53BP1‐mediated recruitment of RASSF1A to ribosomal DNA breaks promotes local ATM signaling

DNA lesions occur across the genome and constitute a threat to cell viability; however, damage at specific genomic loci has a relatively greater impact on overall genome stability. The ribosomal RNA gene repeats (rDNA) are emerging fragile sites. Recent progress in understanding how the rDNA damage response is organized has highlighted a key role of adaptor proteins. Here, we show that the scaffold tumor suppressor RASSF1A is recruited to rDNA breaks. RASSF1A recruitment to double‐strand breaks is mediated by 53BP1 and depends on RASSF1A phosphorylation at Serine 131 by ATM kinase. Employing targeted rDNA damage, we uncover that RASSF1A recruitment promotes local ATM signaling. RASSF1A silencing, a common epigenetic event during malignant transformation, results in persistent breaks, rDNA copy number alterations and decreased cell viability. Overall, we identify a novel role for RASSF1A at rDNA break sites, provide mechanistic insight into how the DNA damage response is organized in a chromatin context, and provide further evidence for how silencing of the RASSF1A tumor suppressor contributes to genome instability.

[1]  B. Reina-San-Martin,et al.  Heterochromatic repeat clustering imposes a physical barrier on homologous recombination to prevent chromosomal translocations , 2021, Molecular cell.

[2]  E. Berns,et al.  CX-5461 activates the DNA damage response and demonstrates therapeutic efficacy in high-grade serous ovarian cancer , 2020, Nature Communications.

[3]  E. Soutoglou,et al.  How to maintain the genome in nuclear space. , 2020, Current opinion in cell biology.

[4]  M. Stucki,et al.  Treacle controls the nucleolar response to rDNA breaks via TOPBP1 recruitment and ATR activation , 2020, Nature Communications.

[5]  T. de Lange,et al.  53BP1: a DSB escort , 2020, Genes & development.

[6]  G. Zalcman,et al.  RASSF1A, puppeteer of cellular homeostasis, fights tumorigenesis, and metastasis—an updated review , 2019, Cell Death & Disease.

[7]  Jean-Philippe Lambert,et al.  JMJD6 participates in the maintenance of ribosomal DNA integrity in response to DNA damage , 2019, bioRxiv.

[8]  P. Mangeot,et al.  A cohesin/HUSH- and LINC-dependent pathway controls ribosomal DNA double-strand break repair , 2019, Genes & development.

[9]  J. Gerton,et al.  Superresolution microscopy reveals linkages between ribosomal DNA on heterologous chromosomes , 2019, The Journal of cell biology.

[10]  C. Bassi,et al.  Methylation Dynamics of RASSF1A and Its Impact on Cancer , 2019, Cancers.

[11]  M. Altmeyer,et al.  Phase separation of 53BP1 determines liquid‐like behavior of DNA repair compartments , 2019, The EMBO journal.

[12]  I. Chiolo,et al.  Actin' between phase separated domains for heterochromatin repair. , 2019, DNA repair.

[13]  D. H. Larsen,et al.  Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair , 2019, Nucleic acids research.

[14]  Daniela Pankova,et al.  RASSF1A is required for the maintenance of nuclear actin levels , 2019, bioRxiv.

[15]  R. Wolthuis,et al.  Keeping ribosomal DNA intact: a repeating challenge , 2018, Chromosome Research.

[16]  M. Skrzypczak,et al.  Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures , 2018, Molecular cell.

[17]  S. Rottenberg,et al.  53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ , 2018, Nature.

[18]  Vassilis G Gorgoulis,et al.  Integrating the DNA damage and protein stress responses during cancer development and treatment , 2018, The Journal of pathology.

[19]  Eytan Zlotorynski Shieldin the ends for 53BP1 , 2018, Nature Reviews Molecular Cell Biology.

[20]  E. O’Neill,et al.  MST2 kinase suppresses rDNA transcription in response to DNA damage by phosphorylating nucleolar histone H2B , 2018, The EMBO journal.

[21]  J. Bartek,et al.  Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis , 2018, Oncogene.

[22]  S. Gasser,et al.  Chromatin and nucleosome dynamics in DNA damage and repair , 2017, Genes & development.

[23]  P. Jeggo,et al.  Chromatin modifiers and remodellers in DNA repair and signalling , 2017, Philosophical Transactions of the Royal Society B: Biological Sciences.

[24]  B. Lemos,et al.  Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation , 2017, PLoS genetics.

[25]  Linheng Li,et al.  Ribosomal DNA copy number loss and sequence variation in cancer , 2017, PLoS genetics.

[26]  Jian Xian,et al.  CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours , 2017, Nature Communications.

[27]  M. Mann,et al.  SCAI promotes DNA double-strand break repair in distinct chromosomal contexts , 2016, Nature Cell Biology.

[28]  B. Reina-San-Martin,et al.  Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin. , 2016, Molecular cell.

