The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion

Chromosome segregation depends on sister chromatid cohesion which is established by cohesin during DNA replication. Cohesive cohesin complexes become acetylated to prevent their precocious release by WAPL before cells have reached mitosis. To obtain insight into how DNA replication, cohesion establishment and cohesin acetylation are coordinated, we analysed the interaction partners of 55 human proteins implicated in these processes by mass spectrometry. This proteomic screen revealed that on chromatin the cohesin acetyltransferase ESCO2 associates with the MCM2‐7 subcomplex of the replicative Cdc45‐MCM‐GINS helicase. The analysis of ESCO2 mutants defective in MCM binding indicates that these interactions are required for proper recruitment of ESCO2 to chromatin, cohesin acetylation during DNA replication, and centromeric cohesion. We propose that MCM binding enables ESCO2 to travel with replisomes to acetylate cohesive cohesin complexes in the vicinity of replication forks so that these complexes can be protected from precocious release by WAPL. Our results also indicate that ESCO1 and ESCO2 have distinct functions in maintaining cohesion between chromosome arms and centromeres, respectively.

[1]  D. Koshland,et al.  Distinct targets of the Eco1 acetyltransferase modulate cohesion in S phase and in response to DNA damage. , 2009, Molecular cell.

[2]  Chris Berdik.  Bladder cancer: 4 big questions , 2017, Nature.

[3]  Michael W. Davidson,et al.  Highly stable loading of Mcm proteins onto chromatin in living cells requires replication to unload , 2011, The Journal of cell biology.

[4]  Nuno A. Fonseca,et al.  Two independent modes of chromatin organization revealed by cohesin removal , 2017, Nature.

[5]  T. Hirano,et al.  Dynamic molecular linkers of the genome: the first decade of SMC proteins. , 2005, Genes & development.

[6]  Christian Cole,et al.  JPred4: a protein secondary structure prediction server , 2015, Nucleic Acids Res..

[7]  Karl Mechtler,et al.  BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals , 2008, Nature Methods.

[8]  Ilya M Flyamer,et al.  A mechanism of cohesin‐dependent loop extrusion organizes zygotic genome architecture , 2017, bioRxiv.

[9]  M. Kenna,et al.  Mechanical Link between Cohesion Establishment and DNA Replication: Ctf7p/Eco1p, a Cohesion Establishment Factor, Associates with Three Different Replication Factor C Complexes , 2003, Molecular and Cellular Biology.

[10]  Kim Nasmyth,et al.  Closing the cohesin ring: Structure and function of its Smc3-kleisin interface , 2014, Science.

[11]  K. Nasmyth,et al.  Cohesins: Chromosomal Proteins that Prevent Premature Separation of Sister Chromatids , 1997, Cell.

[12]  S. Pradhan,et al.  MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity , 2014, Molecular biology international.

[13]  Mihoko Kai,et al.  Establishment and maintenance of sister chromatid cohesion in fission yeast by a unique mechanism , 2001, The EMBO journal.

[14]  J. Ellenberg,et al.  Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins , 2017, The EMBO journal.

[15]  Eishi Noguchi,et al.  Human Timeless and Tipin stabilize replication forks and facilitate sister-chromatid cohesion , 2010, Journal of Cell Science.

[16]  Francesca Forzano,et al.  The molecular mechanism underlying Roberts syndrome involves loss of ESCO2 acetyltransferase activity. , 2008, Human molecular genetics.

[17]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[18]  Christel Krueger,et al.  Cohesin Is Required for Higher-Order Chromatin Conformation at the Imprinted IGF2-H19 Locus , 2009, PLoS genetics.

[19]  Jian-hua Song,et al.  Sororin cooperates with the acetyltransferase Eco2 to ensure DNA replication-dependent sister chromatid cohesion , 2010, Proceedings of the National Academy of Sciences.

[20]  K. Nasmyth.  Cohesin: a catenase with separate entry and exit gates? , 2011, Nature Cell Biology.

