FANCD2 Binding to H4K20me2 via a Methyl-Binding Domain Is Essential for Efficient DNA Cross-Link Repair

Fanconi anemia (FA) is an inherited disease characterized by bone marrow failure and increased cancer risk. FA is caused by mutation of any 1 of 22 genes, and the FA proteins function cooperatively to repair DNA interstrand cross-links (ICLs). A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins, which occurs within chromatin. How FANCD2 and FANCI are anchored to chromatin remains unknown. ABSTRACT Fanconi anemia (FA) is an inherited disease characterized by bone marrow failure and increased cancer risk. FA is caused by mutation of any 1 of 22 genes, and the FA proteins function cooperatively to repair DNA interstrand cross-links (ICLs). A central step in the activation of the FA pathway is the monoubiquitination of the FANCD2 and FANCI proteins, which occurs within chromatin. How FANCD2 and FANCI are anchored to chromatin remains unknown. In this study, we identify and characterize a FANCD2 histone-binding domain (HBD) and embedded methyl-lysine-binding domain (MBD) and demonstrate binding specificity for H4K20me2. Disruption of the HBD/MBD compromises FANCD2 chromatin binding and nuclear focus formation and its ability to promote error-free DNA interstrand cross-link repair, leading to increased error-prone repair and genome instability. Our study functionally describes the first FA protein chromatin reader domain and establishes an important link between this human genetic disease and chromatin plasticity.

[1]  H. Kimura,et al.  Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2 , 2018, Molecular cell.

[2]  Z. Mao,et al.  Histone H3K27 methylation modulates the dynamics of FANCD2 on chromatin to facilitate NHEJ and genome stability , 2018, Journal of Cell Science.

[3]  N. Howlett,et al.  Understanding the Histone DNA Repair Code: H4K20me2 Makes Its Mark , 2018, Molecular Cancer Research.

[4]  Minoru Takata,et al.  Biallelic mutations in the ubiquitin ligase RFWD3 cause Fanconi anemia , 2017, The Journal of clinical investigation.

[5]  N. Howlett,et al.  Modulation of the Fanconi anemia pathway via chemically induced changes in chromatin structure , 2017, Oncotarget.

[6]  Marie-christine Caron,et al.  The identification of FANCD2 DNA binding domains reveals nuclear localization sequences , 2017, Nucleic acids research.

[7]  P. Andreassen,et al.  Coordination of the recruitment of the FANCD2 and PALB2 Fanconi anemia proteins by an ubiquitin signaling network , 2016, Chromosoma.

[8]  A. Shimamura,et al.  Recent discoveries in the molecular pathogenesis of the inherited bone marrow failure syndrome Fanconi anemia. , 2017, Blood reviews.

[9]  N. Howlett,et al.  The PTEN phosphatase functions cooperatively with the Fanconi anemia proteins in DNA crosslink repair , 2016, Scientific Reports.

[10]  M. Cohn,et al.  The FANCD2–FANCI complex is recruited to DNA interstrand crosslinks before monoubiquitination of FANCD2 , 2016, Nature Communications.

[11]  A. Gingras,et al.  The TIP60 Complex Regulates Bivalent Chromatin Recognition by 53BP1 through Direct H4K20me Binding and H2AK15 Acetylation. , 2016, Molecular cell.

[12]  F. Rosselli,et al.  Impaired TIP60-mediated H4K16 acetylation accounts for the aberrant chromatin accumulation of 53BP1 and RAP80 in Fanconi anemia pathway-deficient cells , 2015, Nucleic acids research.

[13]  J. Walter,et al.  BRCA1 promotes unloading of the CMG helicase from a stalled DNA replication fork. , 2014, Molecular cell.

[14]  H. Walden,et al.  The Fanconi anemia DNA repair pathway: structural and functional insights into a complex disorder. , 2014, Annual review of biophysics.

[15]  P. Knipscheer,et al.  XPF-ERCC1 acts in Unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4. , 2014, Molecular cell.

