Double-strand Breaks in Ribosomal RNA Genes Activate a Distinct Signaling and Chromatin Response to Facilitate Nucleolar Restructuring and Repair

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2019 Jun 12

PMID 31184714

Citations 41

Authors

Lea M Korsholm

Zita Gal

Lin Lin

Oliver Quevedo

Diana A Ahmad

Ekaterina Dulina

Yonglun Luo

Jiri Bartek

Dorthe H Larsen

Affiliations

Soon will be listed here.

Abstract

The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.

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References

Pefani D, Tognoli M, Pirincci Ercan D, Gorgoulis V, ONeill E . MST2 kinase suppresses rDNA transcription in response to DNA damage by phosphorylating nucleolar histone H2B. EMBO J. 2018; 37(15). PMC: 6068430. DOI: 10.15252/embj.201798760. View

Berkovich E, Monnat Jr R, Kastan M . Roles of ATM and NBS1 in chromatin structure modulation and DNA double-strand break repair. Nat Cell Biol. 2007; 9(6):683-90. DOI: 10.1038/ncb1599. View

Kruhlak M, Crouch E, Orlov M, Montano C, Gorski S, Nussenzweig A . The ATM repair pathway inhibits RNA polymerase I transcription in response to chromosome breaks. Nature. 2007; 447(7145):730-4. DOI: 10.1038/nature05842. View

Aymard F, Aguirrebengoa M, Guillou E, Javierre B, Bugler B, Arnould C . Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat Struct Mol Biol. 2017; 24(4):353-361. PMC: 5385132. DOI: 10.1038/nsmb.3387. View

Velimezi G, Liontos M, Vougas K, Roumeliotis T, Bartkova J, Sideridou M . Functional interplay between the DNA-damage-response kinase ATM and ARF tumour suppressor protein in human cancer. Nat Cell Biol. 2013; 15(8):967-77. DOI: 10.1038/ncb2795. View

Toledo L, Altmeyer M, Rask M, Lukas C, Larsen D, Povlsen L . ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell. 2013; 155(5):1088-103. DOI: 10.1016/j.cell.2013.10.043. View

Bartek J, Lukas J . DNA damage checkpoints: from initiation to recovery or adaptation. Curr Opin Cell Biol. 2007; 19(2):238-45. DOI: 10.1016/j.ceb.2007.02.009. View

Chiolo I, Minoda A, Colmenares S, Polyzos A, Costes S, Karpen G . Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell. 2011; 144(5):732-44. PMC: 3417143. DOI: 10.1016/j.cell.2011.02.012. View

Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grofte M . TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes. Cell. 2012; 150(4):697-709. DOI: 10.1016/j.cell.2012.06.039. View

10.

Lindstrom M, Jurada D, Bursac S, Orsolic I, Bartek J, Volarevic S . Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis. Oncogene. 2018; 37(18):2351-2366. PMC: 5931986. DOI: 10.1038/s41388-017-0121-z. View

11.

Melander F, Bekker-Jensen S, Falck J, Bartek J, Mailand N, Lukas J . Phosphorylation of SDT repeats in the MDC1 N terminus triggers retention of NBS1 at the DNA damage-modified chromatin. J Cell Biol. 2008; 181(2):213-26. PMC: 2315670. DOI: 10.1083/jcb.200708210. View

12.

Tsouroula K, Furst A, Rogier M, Heyer V, Maglott-Roth A, Ferrand A . Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin. Mol Cell. 2016; 63(2):293-305. DOI: 10.1016/j.molcel.2016.06.002. View

13.

Williams R, Williams J, Tainer J . Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem Cell Biol. 2007; 85(4):509-20. DOI: 10.1139/O07-069. View

14.

Sokka M, Rilla K, Miinalainen I, Pospiech H, Syvaoja J . High levels of TopBP1 induce ATR-dependent shut-down of rRNA transcription and nucleolar segregation. Nucleic Acids Res. 2015; 43(10):4975-89. PMC: 4446431. DOI: 10.1093/nar/gkv371. View

15.

Ciccia A, Huang J, Izhar L, Sowa M, Harper J, Elledge S . Treacher Collins syndrome TCOF1 protein cooperates with NBS1 in the DNA damage response. Proc Natl Acad Sci U S A. 2014; 111(52):18631-6. PMC: 4284564. DOI: 10.1073/pnas.1422488112. View

16.

Sirri V, Urcuqui-Inchima S, Roussel P, Hernandez-Verdun D . Nucleolus: the fascinating nuclear body. Histochem Cell Biol. 2007; 129(1):13-31. PMC: 2137947. DOI: 10.1007/s00418-007-0359-6. View

17.

Aymard F, Bugler B, Schmidt C, Guillou E, Caron P, Briois S . Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks. Nat Struct Mol Biol. 2014; 21(4):366-74. PMC: 4300393. DOI: 10.1038/nsmb.2796. View

18.

Killen M, Stults D, Adachi N, Hanakahi L, Pierce A . Loss of Bloom syndrome protein destabilizes human gene cluster architecture. Hum Mol Genet. 2009; 18(18):3417-28. DOI: 10.1093/hmg/ddp282. View

19.

Adams K, Medhurst A, Dart D, Lakin N . Recruitment of ATR to sites of ionising radiation-induced DNA damage requires ATM and components of the MRN protein complex. Oncogene. 2006; 25(28):3894-904. PMC: 1852851. DOI: 10.1038/sj.onc.1209426. View

20.

Iacovoni J, Caron P, Lassadi I, Nicolas E, Massip L, Trouche D . High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome. EMBO J. 2010; 29(8):1446-57. PMC: 2868577. DOI: 10.1038/emboj.2010.38. View