[21]  K. Nasmyth,et al.  Tension between two kinetochores suffices for their bi-orientation on the mitotic spindle , 2004, Nature.

[22]  J. Diffley,et al.  Regulating DNA replication in eukarya. , 2013, Cold Spring Harbor perspectives in biology.

[23]  T. Hirano,et al.  Human Wapl Is a Cohesin-Binding Protein that Promotes Sister-Chromatid Resolution in Mitotic Prophase , 2006, Current Biology.

[24]  A. Desai,et al.  A Combined Approach for the Localization and Tandem Affinity Purification of Protein Complexes from Metazoans , 2005, Science's STKE.

[25]  Karl Mechtler,et al.  Eco1 Is a Novel Acetyltransferase that Can Acetylate Proteins Involved in Cohesion , 2002, Current Biology.

[26]  A. Musacchio,et al.  The Aurora B Kinase in Chromosome Bi-Orientation and Spindle Checkpoint Signaling , 2015, Front. Oncol..

[27]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[28]  J. Diffley,et al.  ATPase-Dependent Quality Control of DNA Replication Origin Licensing , 2013, Nature.

[29]  G. Eichele,et al.  The non-redundant function of cohesin acetyltransferase Esco2 , 2012, Nucleus.

[30]  John R. Yates,et al.  Sequential Primed Kinases Create a Damage-Responsive Phosphodegron on Eco1 , 2012, Nature Structural &Molecular Biology.

[31]  Susannah Rankin,et al.  Esco1 and Esco2 regulate distinct cohesin functions during cell cycle progression , 2017, Proceedings of the National Academy of Sciences.

[32]  Michael D. Wilson,et al.  ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. , 2009, Methods.

[33]  P. Fraser,et al.  Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus , 2009, Nature.

[34]  K. Nasmyth,et al.  Rec8-containing cohesin maintains bivalents without turnover during the growing phase of mouse oocytes. , 2010, Genes & development.

[35]  P. Jallepalli,et al.  Cohesin acetylation speeds the replication fork , 2009, Nature.

[36]  T. Itoh,et al.  Budding Yeast Wpl1(Rad61)-Pds5 Complex Counteracts Sister Chromatid Cohesion-Establishing Reaction , 2009, Current Biology.

[37]  Xiaohui Yang,et al.  Arabidopsis thaliana WAPL Is Essential for the Prophase Removal of Cohesin during Meiosis , 2014, PLoS genetics.

[38]  Ruedi Aebersold,et al.  Characterization of a DNA exit gate in the human cohesin ring , 2014, Science.

[39]  J. Javerzat,et al.  Psm3 Acetylation on Conserved Lysine Residues Is Dispensable for Viability in Fission Yeast but Contributes to Eso1-Mediated Sister Chromatid Cohesion by Antagonizing Wpl1 , 2011, Molecular and Cellular Biology.

[40]  J. Diffley,et al.  MCM: one ring to rule them all. , 2016, Current opinion in structural biology.

[41]  P. Hieter,et al.  Ctf7p is essential for sister chromatid cohesion and links mitotic chromosome structure to the DNA replication machinery. , 1999, Genes & development.

[42]  Andrej Sali,et al.  Comparative Protein Structure Modeling Using MODELLER , 2014, Current protocols in bioinformatics.

[43]  H. Masumoto,et al.  A human centromere protein, CENP-B, has a DNA binding domain containing four potential alpha helices at the NH2 terminus, which is separable from dimerizing activity , 1992, The Journal of cell biology.

[44]  Katsuhiko Shirahige,et al.  Establishment of sister chromatid cohesion at the S. cerevisiae replication fork. , 2006, Molecular cell.

[45]  J. Ellenberg,et al.  Wapl is an essential regulator of chromatin structure and chromosome segregation , 2013, Nature.

[46]  Olga G. Troyanskaya,et al.  An effective statistical evaluation of ChIPseq dataset similarity , 2012, Bioinform..