[16]  Michal Zimmermann,et al.  53BP1: pro choice in DNA repair. , 2014, Trends in cell biology.

[17]  N. Howlett,et al.  Coordinate Nuclear Targeting of the FANCD2 and FANCI Proteins via a FANCD2 Nuclear Localization Signal , 2013, PloS one.

[18]  D. Durocher,et al.  53BP1 is a reader of the DNA damage-induced H2A Lys15 ubiquitin mark , 2013, Nature.

[19]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[20]  G. Schotta,et al.  Histone H4 Lysine 20 methylation: key player in epigenetic regulation of genomic integrity , 2013, Nucleic acids research.

[21]  Molly C. Kottemann,et al.  Fanconi anaemia and the repair of Watson and Crick DNA crosslinks , 2013, Nature.

[22]  R. Greenberg,et al.  Acetylation Limits 53BP1 Association with Damaged Chromatin to Promote Homologous Recombination , 2012, Nature Structural &Molecular Biology.

[23]  N. Howlett,et al.  Regulation of the Fanconi anemia pathway by a CUE ubiquitin-binding domain in the FANCD2 protein. , 2012, Blood.

[24]  H. Kimura,et al.  Histone chaperone activity of Fanconi anemia proteins, FANCD2 and FANCI, is required for DNA crosslink repair , 2012, The EMBO journal.

[25]  Hong Wu,et al.  A distinct replication fork protection pathway connects Fanconi anemia tumor suppressors to RAD51-BRCA1/2. , 2012, Cancer cell.

[26]  Benjamin E. Gross,et al.  The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. , 2012, Cancer discovery.

[27]  T. Ludwig,et al.  BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair. , 2012, Molecular cell.

[28]  H. Kurumizaka,et al.  DNA robustly stimulates FANCD2 monoubiquitylation in the complex with FANCI , 2012, Nucleic acids research.

[29]  S. Khorasanizadeh,et al.  Epigenetic virtues of chromodomains , 2011, Critical reviews in biochemistry and molecular biology.

[30]  S. Elledge,et al.  Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway , 2011, Science.

[31]  V. Rybin,et al.  Chromatin-modifying Complex Component Nurf55/p55 Associates with Histones H3 and H4 and Polycomb Repressive Complex 2 Subunit Su(z)12 through Partially Overlapping Binding Sites , 2011, The Journal of Biological Chemistry.

[32]  M. Jasin,et al.  NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript NIH Public Access Author Manuscript , 2006 .

[33]  Xiaofeng Jiang,et al.  The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair , 2010, The Journal of cell biology.

[34]  Z. Hořejší,et al.  Preventing nonhomologous end joining suppresses DNA repair defects of Fanconi anemia. , 2010, Molecular cell.

[35]  M. Sivasubramaniam,et al.  Ku70 Corrupts DNA Repair in the Absence of the Fanconi Anemia Pathway , 2010, Science.

[36]  S. Elledge,et al.  The Fanconi Anemia Pathway Promotes Replication-Dependent DNA Interstrand Cross-Link Repair , 2009, Science.

[37]  T. Glover,et al.  Functional Interaction between the Fanconi Anemia D2 Protein and Proliferating Cell Nuclear Antigen (PCNA) via a Conserved Putative PCNA Interaction Motif* , 2009, The Journal of Biological Chemistry.

[38]  N. Lowndes,et al.  53BP1: function and mechanisms of focal recruitment. , 2009, Biochemical Society transactions.

[39]  J. Whetstine,et al.  Histone H3 methylation links DNA damage detection to activation of the Tip60 tumor suppressor , 2009, Nature Cell Biology.

[40]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[41]  D. Reinberg,et al.  Monomethylation of Histone H4-Lysine 20 Is Involved in Chromosome Structure and Stability and Is Essential for Mouse Development , 2009, Molecular and Cellular Biology.

