S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion.

Cohesion establishment and maintenance are carried out by proteins that modify the activity of Cohesin, an essential complex that holds sister chromatids together. Constituents of the replication fork, such as the DNA polymerase alpha-binding protein Ctf4, contribute to cohesion in ways that are poorly understood. To identify additional cohesion components, we analyzed a ctf4Delta synthetic lethal screen performed on microarrays. We focused on a subset of ctf4Delta-interacting genes with genetic instability of their own. Our analyses revealed that 17 previously studied genes are also necessary for the maintenance of robust association of sisters in metaphase. Among these were subunits of the MRX complex, which forms a molecular structure similar to Cohesin. Further investigation indicated that the MRX complex did not contribute to metaphase cohesion independent of Cohesin, although an additional role may be contributed by XRS2. In general, results from the screen indicated a sister chromatid cohesion role for a specific subset of genes that function in DNA replication and repair. This subset is particularly enriched for genes that support the S-phase checkpoint. We suggest that these genes promote and protect a chromatin environment conducive to robust cohesion.

[1]  H. Ogawa,et al.  Interaction of Mre11 and Rad50: two proteins required for DNA repair and meiosis-specific double-strand break formation in Saccharomyces cerevisiae. , 1995, Genetics.

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

[3]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

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

[5]  D. Koshland,et al.  SMC Complexes--Wrapped Up in Controversy , 2003, Science.

[6]  J. Bartek,et al.  MDC1 is required for the intra-S-phase DNA damage checkpoint , 2003, Nature.

[7]  Martin Kupiec,et al.  ELG1, a yeast gene required for genome stability, forms a complex related to replication factor C , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Peter K. Sorger,et al.  Transient Sister Chromatid Separation and Elastic Deformation of Chromosomes during Mitosis in Budding Yeast , 2000, Cell.

[9]  R. Kolodner,et al.  Suppression of Spontaneous Chromosomal Rearrangements by S Phase Checkpoint Functions in Saccharomyces cerevisiae , 2001, Cell.

[10]  T. Formosa,et al.  The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein , 1997, Molecular and cellular biology.

[11]  F. Fabre,et al.  The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments , 2003, Nature.

[12]  Caroline M. Li,et al.  Saccharomyces cerevisiae DNA polymerase epsilon and polymerase sigma interact physically and functionally, suggesting a role for polymerase epsilon in sister chromatid cohesion. , 2003, Molecular and cellular biology.

[13]  Kyoko Yokomori,et al.  The alternative Ctf18-Dcc1-Ctf8-replication factor C complex required for sister chromatid cohesion loads proliferating cell nuclear antigen onto DNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Daniel Durocher,et al.  Elg1 Forms an Alternative PCNA-Interacting RFC Complex Required to Maintain Genome Stability , 2003, Current Biology.

[15]  S. Gygi,et al.  Identification of RFC(Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. , 2001, Molecular cell.

[16]  K. Tanimoto,et al.  NBS1 localizes to gamma-H2AX foci through interaction with the FHA/BRCT domain. , 2002, Current biology : CB.

[17]  E. Foss Tof1p regulates DNA damage responses during S phase in Saccharomyces cerevisiae. , 2001, Genetics.

[18]  Ying Li,et al.  DNA helicase Srs2 disrupts the Rad51 presynaptic filament , 2003, Nature.

[19]  R. Anand Yeast artificial chromosomes (YACs) and the analysis of complex genomes. , 1992, Trends in biotechnology.

[20]  Ronald W. Davis,et al.  Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. , 1999, Science.

[21]  R. Jessberger The many functions of smc proteins in chromosome dynamics , 2002, Nature Reviews Molecular Cell Biology.

[22]  Stephen J. Elledge,et al.  MDC1 is a mediator of the mammalian DNA damage checkpoint , 2003, Nature.

[23]  P. Russell,et al.  Mrc1 channels the DNA replication arrest signal to checkpoint kinase Cds1 , 2001, Nature Cell Biology.

[24]  T. Formosa,et al.  Dna2 mutants reveal interactions with Dna polymerase alpha and Ctf4, a Pol alpha accessory factor, and show that full Dna2 helicase activity is not essential for growth. , 1999, Genetics.

[25]  D. Toczyski,et al.  A unified view of the DNA-damage checkpoint. , 2002, Current opinion in cell biology.

[26]  M. Kastan,et al.  Involvement of the cohesin protein, Smc1, in Atm-dependent and independent responses to DNA damage. , 2002, Genes & development.

[27]  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.

[28]  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.

[29]  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.

[30]  Michel C. Nussenzweig,et al.  Genomic Instability in Mice Lacking Histone H2AX , 2002, Science.

[31]  K. Tanimoto,et al.  NBS1 Localizes to γ-H2AX Foci through Interaction with the FHA/BRCT Domain , 2002, Current Biology.