[47]  D. Cortez,et al.  Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA , 2012, Nature Protocols.

[48]  V. Guacci,et al.  A Direct Link between Sister Chromatid Cohesion and Chromosome Condensation Revealed through the Analysis of MCD1 in S. cerevisiae , 1997, Cell.

[49]  D T Jones,et al.  Protein secondary structure prediction based on position-specific scoring matrices. , 1999, Journal of molecular biology.

[50]  D. Cortez,et al.  Analysis of protein dynamics at active, stalled, and collapsed replication forks. , 2011, Genes & development.

[51]  K. Shirahige,et al.  Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2 , 2015, Current Biology.

[52]  J. Peters,et al.  Wapl Controls the Dynamic Association of Cohesin with Chromatin , 2006, Cell.

[53]  G. Casari,et al.  A reversible gene trap collection empowers haploid genetics in human cells , 2013, Nature Methods.

[54]  Jingrong Chen,et al.  Cohesin Acetylation Promotes Sister Chromatid Cohesion Only in Association with the Replication Machinery* , 2012, The Journal of Biological Chemistry.

[55]  Elizabeth D Rosenman,et al.  Two Putative Acetyltransferases, San and Deco, Are Required for Establishing Sister Chromatid Cohesion in Drosophila , 2003, Current Biology.

[56]  M. Washington,et al.  R.I.P. to the PIP: PCNA‐binding motif no longer considered specific , 2016, BioEssays : news and reviews in molecular, cellular and developmental biology.

[57]  Alison B. Ansbach,et al.  RFCCtf18 and the Swi1-Swi3 complex function in separate and redundant pathways required for the stabilization of replication forks to facilitate sister chromatid cohesion in Schizosaccharomyces pombe. , 2007, Molecular biology of the cell.

[58]  R. Durbin,et al.  Systematic Analysis of Human Protein Complexes Identifies Chromosome Segregation Proteins , 2010, Science.

[59]  E Warbrick,et al.  PCNA binding through a conserved motif. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[60]  Karl Mechtler,et al.  Building sister chromatid cohesion: smc3 acetylation counteracts an antiestablishment activity. , 2009, Molecular cell.

[61]  J. German,et al.  Roberts's syndrome , 1981, Clinical genetics.

[62]  Karl Mechtler,et al.  Sororin Is Required for Stable Binding of Cohesin to Chromatin and for Sister Chromatid Cohesion in Interphase , 2007, Current Biology.

[63]  K. Nasmyth,et al.  Yeast cohesin complex requires a conserved protein, Eco1p(Ctf7), to establish cohesion between sister chromatids during DNA replication. , 1999, Genes & development.

[64]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[65]  J. Diffley,et al.  How the Eukaryotic Replisome Achieves Rapid and Efficient DNA Replication , 2017, Molecular cell.

[66]  Nicholas A. Lyons,et al.  Cdk1-dependent destruction of Eco1 prevents cohesion establishment after S phase. , 2011, Molecular cell.

[67]  A. Deutschbauer,et al.  Sister-chromatid cohesion mediated by the alternative RF-CCtf18/Dcc1/Ctf8, the helicase Chl1 and the polymerase-α-associated protein Ctf4 is essential for chromatid disjunction during meiosis II , 2004, Journal of Cell Science.

[68]  M. Méchali,et al.  DNA replication origin activation in space and time , 2015, Nature Reviews Molecular Cell Biology.

[69]  Daniel Rico,et al.  Cohesin organizes chromatin loops at DNA replication factories. , 2010, Genes & development.

[70]  P. Bates,et al.  Ctf4 Links DNA Replication with Sister Chromatid Cohesion Establishment by Recruiting the Chl1 Helicase to the Replisome , 2016, Molecular cell.

[71]  O. Stemmann,et al.  Prophase pathway‐dependent removal of cohesin from human chromosomes requires opening of the Smc3–Scc1 gate , 2013, The EMBO journal.