[29]  Daniela Pankova,et al.  TGF-β Targets the Hippo Pathway Scaffold RASSF1A to Facilitate YAP/SMAD2 Nuclear Translocation. , 2016, Molecular cell.

[30]  Lan K. Nguyen,et al.  MST2-RASSF protein-protein interactions through SARAH domains , 2016, Briefings Bioinform..

[31]  Diana M. Mitrea,et al.  Coexisting Liquid Phases Underlie Nucleolar Subcompartments , 2016, Cell.

[32]  N. Mailand,et al.  Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers , 2016, Nature Reviews Molecular Cell Biology.

[33]  E. O’Neill,et al.  Hippo pathway and protection of genome stability in response to DNA damage , 2016, The FEBS journal.

[34]  R. Medema,et al.  Breaks in the 45S rDNA Lead to Recombination-Mediated Loss of Repeats. , 2016, Cell reports.

[35]  Robert A. Baldock,et al.  ATM Localization and Heterochromatin Repair Depend on Direct Interaction of the 53BP1-BRCT2 Domain with γH2AX , 2015, Cell Reports.

[36]  R. Greenberg,et al.  ATM Dependent Silencing Links Nucleolar Chromatin Reorganization to DNA Damage Recognition. , 2015, Cell reports.

[37]  Junjie Chen,et al.  Cell cycle-dependent inhibition of 53BP1 signaling by BRCA1 , 2015, Cell Discovery.

[38]  E. O’Neill,et al.  Clinical utility of RASSF1A methylation in human malignancies , 2015, British Journal of Cancer.

[39]  B. McStay,et al.  A localized nucleolar DNA damage response facilitates recruitment of the homology-directed repair machinery independent of cell cycle stage , 2015, Genes & development.

[40]  M. Jasin,et al.  Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. , 2015, Cold Spring Harbor perspectives in biology.

[41]  B. Lemos,et al.  Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes , 2015, Proceedings of the National Academy of Sciences.

[42]  T. Misteli,et al.  Activation of DNA damage response signaling by condensed chromatin. , 2014, Cell reports.

[43]  Jennifer A. Clark,et al.  The RASSF1A Tumor Suppressor Regulates XPA-Mediated DNA Repair , 2014, Molecular and Cellular Biology.

[44]  L. V. D. Weyden,et al.  RASSF1A–LATS1 signalling stabilizes replication forks by restricting CDK2-mediated phosphorylation of BRCA2 , 2014, Nature Cell Biology.

[45]  S. Smerdon,et al.  The NBS1–Treacle complex controls ribosomal RNA transcription in response to DNA damage , 2014, Nature Cell Biology.

[46]  P. Sung,et al.  53BP1, BRCA1, and the Choice between Recombination and End Joining at DNA Double-Strand Breaks , 2014, Molecular and Cellular Biology.

[47]  Austen R. D. Ganley,et al.  The shared genomic architecture of human nucleolar organizer regions , 2013, Genome research.

[48]  T. Misteli,et al.  Spatial Dynamics of Chromosome Translocations in Living Cells , 2013, Science.

[49]  Marco Durante,et al.  DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin , 2011, Nucleic acids research.

[50]  Aki Minoda,et al.  Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair , 2011, Cell.

[51]  S. Baksh,et al.  Functional importance of RASSF1A microtubule localization and polymorphisms , 2010, Oncogene.

[52]  H. Maki,et al.  Abundance of Ribosomal RNA Gene Copies Maintains Genome Integrity , 2010, Science.

[53]  P. Jeggo,et al.  53BP1 promotes ATM activity through direct interactions with the MRN complex , 2010, The EMBO journal.

[54]  A. Shibata,et al.  53BP1-dependent robust localized KAP-1 phosphorylation is essential for heterochromatic DNA double-strand break repair , 2010, Nature Cell Biology.

[55]  S. Arnold,et al.  Human rRNA gene clusters are recombinational hotspots in cancer. , 2009, Cancer research.

[56]  J. Bartek,et al.  The DNA-damage response in human biology and disease , 2009, Nature.

[57]  A. Pierce,et al.  Genomic architecture and inheritance of human ribosomal RNA gene clusters. , 2007, Genome research.

[58]  Jiri Bartek,et al.  RNF8 Ubiquitylates Histones at DNA Double-Strand Breaks and Promotes Assembly of Repair Proteins , 2007, Cell.

[59]  Walter Kolch,et al.  RASSF1A elicits apoptosis through an MST2 pathway directing proapoptotic transcription by the p73 tumor suppressor protein. , 2007, Molecular cell.

[60]  T. Misteli,et al.  The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks , 2007, Nature.

[61]  T. Halazonetis,et al.  53BP1 and NFBD1/MDC1-Nbs1 function in parallel interacting pathways activating ataxia-telangiectasia mutated (ATM) in response to DNA damage. , 2003, Cancer research.

[62]  Jiri Bartek,et al.  53BP1 functions in an ATM-dependent checkpoint pathway that is constitutively activated in human cancer , 2002, Nature Cell Biology.