[32]  Stephen J. Elledge,et al.  Mrc1 transduces signals of DNA replication stress to activate Rad53 , 2001, Nature Cell Biology.

[33]  J. Boeke,et al.  DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray , 2003, Nature Genetics.

[34]  Charles Boone,et al.  Elg1 forms an alternative RFC complex important for DNA replication and genome integrity , 2003, The EMBO journal.

[35]  J. Blow,et al.  DNA replication: Stable driving prevents fatal smashes , 2001, Current Biology.

[36]  Matthias Platzer,et al.  Nibrin, a Novel DNA Double-Strand Break Repair Protein, Is Mutated in Nijmegen Breakage Syndrome , 1998, Cell.

[37]  A. Carr,et al.  Cytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Haber,et al.  Recombination‐induced CAG trinucleotide repeat expansions in yeast involve the MRE11–RAD50–XRS2 complex , 2000, The EMBO journal.

[39]  J. Haber,et al.  Multiple Pathways of Recombination Induced by Double-Strand Breaks in Saccharomyces cerevisiae , 1999, Microbiology and Molecular Biology Reviews.

[40]  I. Hickson,et al.  DNA helicase deficiencies associated with cancer predisposition and premature ageing disorders. , 2001, Human molecular genetics.

[41]  Brian E Snydsman,et al.  Chl4p and iml3p are two new members of the budding yeast outer kinetochore. , 2003, Molecular biology of the cell.

[42]  F. Fabre,et al.  Mutations in XRS2 and RAD50 delay but do not prevent mating-type switching in Saccharomyces cerevisiae , 1994, Molecular and cellular biology.

[43]  John R Yates,et al.  The hMre11/hRad50 Protein Complex and Nijmegen Breakage Syndrome: Linkage of Double-Strand Break Repair to the Cellular DNA Damage Response , 1998, Cell.

[44]  T. Stankovic,et al.  The DNA Double-Strand Break Repair Gene hMRE11 Is Mutated in Individuals with an Ataxia-Telangiectasia-like Disorder , 1999, Cell.

[45]  A. Tomkinson,et al.  Yeast Xrs2 Binds DNA and Helps Target Rad50 and Mre11 to DNA Ends* , 2003, Journal of Biological Chemistry.

[46]  Caroline M. Li,et al.  Saccharomyces cerevisiae DNA Polymerase ε and Polymerase σ Interact Physically and Functionally, Suggesting a Role for Polymerase ε in Sister Chromatid Cohesion , 2003, Molecular and Cellular Biology.

[47]  I. Herskowitz,et al.  Control of cell type in yeast by the mating type locus. The alpha 1-alpha 2 hypothesis. , 1981, Journal of molecular biology.

[48]  L. Symington Role of RAD52 Epistasis Group Genes in Homologous Recombination and Double-Strand Break Repair , 2002, Microbiology and Molecular Biology Reviews.

[49]  A. Franchitto,et al.  Bloom's syndrome protein is required for correct relocalization of RAD50/MRE11/NBS1 complex after replication fork arrest , 2002, The Journal of cell biology.

[50]  Shinya Matsuura,et al.  Nijmegen breakage syndrome gene, NBS1, and molecular links to factors for genome stability , 2002, Oncogene.

[51]  Junjie Chen,et al.  Cloning and Characterization of hCTF18, hCTF8, and hDCC1 , 2003, Journal of Biological Chemistry.

[52]  S. Elledge,et al.  BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. , 2000, Genes & development.

[53]  I. Herskowitz,et al.  Control of cell type in yeast by the mating type locus: The α1-α2 hypothesis☆ , 1981 .

[54]  E. Y. Lee,et al.  Functional analysis of FHA and BRCT domains of NBS1 in chromatin association and DNA damage responses. , 2002, Nucleic acids research.

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

[56]  S. Jackson,et al.  The MRE11 complex: at the crossroads of DNA repair and checkpoint signalling , 2002, Nature Reviews Molecular Cell Biology.

[57]  K. Nasmyth THE GENOME : Joining , Resolving , and Separating Sister Chromatids During Mitosis and Meiosis , 2006 .

[58]  J. Petrini,et al.  DNA replication-dependent nuclear dynamics of the Mre11 complex. , 2003, Molecular cancer research : MCR.

[59]  D. Koshland,et al.  Molecular biology. SMC complexes--wrapped up in controversy. , 2003, Science.

[60]  J. Petrini,et al.  A DNA damage response pathway controlled by Tel1 and the Mre11 complex. , 2001, Molecular cell.

[61]  T. Formosa,et al.  Evidence that POB1, a Saccharomyces cerevisiae protein that binds to DNA polymerase alpha, acts in DNA metabolism in vivo , 1992, Molecular and cellular biology.

[62]  R. C. Johnston,et al.  Distinct chromosome segregation roles for spindle checkpoint proteins. , 2002, Molecular biology of the cell.

