Kinetochores Coordinate Pericentromeric Cohesion and Early DNA Replication by Cdc7-Dbf4 Kinase Recruitment

Summary Centromeres play several important roles in ensuring proper chromosome segregation. Not only do they promote kinetochore assembly for microtubule attachment, but they also support robust sister chromatid cohesion at pericentromeres and facilitate replication of centromeric DNA early in S phase. However, it is still elusive how centromeres orchestrate all these functions at the same site. Here, we show that the budding yeast Dbf4-dependent kinase (DDK) accumulates at kinetochores in telophase, facilitated by the Ctf19 kinetochore complex. This promptly recruits Sld3–Sld7 replication initiator proteins to pericentromeric replication origins so that they initiate replication early in S phase. Furthermore, DDK at kinetochores independently recruits the Scc2–Scc4 cohesin loader to centromeres in G1 phase. This enhances cohesin loading and facilitates robust pericentromeric cohesion in S phase. Thus, we have found the central mechanism by which kinetochores orchestrate early S phase DNA replication and robust sister chromatid cohesion at microtubule attachment sites.

[1]  K. Nasmyth,et al.  Identification of Cohesin Association Sites at Centromeres and along Chromosome Arms , 1999, Cell.

[2]  Tomoyuki U. Tanaka,et al.  Kinetochore microtubule interaction during S phase in Saccharomyces cerevisiae. , 2007, Genes & development.

[3]  H. Aburatani,et al.  Genomic approach for the understanding of dynamic aspect of chromosome behavior. , 2006, Methods in enzymology.

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

[5]  S. Schreiber,et al.  Identification of an 11-kDa FKBP12-rapamycin-binding domain within the 289-kDa FKBP12-rapamycin-associated protein and characterization of a critical serine residue. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[6]  S. Henikoff,et al.  Centromeres Are Specialized Replication Domains in Heterochromatin , 2001, The Journal of cell biology.

[7]  Renata Retkute,et al.  Mathematical modelling of whole chromosome replication , 2010, Nucleic acids research.

[8]  D. Gilbert,et al.  The spatial position and replication timing of chromosomal domains are both established in early G1 phase. , 1999, Molecular cell.

[9]  S. Bell,et al.  Eukaryotic Origin-Dependent DNA Replication In Vitro Reveals Sequential Action of DDK and S-CDK Kinases , 2011, Cell.

[10]  J. Huberman,et al.  Early-replicating heterochromatin. , 2003, Genes & development.

[11]  Takuro Nakagawa,et al.  The heterochromatin protein Swi6/HP1 activates replication origins at the pericentromeric region and silent mating-type locus , 2009, Nature Cell Biology.

[12]  K. Labib How do Cdc7 and cyclin-dependent kinases trigger the initiation of chromosome replication in eukaryotic cells? , 2010, Genes & development.

[13]  J. Hurwitz,et al.  Cdc7-Drf1 kinase links chromosome cohesion to the initiation of DNA replication in Xenopus egg extracts. , 2008, Genes & development.

[14]  S. Biggins,et al.  Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. , 2009, Genes & development.

[15]  H. Araki Initiation of chromosomal DNA replication in eukaryotic cells; contribution of yeast genetics to the elucidation. , 2011, Genes & genetic systems.

[16]  K. Bloom,et al.  Acquisition and processing of a conditional dicentric chromosome in Saccharomyces cerevisiae , 1989, Molecular and cellular biology.

[17]  N. Barkai,et al.  Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase , 2010, PLoS genetics.

[18]  S. Biggins,et al.  Pericentromeric sister chromatid cohesion promotes kinetochore biorientation. , 2009, Molecular biology of the cell.

[19]  Robin C. Allshire,et al.  Hsk1–Dfp1 is required for heterochromatin-mediated cohesion at centromeres , 2003, Nature Cell Biology.

[20]  T. Hirano,et al.  Scc2 Couples Replication Licensing to Sister Chromatid Cohesion in Xenopus Egg Extracts , 2004, Current Biology.

[21]  Ryuichiro Nakato,et al.  Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing , 2011, Current Biology.

