RSC Mobilizes Nucleosomes To Improve Accessibility of Repair Machinery to the Damaged Chromatin

ABSTRACT Repair of DNA double-strand breaks (DSBs) protects cells and organisms, as well as their genome integrity. Since DSB repair occurs in the context of chromatin, chromatin must be modified to prevent it from inhibiting DSB repair. Evidence supports the role of histone modifications and ATP-dependent chromatin remodeling in repair and signaling of chromosome DSBs. The key questions are, then, what the nature of chromatin altered by DSBs is and how remodeling of chromatin facilitates DSB repair. Here we report a chromatin alteration caused by a single HO endonuclease-generated DSB at the Saccharomyces cerevisiae MAT locus. The break induces rapid nucleosome migration to form histone-free DNA of a few hundred base pairs immediately adjacent to the break. The DSB-induced nucleosome repositioning appears independent of end processing, since it still occurs when the 5′-to-3′ degradation of the DNA end is markedly reduced. The tetracycline-controlled depletion of Sth1, the ATPase of RSC, or deletion of RSC2 severely reduces chromatin remodeling and loading of Mre11 and Yku proteins at the DSB. Depletion of Sth1 also reduces phosphorylation of H2A, processing, and joining of DSBs. We propose that RSC-mediated chromatin remodeling at the DSB prepares chromatin to allow repair machinery to access the break and is vital for efficient DSB repair.

[1]  A. Imbalzano,et al.  Mammalian SWI/SNF complexes facilitate DNA double‐strand break repair by promoting γ‐H2AX induction , 2006, The EMBO journal.

[2]  J. Lieberman,et al.  γ-H2AX Dephosphorylation by Protein Phosphatase 2A Facilitates DNA Double-Strand Break Repair , 2005 .

[3]  F. Winston,et al.  Recent advances in understanding chromatin remodeling by Swi/Snf complexes. , 2003, Current opinion in genetics & development.

[4]  Alexander W. Bird,et al.  Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair , 2002, Nature.

[5]  J. T. Kadonaga,et al.  The Many Faces of Chromatin Remodeling SWItching beyond Transcription , 2001, Cell.

[6]  T. Tsukiyama,et al.  Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. , 2003, Molecular cell.

[7]  M. Groudine,et al.  Controlling the double helix , 2003, Nature.

[8]  B. Maier-Davis,et al.  Chromatin remodeling by nucleosome disassembly in vitro. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[9]  N. Krogan,et al.  INO80 and γ-H2AX Interaction Links ATP-Dependent Chromatin Remodeling to DNA Damage Repair , 2004, Cell.

[10]  D. Sterner,et al.  Acetylation of Histones and Transcription-Related Factors , 2000, Microbiology and Molecular Biology Reviews.

[11]  J. Tyler,et al.  Localized Histone Acetylation and Deacetylation Triggered by the Homologous Recombination Pathway of Double-Strand DNA Repair , 2005, Molecular and Cellular Biology.

[12]  N. Kleckner,et al.  The Single-End Invasion An Asymmetric Intermediate at the Double-Strand Break to Double-Holliday Junction Transition of Meiotic Recombination , 2001, Cell.

[13]  C. Peterson,et al.  Cellular machineries for chromosomal DNA repair. , 2004, Genes & development.

[14]  R. Simpson,et al.  High-Resolution Structural Analysis of Chromatin at Specific Loci: Saccharomyces cerevisiae Silent Mating Type Locus HMLα , 1998, Molecular and Cellular Biology.

[15]  Stephen P. Jackson,et al.  A role for Saccharomyces cerevisiae histone H2A in DNA repair , 2000, Nature.

[16]  Barbara Hohn,et al.  Recruitment of the INO80 Complex by H2A Phosphorylation Links ATP-Dependent Chromatin Remodeling with DNA Double-Strand Break Repair , 2004, Cell.

[17]  B. Cairns,et al.  The RSC Chromatin Remodeling Complex Bears an Essential Fungal-Specific Protein Module With Broad Functional Roles , 2006, Genetics.

[18]  K. Khanna,et al.  DNA double-strand breaks: signaling, repair and the cancer connection , 2001, Nature Genetics.

[19]  G. Mizuguchi,et al.  ATP-dependent remodeling of chromatin. , 1998, Cold Spring Harbor symposia on quantitative biology.

[20]  J. Lieberman,et al.  A phosphatase complex that dephosphorylates γH2AX regulates DNA damage checkpoint recovery , 2006, Nature.