[63]  S. Gasser,et al.  DNA polymerase stabilization at stalled replication forks requires Mec1 and the RecQ helicase Sgs1 , 2003, The EMBO journal.

[64]  R. Rothstein,et al.  Rad52 forms DNA repair and recombination centers during S phase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[65]  K. Middleton,et al.  KAR3-encoded kinesin is a minus-end-directed motor that functions with centromere binding proteins (CBF3) on an in vitro yeast kinetochore. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[66]  R. Ozawa,et al.  A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Katsuhiko Shirahige,et al.  S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex , 2003, Nature.

[68]  F. Spencer,et al.  CTF4 (CHL15) Mutants Exhibit Defective DNA Metabolism in the Yeast Saccharomyces cerevisiae , 1992, Molecular and cellular biology.

[69]  C. Mathew,et al.  Interaction of FANCD2 and NBS1 in the DNA damage response , 2002, Nature Cell Biology.

[70]  Jun Qin,et al.  SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint. , 2002, Genes & development.

[71]  A. Taylor,et al.  Specific Recruitment of Human Cohesin to Laser-induced DNA Damage* , 2002, The Journal of Biological Chemistry.

[72]  P. Meluh,et al.  KAR3, a kinesin-related gene required for yeast nuclear fusion , 1990, Cell.

[73]  S. Jackson,et al.  The yeast Xrs2 complex functions in S phase checkpoint regulation. , 2001, Genes & development.

[74]  Kunihiro Matsumoto,et al.  Chl12 (Ctf18) Forms a Novel Replication Factor C-Related Complex and Functions Redundantly with Rad24 in the DNA Replication Checkpoint Pathway , 2001, Molecular and Cellular Biology.

[75]  K. Bloom,et al.  Differential kinetochore protein requirements for establishment versus propagation of centromere activity in Saccharomyces cerevisiae , 2003, The Journal of cell biology.

[76]  Gary D Bader,et al.  Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants , 2001, Science.

[77]  B. Everitt,et al.  Statistical methods for rates and proportions , 1973 .

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

[79]  P. Plevani,et al.  Srs2 DNA helicase is involved in checkpoint response and its regulation requires a functional Mec1‐dependent pathway and Cdk1 activity , 2000, The EMBO journal.

[80]  A Chakravarti,et al.  High-throughput variation detection and genotyping using microarrays. , 2001, Genome research.

[81]  J. Diffley,et al.  A central role for DNA replication forks in checkpoint activation and response. , 2003, Molecular cell.

[82]  S. Jackson,et al.  The complex matter of DNA double-strand break detection. , 2001, Biochemical Society transactions.

[83]  J. Haber,et al.  Recovery from checkpoint-mediated arrest after repair of a double-strand break requires Srs2 helicase. , 2002, Molecular cell.

[84]  A. Carr,et al.  Fission yeast Rad50 stimulates sister chromatid recombination and links cohesion with repair , 2001, The EMBO journal.

[85]  F. Spencer,et al.  CTF 4 ( CHL 15 ) Mutants Exhibit Defective DNA Metabolism in the Yeast Saccharomyces cerevisiae , 2022 .

[86]  D. Burke,et al.  The spindle checkpoint of the yeast Saccharomyces cerevisiae requires kinetochore function and maps to the CBF3 domain. , 2001, Genetics.

[87]  M. Christman,et al.  Pol κ: A DNA Polymerase Required for Sister Chromatid Cohesion , 2000 .

[88]  M. Bibikova,et al.  Mre11 protein complex prevents double-strand break accumulation during chromosomal DNA replication. , 2001, Molecular cell.

[89]  R. Kanaar,et al.  Chromosome Organization: Reaching out to Embrace New Models , 2002, Current Biology.

[90]  J. Yates,et al.  Cid13 Is a Cytoplasmic Poly(A) Polymerase that Regulates Ribonucleotide Reductase mRNA , 2002, Cell.

[91]  P. Mosesso,et al.  Werner's syndrome protein is required for correct recovery after replication arrest and DNA damage induced in S-phase of cell cycle. , 2001, Molecular biology of the cell.

[92]  H. Klein Mutations in recombinational repair and in checkpoint control genes suppress the lethal combination of srs2Delta with other DNA repair genes in Saccharomyces cerevisiae. , 2001, Genetics.

[93]  M. Christman,et al.  Pol kappa: A DNA polymerase required for sister chromatid cohesion. , 2000, Science.

[94]  P. Farnham,et al.  Mre11 Complex and DNA Replication: Linkage to E2F and Sites of DNA Synthesis , 2001, Molecular and Cellular Biology.

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

[96]  S. Gasser,et al.  RecQ helicases: at the heart of genetic stability , 2002, FEBS letters.

[97]  T. Weinert,et al.  Toward maintaining the genome: DNA damage and replication checkpoints. , 2002, Annual review of genetics.