[22]  K. Nasmyth,et al.  ATP Hydrolysis Is Required for Relocating Cohesin from Sites Occupied by Its Scc2/4 Loading Complex , 2011, Current Biology.

[23]  J. Derisi,et al.  The Kinetochore Is an Enhancer of Pericentric Cohesin Binding , 2004, PLoS biology.

[24]  S. Gygi,et al.  Recruitment of Xenopus Scc2 and cohesin to chromatin requires the pre-replication complex , 2004, Nature Cell Biology.

[25]  D. Magliano,et al.  A 330 kb CENP‐A binding domain and altered replication timing at a human neocentromere , 2001, The EMBO journal.

[26]  W. L. Fangman,et al.  Cell cycle-dependent establishment of a late replication program. , 1997, Science.

[27]  Ryuichiro Nakato,et al.  DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data , 2013, Genes to cells : devoted to molecular & cellular mechanisms.

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

[29]  Toyoaki Natsume,et al.  Spatial regulation and organization of DNA replication within the nucleus , 2009, Chromosome Research.

[30]  P. Megee,et al.  The enhancement of pericentromeric cohesin association by conserved kinetochore components promotes high-fidelity chromosome segregation and is sensitive to microtubule-based tension. , 2007, Genes & development.

[31]  O. Aparicio,et al.  Location, location, location: it's all in the timing for replication origins. , 2013, Genes & development.

[32]  L. Drury,et al.  Dbf4p, an Essential S Phase-Promoting Factor, Is Targeted for Degradation by the Anaphase-Promoting Complex , 2000, Molecular and Cellular Biology.

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

[34]  Stefan Westermann,et al.  CENP-T proteins are conserved centromere receptors of the Ndc80 complex , 2012, Nature Cell Biology.

[35]  M. Raghuraman,et al.  Functional Centromeres Determine the Activation Time of Pericentric Origins of DNA Replication in Saccharomyces cerevisiae , 2012, PLoS genetics.

[36]  S. Kelly,et al.  Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei , 2012, Cell reports.

[37]  Carolin A. Müller,et al.  Conservation of replication timing reveals global and local regulation of replication origin activity , 2012, Genome research.

[38]  Ronald W. Davis,et al.  Replication dynamics of the yeast genome. , 2001, Science.

[39]  Julian Haase,et al.  Pericentric Chromatin Is Organized into an Intramolecular Loop in Mitosis , 2008, Current Biology.

[40]  Kim Nasmyth,et al.  Cohesin: its roles and mechanisms. , 2009, Annual review of genetics.

[41]  M. Gartenberg Heterochromatin and the cohesion of sister chromatids , 2009, Chromosome Research.

[42]  Tomoyuki U. Tanaka Bi-orienting chromosomes on the mitotic spindle. , 2002, Current opinion in cell biology.

[43]  Juri Rappsilber,et al.  Cohesin-Dependent Association of Scc2/4 with the Centromere Initiates Pericentromeric Cohesion Establishment , 2013, Current Biology.

[44]  J. Julian Blow,et al.  Live-Cell Imaging Reveals Replication of Individual Replicons in Eukaryotic Replication Factories , 2006, Cell.

[45]  William Stafford Noble,et al.  A Three-Dimensional Model of the Yeast Genome , 2010, Nature.

[46]  B. Stillman,et al.  Cdc7p–Dbf4p kinase binds to chromatin during S phase and is regulated by both the APC and the RAD53 checkpoint pathway , 1999, The EMBO journal.

[47]  T. Itoh,et al.  Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases. , 2012, Molecular cell.

[48]  V. Guacci,et al.  Centromere position in budding yeast: evidence for anaphase A. , 1997, Molecular biology of the cell.

[49]  J. Diffley,et al.  The initiation of chromosomal DNA replication in eukaryotes. , 1990, Trends in genetics : TIG.

[50]  A. Marston,et al.  Establishment of Cohesion at the Pericentromere by the Ctf19 Kinetochore Subcomplex and the Replication Fork-Associated Factor, Csm3 , 2009, PLoS genetics.

[51]  K. Nasmyth,et al.  An Smc3 acetylation cycle is essential for establishment of sister chromatid cohesion. , 2010, Molecular cell.