[21]  F. Alt,et al.  Increased ionizing radiation sensitivity and genomic instability in the absence of histone H2AX , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[22]  T. Hughes,et al.  Exploration of Essential Gene Functions via Titratable Promoter Alleles , 2004, Cell.

[23]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[24]  Nevan J Krogan,et al.  INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. , 2004, Cell.

[25]  B. Cairns,et al.  Chromatin remodeling complexes: strength in diversity, precision through specialization. , 2005, Current opinion in genetics & development.

[26]  M. Yaniv,et al.  Increased DNA Damage Sensitivity and Apoptosis in Cells Lacking the Snf5/Ini1 Subunit of the SWI/SNF Chromatin Remodeling Complex , 2006, Molecular and Cellular Biology.

[27]  Jeremy M. Stark,et al.  Double-strand breaks and tumorigenesis. , 2001, Trends in cell biology.

[28]  J. Haber,et al.  Saccharomyces Ku70, Mre11/Rad50, and RPA Proteins Regulate Adaptation to G2/M Arrest after DNA Damage , 1998, Cell.

[29]  Haico van Attikum,et al.  The histone code at DNA breaks: a guide to repair? , 2005, Nature Reviews Molecular Cell Biology.

[30]  Marco Foiani,et al.  DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1 , 2004, Nature.

[31]  Jian Huang,et al.  ATP-Dependent Chromatin-Remodeling Complexes in DNA Double-Strand Break Repair: Remodeling, Pairing and (Re)pairing , 2005, Cell cycle.

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

[33]  M. Osley,et al.  Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae , 2005, Nature.

[34]  V. Yamazaki,et al.  A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage , 2000, Current Biology.

[35]  J. Haber,et al.  Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae , 1996, Molecular and cellular biology.

[36]  A. Tomkinson,et al.  Mending the break: two DNA double-strand break repair machines in eukaryotes. , 2003, Progress in nucleic acid research and molecular biology.

[37]  Ali Jazayeri,et al.  Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Sung-Hee Ahn,et al.  Phosphorylation of Histone H4 Serine 1 during DNA Damage Requires Casein Kinase II in S. cerevisiae , 2005, Current Biology.

[39]  Anjanabha Saha,et al.  Chromatin remodeling by RSC involves ATP-dependent DNA translocation. , 2002, Genes & development.

[40]  M. Parthun,et al.  The nuclear Hat1p/Hat2p complex: a molecular link between type B histone acetyltransferases and chromatin assembly. , 2004, Molecular cell.

[41]  Sang Eun Lee,et al.  The Yeast Chromatin Remodeler RSC Complex Facilitates End Joining Repair of DNA Double-Strand Breaks , 2005, Molecular and Cellular Biology.

[42]  T. Tsukiyama,et al.  Chromatin remodeling and transcription. , 1997, Current opinion in genetics & development.

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

[44]  J. Haber,et al.  Complementation between N-terminal Saccharomyces cerevisiae mre11 alleles in DNA repair and telomere length maintenance. , 2002, DNA repair.

[45]  C. Allis,et al.  Histone acetyltransferases. , 2001, Annual review of biochemistry.

[46]  J. Hayes,et al.  Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. , 2005, Molecular cell.

[47]  W. Wang,et al.  The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms for diverse functions. , 2003, Current topics in microbiology and immunology.

[48]  R. Rothstein,et al.  Choreography of the DNA Damage Response Spatiotemporal Relationships among Checkpoint and Repair Proteins , 2004, Cell.

[49]  S. Jackson,et al.  Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. , 2004, Molecular cell.

[50]  Michael Lichten,et al.  Distribution and Dynamics of Chromatin Modification Induced by a Defined DNA Double-Strand Break , 2004, Current Biology.

[51]  Michael Lichten,et al.  DNA damage response pathway uses histone modification to assemble a double-strand break-specific cohesin domain. , 2004, Molecular cell.

[52]  B. Cairns,et al.  Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. , 2005, Genes & development.

[53]  J. Haber,et al.  Role of yeast SIR genes and mating type in directing DNA double-strand breaks to homologous and non-homologous repair paths , 1999, Current Biology.

[54]  M. Parthun,et al.  Recruitment of the Type B Histone Acetyltransferase Hat1p to Chromatin Is Linked to DNA Double-Strand Breaks , 2006, Molecular and Cellular Biology.