[72]  Philip East,et al.  Eco1-Dependent Cohesin Acetylation During Establishment of Sister Chromatid Cohesion , 2008, Science.

[73]  E. Jabs,et al.  Roberts syndrome is caused by mutations in ESCO2, a human homolog of yeast ECO1 that is essential for the establishment of sister chromatid cohesion , 2005, Nature Genetics.

[74]  Steven P. Gygi,et al.  A Molecular Determinant for the Establishment of Sister Chromatid Cohesion , 2008, Science.

[75]  Grant W. Brown,et al.  Identification of protein complexes required for efficient sister chromatid cohesion. , 2004, Molecular biology of the cell.

[76]  K. Shirahige,et al.  Postreplicative Formation of Cohesion Is Required for Repair and Induced by a Single DNA Break , 2007, Science.

[77]  M. Lampson,et al.  Sensing Chromosome Bi-Orientation by Spatial Separation of Aurora B Kinase from Kinetochore Substrates , 2009, Science.

[78]  J. Diffley,et al.  Regulated Eukaryotic DNA Replication Origin Firing with Purified Proteins , 2015, Nature.

[79]  Xuewen Pan,et al.  Acetylation of Smc3 by Eco1 is required for S phase sister chromatid cohesion in both human and yeast. , 2008, Molecular cell.

[80]  T. Hirano,et al.  Identification of Xenopus SMC protein complexes required for sister chromatid cohesion. , 1998, Genes & development.

[81]  Stephanie M Cohen,et al.  Early S phase DNA replication: a search for targets of carcinogenesis. , 2007, Advances in enzyme regulation.

[82]  M. Kirschner,et al.  Sororin, a substrate of the anaphase-promoting complex, is required for sister chromatid cohesion in vertebrates. , 2005, Molecular cell.

[83]  E. Noguchi,et al.  The Replication Fork: Understanding the Eukaryotic Replication Machinery and the Challenges to Genome Duplication , 2013, Genes.

[84]  P. Ménard,et al.  Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components , 2014, Nature Cell Biology.

[85]  David J Young,et al.  High‐throughput mapping of origins of replication in human cells , 2007, EMBO reports.

[86]  T. Hunt,et al.  Tipin/Tim1/And1 protein complex promotes Polα chromatin binding and sister chromatid cohesion , 2009, The EMBO journal.

[87]  P. Jallepalli,et al.  Cohesin recruits the Esco1 acetyltransferase genome wide to repress transcription and promote cohesion in somatic cells , 2015, Proceedings of the National Academy of Sciences.

[88]  Kim Nasmyth,et al.  Cohesion between sister chromatids must be established during DNA replication , 1998, Current Biology.

[89]  K. Nasmyth,et al.  The cohesin ring concatenates sister DNA molecules , 2008, Nature.

[90]  F. Spencer,et al.  Saccharomyces cerevisiae CTF18 and CTF4 Are Required for Sister Chromatid Cohesion , 2001, Molecular and Cellular Biology.

[91]  J. Ellenberg,et al.  Live-Cell Imaging Reveals a Stable Cohesin-Chromatin Interaction after but Not before DNA Replication , 2006, Current Biology.

[92]  K. Nasmyth,et al.  Cohesin’s DNA Exit Gate Is Distinct from Its Entrance Gate and Is Regulated by Acetylation , 2012, Cell.

[93]  F. Uhlmann,et al.  Budding Yeast Wapl Controls Sister Chromatid Cohesion Maintenance and Chromosome Condensation , 2013, Current Biology.

[94]  A. Hunter,et al.  Cytogenetic findings in Roberts-SC phocomelia syndrome(s). , 1979, American journal of medical genetics.

[95]  Howard J. Worman,et al.  Nuclear Membrane Dynamics and Reassembly in Living Cells: Targeting of an Inner Nuclear Membrane Protein in Interphase and Mitosis , 1997, The Journal of cell biology.

