 Cdc18 Cdc6 Cdc6a, Cdc6b [Orc1/Cdc6]-1, 2, 3 DnaC Cdt1/Rlf-B Tah11/Sid2/Cdt1 Cdt1 Dup/Cdt1 Cdt1a, Cdt1b Whip g MCM helicase MCM helicase MCM helicase MCM helicase MCM helicase Mcm DnaB Mcm2 Mcm2 Mcm2/Nda1/Cdc19 Mcm2 Mcm2 Mcm3 Mcm3 Mcm3 Mcm3 Mcm3 Mcm4 Mcm4/Cdc54 Mcm4/Cdc21 Mcm4/Dpa Mcm4 Mcm5 Mcm5/Cdc46/Bob1 Mcm5/Nda4 Mcm5 Mcm5 Mcm6 Mcm6 Mcm6/Mis5 Mcm6 Mcm6 Mcm7 Mcm7/Cdc47 Mcm7 Mcm7 Mcm7/Prolifera Gmnn/Geminin Geminin Mcm9 Mcm9 Hbo1 Chm/Hat1 Ham1 Ham2 DiaA Ihfa Ihfb Fis SeqA Replication fork assembly Hs Sc Sp Dm At Sso Eco Mcm8 Rec/Mcm8 Mcm8 Mcm10 Mcm10/Dna43 Mcm10/Cdc23 Mcm10 Mcm10 DDK complex DDK complex DDK complex DDK complex Cdc7 Cdc7 Hsk1 l(1)G0148 Hsk1-like 1 Dbf4/Ask Dbf4 Dfp1/Him1/Rad35 Chif/chiffon Drf1 Continued 2 Replication fork assembly (Continued ) Hs Sc Sp Dm At Sso Eco CDK complex CDK complex CDK complex CDK complex CDK complex Cdk1 Cdc28/Cdk1 Cdc2/Cdk1 Cdc2 CdkA Cdk2 Cdc2c CcnA1, A2 CycA CycA1, A2,
    [Show full text]
  • The Replisome Guides Nucleosome Assembly During DNA Replication Wenshuo Zhang, Jianxun Feng and Qing Li*
    Zhang et al. Cell Biosci (2020) 10:37 https://doi.org/10.1186/s13578-020-00398-z Cell & Bioscience REVIEW Open Access The replisome guides nucleosome assembly during DNA replication Wenshuo Zhang, Jianxun Feng and Qing Li* Abstract Nucleosome assembly during DNA replication is tightly coupled to ongoing DNA synthesis. This process, termed DNA replication-coupled (RC) nucleosome assembly, is essential for chromatin replication and has a great impact on both genome stability maintenance and epigenetic inheritance. This review discusses a set of recent fndings regarding the role of replisome components contributing to RC nucleosome assembly. Starting with a brief introduction to the fac- tors involved in nucleosome assembly and some aspects of the architecture of the eukaryotic replisome, we discuss studies from yeast to mammalian cells and the interactions of replisome components with histones and histone chaperones. We describe the proposed functions of replisome components during RC nucleosome assembly and discuss their impacts on histone segregation and implications for epigenetic inheritance. Keywords: Replisome component, Nucleosome assembly, Chromatin replication, Histone chaperone Background state. Tis process, called DNA replication-coupled (RC) A brief introduction to DNA replication‑coupled (RC) nucleosome assembly, is an essential step for chromatin nucleosome assembly replication [2, 4, 6]. Eukaryotic DNA replication occurs in the context of Nucleosome assembly during DNA replication occurs the chromatin environment [1]. Chromatin, the carrier in a stepwise fashion. Early studies using a chemical of genetic and epigenetic information and guardian of cross-linking technique combined with radioisotope genome stability, must be duplicated in daughter cells labeling methods demonstrated that parental histone to ensure continuity between generations.
    [Show full text]
  • Telomere Maintenance Pathway Activity Analysis Enables Tissue- and Gene-Level Inferences
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.01.429081; this version posted February 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Telomere maintenance pathway activity analysis enables tissue- and gene-level inferences Lilit Nersisyan1,2*, Arman Simonyan1, Hans Binder3, Arsen Arakelyan1,2 1 Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia 2 Pathverse, LLC, Yerevan, Armenia 3 Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany * Correspondence: Lilit Nersisyan Keywords: telomere maintenance mechanisms, telomerase, alternative lengthening of telomeres, pathway signal flow, testis ABSTRACT Telomere maintenance is one of the mechanisms ensuring indefinite divisions of cancer and stem cells. Good understanding of telomere maintenance mechanisms (TMM) is important for studying cancers and designing therapies. However, molecular factors triggering selective activation of either the telomerase dependent (TEL) or the alternative lengthening of telomeres (ALT) pathway are poorly understood. In addition, more accurate and easy-to-use methodologies are required for TMM phenotyping. In this study, we have performed literature based reconstruction of signaling pathways for the ALT and TEL TMMs. Gene expression data were used for computational assessment of TMM pathway activities and compared with experimental assays for TEL and ALT. Explicit consideration of pathway topology makes bioinformatics analysis more informative compared to computational methods based on simple summary measures of gene expression. Application to healthy human tissues showed high ALT and TEL pathway activities in testis, and identified genes and pathways that may trigger TMM activation.
    [Show full text]
  • Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms
    International Journal of Molecular Sciences Review Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms Megan Schmit and Anja-Katrin Bielinsky * Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA; [email protected] * Correspondence: [email protected] Abstract: Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner. Keywords: Meier-Gorlin syndrome; natural killer cell deficiency; X-linked pigmentary reticulate disorder; Van Esch-O’Driscoll disease; IMAGe syndrome; FILS syndrome; Rothmund-Thomson syndrome; Baller-Gerold syndrome; RAPADILINO Citation: Schmit, M.; Bielinsky, A.-K. Congenital Diseases of DNA Replication: Clinical Phenotypes and 1. Introduction Molecular Mechanisms. Int. J. Mol. 1.1. Replication Initiation Sci.
    [Show full text]
  • Gene Section Mini Review
    Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Mini Review POLE (DNA polymerase epsilon, catalytic subunit) Enric Domingo Department of Oncology, University of Oxford, Oxford, United Kingdom / [email protected] Published in Atlas Database: May 2018 Online updated version : http://AtlasGeneticsOncology.org/Genes/POLEID41773ch12q24.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/70021/05-2018-POLEID41773ch12q24.pdf DOI: 10.4267/2042/70021 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2019 Atlas of Genetics and Cytogenetics in Oncology and Haematology eukaryotes and is responsible of the replication of the Abstract leading strand. POLE contains both the catalytic Review on POLE, with data on DNA, on the protein active site and the proofreading exonuclease domain encoded, and where the gene is implicated. (residues 223-517). Accordingly, the POLE gene Keywords confers to Polε both replicative and 3' to 5' repair capabilities for the new strand. POLE; DNA repair; DNA replication; DNA replicase Expression Identity Broadly expressed. Localisation Other names: POLE1 Nuclear. HGNC (Hugo): POLE Function Location: 12q24.33 Polε is responsible of the polymerization of the Local order: 132,623,762-132,687,359 leading strand during DNA replication in yeast and humans. It also possesses 3' to 5' exonuclease DNA/RNA capability to repair missincorporated nucleotides during DNA replication. Polε is also involved in Description DNA repair pathways such as mismatch repair POLE gene is 63.6 kb long and composed of 49 (MMR), base excision repair (BER), nucleotide coding exons, where the first and last one also have excision repair (NER) or double-strand break repair.
    [Show full text]