[42]  Min Huang,et al.  Inactivation of murine Usp1 results in genomic instability and a Fanconi anemia phenotype. , 2009, Developmental cell.

[43]  G. Schotta,et al.  A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse. , 2008, Genes & development.

[44]  R. Kingston,et al.  Structural basis of histone H4 recognition by p55. , 2008, Genes & development.

[45]  K. Helin,et al.  The histone methyltransferase SET8 is required for S-phase progression , 2007, The Journal of cell biology.

[46]  Anindya Dutta,et al.  UBE2T, the Fanconi Anemia Core Complex, and FANCD2 Are Recruited Independently to Chromatin: a Basis for the Regulation of FANCD2 Monoubiquitination , 2007, Molecular and Cellular Biology.

[47]  E. Spiteri,et al.  FANCI is a second monoubiquitinated member of the Fanconi anemia pathway , 2007, Nature Structural &Molecular Biology.

[48]  G. Pals,et al.  Hypomorphic mutations in the gene encoding a key Fanconi anemia protein, FANCD2, sustain a significant group of FA-D2 patients with severe phenotype. , 2007, American journal of human genetics.

[49]  S. Elledge,et al.  Identification of the FANCI Protein, a Monoubiquitinated FANCD2 Paralog Required for DNA Repair , 2007, Cell.

[50]  R. Marcos,et al.  Histone H2AX and Fanconi anemia FANCD2 function in the same pathway to maintain chromosome stability , 2007, The EMBO journal.

[51]  R. Steward,et al.  Aberrant monomethylation of histone H4 lysine 20 activates the DNA damage checkpoint in Drosophila melanogaster , 2007, The Journal of cell biology.

[52]  Georges Mer,et al.  Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair , 2006, Cell.

[53]  B. Chen,et al.  ATR-Dependent Phosphorylation of DNA-Dependent Protein Kinase Catalytic Subunit in Response to UV-Induced Replication Stress , 2006, Molecular and Cellular Biology.

[54]  P. Russell,et al.  Histone modification-dependent and -independent pathways for recruitment of checkpoint protein Crb2 to double-strand breaks. , 2006, Genes & development.

[55]  A. Horwitz,et al.  Direct DNA Binding Activity of the Fanconi Anemia D2 Protein* , 2005, Journal of Biological Chemistry.

[56]  A. D’Andrea,et al.  The Fanconi anemia pathway is required for the DNA replication stress response and for the regulation of common fragile site stability. , 2005, Human molecular genetics.

[57]  D. Reinberg,et al.  PR-Set7-dependent methylation of histone H4 Lys 20 functions in repression of gene expression and is essential for mitosis. , 2005, Genes & development.

[58]  Zhao-Qi Wang,et al.  Human Fanconi anemia monoubiquitination pathway promotes homologous DNA repair. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. Mata,et al.  Methylation of Histone H4 Lysine 20 Controls Recruitment of Crb2 to Sites of DNA Damage , 2004, Cell.

[60]  Tom J. Petty,et al.  Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks , 2004, Nature.

[61]  A. Brehm,et al.  The Drosophila methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2 , 2004, BMC Molecular Biology.

[62]  Paul Tempst,et al.  PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. , 2002, Molecular cell.

[63]  R. Moses,et al.  Positional cloning of a novel Fanconi anemia gene, FANCD2. , 2001, Molecular cell.

[64]  S. Ganesan,et al.  Interaction of the Fanconi anemia proteins and BRCA1 in a common pathway. , 2001, Molecular cell.

[65]  E. Rogakou,et al.  DNA Double-stranded Breaks Induce Histone H2AX Phosphorylation on Serine 139* , 1998, The Journal of Biological Chemistry.

[66]  Carl Wu,et al.  Drosophila NURF-55, a WD repeat protein involved in histone metabolism. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[67]  S. Olson.  Fanconi Anemia : Guidelines for Diagnosis and Management 28 Test 1 : Chromosome Breakage in Peripheral Blood Lymphocytes , 2015 .