[96]  K. Nasmyth,et al.  From a single double helix to paired double helices and back. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[97]  H. Arakawa,et al.  ESCO1/2's roles in chromosome structure and interphase chromatin organization , 2017, Genes & development.

[98]  B. Tye,et al.  Structure of the eukaryotic MCM complex at 3.8 Å , 2015, Nature.

[99]  S. Jentsch,et al.  PCNA controls establishment of sister chromatid cohesion during S phase. , 2006, Molecular cell.

[100]  F. Grummt,et al.  Interactions and subcellular distribution of DNA replication initiation proteins in eukaryotic cells , 2007, Molecular Genetics and Genomics.

[101]  J. Peters,et al.  Sister chromatid cohesion. , 2012, Cold Spring Harbor perspectives in biology.

[102]  J. Peters,et al.  Sororin actively maintains sister chromatid cohesion , 2016, The EMBO journal.

[103]  Frank Uhlmann,et al.  An Eco1-independent sister chromatid cohesion establishment pathway in S. cerevisiae , 2013, Chromosoma.

[104]  H. Zou,et al.  Two human orthologues of Eco1/Ctf7 acetyltransferases are both required for proper sister-chromatid cohesion. , 2005, Molecular biology of the cell.

[105]  K. Nasmyth,et al.  Disengaging the Smc3/kleisin interface releases cohesin from Drosophila chromosomes during interphase and mitosis , 2013, The EMBO journal.

[106]  K. Nasmyth,et al.  Releasing Activity Disengages Cohesin’s Smc3/Scc1 Interface in a Process Blocked by Acetylation , 2016, Molecular cell.

[107]  D. Gilbert,et al.  Mcm2, but Not Rpa, Is a Component of the Mammalian Early G1-Phase Prereplication Complex , 1999, The Journal of cell biology.

[108]  Simon Tavaré,et al.  BayesPeak: Bayesian analysis of ChIP-seq data , 2009, BMC Bioinformatics.

[109]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[110]  Nenggang Zhang,et al.  A cohesin-RAD21 interactome. , 2012, The Biochemical journal.

[111]  A. Hyman,et al.  Sororin Mediates Sister Chromatid Cohesion by Antagonizing Wapl , 2010, Cell.

[112]  R. Wolthuis,et al.  The Cellular Phenotype of Roberts Syndrome Fibroblasts as Revealed by Ectopic Expression of ESCO2 , 2009, PloS one.

[113]  Erez Lieberman Aiden,et al.  Cohesin Loss Eliminates All Loop Domains , 2017, Cell.

[114]  J. Ellenberg,et al.  CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin , 2017, bioRxiv.

[115]  G. Gimelli,et al.  Roberts syndrome: phenotypic variation, cytogenetic definition and heterozygote detection. , 1991, Annales de genetique.

[116]  Kengo Kinoshita,et al.  PrDOS: prediction of disordered protein regions from amino acid sequence , 2007, Nucleic Acids Res..

[117]  U. Francke,et al.  Inactivating mutations in ESCO2 cause SC phocomelia and Roberts syndrome: no phenotype-genotype correlation. , 2005, American journal of human genetics.

[118]  K. Shirahige,et al.  The Prereplication Complex Recruits XEco2 to Chromatin to Promote Cohesin Acetylation in Xenopus Egg Extracts , 2012, Current Biology.

[119]  J. German.  Roberts' syndrome.I. Cytological evidence for a disturbance in chromatid pairing , 1979, Clinical genetics.

[120]  U. Francke,et al.  Roberts syndrome: a review of 100 cases and a new rating system for severity. , 1993, American journal of medical genetics.

[121]  D. Koshland,et al.  DNA Double-Strand Breaks Trigger Genome-Wide Sister-Chromatid Cohesion Through Eco1 (Ctf7) , 2007, Science.

[122]  V. Guacci,et al.  A novel mechanism for the establishment of sister chromatid cohesion by the ECO1 acetyltransferase , 2015, Molecular biology of the cell.