Transcription-replication conflicts as a source of common fragile site instability caused by BMI1-RNF2 deficiency
Autoři:
Anthony Sanchez aff001; Angelo de Vivo aff001; Peter Tonzi aff002; Jeonghyeon Kim aff001; Tony T. Huang aff002; Younghoon Kee aff001
Působiště autorů:
Department of Cell Biology, Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida, United States of America
aff001; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
aff002
Vyšlo v časopise:
Transcription-replication conflicts as a source of common fragile site instability caused by BMI1-RNF2 deficiency. PLoS Genet 16(3): e32767. doi:10.1371/journal.pgen.1008524
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pgen.1008524
Souhrn
Common fragile sites (CFSs) are breakage-prone genomic loci, and are considered to be hotspots for genomic rearrangements frequently observed in cancers. Understanding the underlying mechanisms for CFS instability will lead to better insight on cancer etiology. Here we show that Polycomb group proteins BMI1 and RNF2 are suppressors of transcription-replication conflicts (TRCs) and CFS instability. Cells depleted of BMI1 or RNF2 showed slower replication forks and elevated fork stalling. These phenotypes are associated with increase occupancy of RNA Pol II (RNAPII) at CFSs, suggesting that the BMI1-RNF2 complex regulate RNAPII elongation at these fragile regions. Using proximity ligase assays, we showed that depleting BMI1 or RNF2 causes increased associations between RNAPII with EdU-labeled nascent forks and replisomes, suggesting increased TRC incidences. Increased occupancy of a fork protective factor FANCD2 and R-loop resolvase RNH1 at CFSs are observed in RNF2 CRISPR-KO cells, which are consistent with increased transcription-associated replication stress in RNF2-deficient cells. Depleting FANCD2 or FANCI proteins further increased genomic instability and cell death of the RNF2-deficient cells, suggesting that in the absence of RNF2, cells depend on these fork-protective factors for survival. These data suggest that the Polycomb proteins have non-canonical roles in suppressing TRC and preserving genomic integrity.
Klíčová slova:
anémia – Cyclins – DNA replication – DNA transcription – Genetic networks – Immunoprecipitation – Protein structure networks – Small interfering RNAs
Zdroje
1. Sarni D, Kerem B. The complex nature of fragile site plasticity and its importance in cancer. Curr Opin Cell Biol. 2016;40:131–6. Epub 2016/04/12. doi: 10.1016/j.ceb.2016.03.017 27062332.
2. Letessier A, Millot GA, Koundrioukoff S, Lachages AM, Vogt N, Hansen RS, et al. Cell-type-specific replication initiation programs set fragility of the FRA3B fragile site. Nature. 2011;470(7332):120–3. Epub 2011/01/25. doi: 10.1038/nature09745 21258320.
3. Franchitto A, Pichierri P. Replication fork recovery and regulation of common fragile sites stability. Cell Mol Life Sci. 2014;71(23):4507–17. Epub 2014/09/14. doi: 10.1007/s00018-014-1718-9 25216703.
4. Oestergaard VH, Lisby M. Transcription-replication conflicts at chromosomal fragile sites-consequences in M phase and beyond. Chromosoma. 2017;126(2):213–22. Epub 2016/11/01. doi: 10.1007/s00412-016-0617-2 27796495.
5. Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer. 2019;58(5):270–83. Epub 2018/12/12. doi: 10.1002/gcc.22721 30536896.
6. Helmrich A, Ballarino M, Nudler E, Tora L. Transcription-replication encounters, consequences and genomic instability. Nat Struct Mol Biol. 2013;20(4):412–8. Epub 2013/04/05. doi: 10.1038/nsmb.2543 23552296.
7. Helmrich A, Stout-Weider K, Hermann K, Schrock E, Heiden T. Common fragile sites are conserved features of human and mouse chromosomes and relate to large active genes. Genome Res. 2006;16(10):1222–30. Epub 2006/09/07. doi: 10.1101/gr.5335506 16954539; PubMed Central PMCID: PMC1581431.
8. Helmrich A, Ballarino M, Tora L. Collisions between replication and transcription complexes cause common fragile site instability at the longest human genes. Molecular cell. 2011;44(6):966–77. Epub 2011/12/27. doi: 10.1016/j.molcel.2011.10.013 22195969.
9. Gomez-Gonzalez B, Aguilera A. Transcription-mediated replication hindrance: a major driver of genome instability. Genes & development. 2019. Epub 2019/05/28. doi: 10.1101/gad.324517.119 31123061.
10. Garcia-Muse T, Aguilera A. Transcription-replication conflicts: how they occur and how they are resolved. Nature reviews Molecular cell biology. 2016;17(9):553–63. Epub 2016/07/21. doi: 10.1038/nrm.2016.88 27435505.
11. Macheret M, Halazonetis TD. Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress. Nature. 2018;555(7694):112–6. Epub 2018/02/22. doi: 10.1038/nature25507 29466339; PubMed Central PMCID: PMC5837010.
12. Kotsantis P, Silva LM, Irmscher S, Jones RM, Folkes L, Gromak N, et al. Increased global transcription activity as a mechanism of replication stress in cancer. Nat Commun. 2016;7:13087. Epub 2016/10/12. doi: 10.1038/ncomms13087 27725641; PubMed Central PMCID: PMC5062618.
13. Jones RM, Mortusewicz O, Afzal I, Lorvellec M, Garcia P, Helleday T, et al. Increased replication initiation and conflicts with transcription underlie Cyclin E-induced replication stress. Oncogene. 2013;32(32):3744–53. Epub 2012/09/05. doi: 10.1038/onc.2012.387 22945645.
14. Hamperl S, Bocek MJ, Saldivar JC, Swigut T, Cimprich KA. Transcription-Replication Conflict Orientation Modulates R-Loop Levels and Activates Distinct DNA Damage Responses. Cell. 2017;170(4):774–86 e19. Epub 2017/08/13. doi: 10.1016/j.cell.2017.07.043 28802045; PubMed Central PMCID: PMC5570545.
15. Santos-Pereira JM, Aguilera A. R loops: new modulators of genome dynamics and function. Nat Rev Genet. 2015;16(10):583–97. Epub 2015/09/16. doi: 10.1038/nrg3961 26370899.
16. Garcia-Rubio ML, Perez-Calero C, Barroso SI, Tumini E, Herrera-Moyano E, Rosado IV, et al. The Fanconi Anemia Pathway Protects Genome Integrity from R-loops. PLoS genetics. 2015;11(11):e1005674. Epub 2015/11/20. doi: 10.1371/journal.pgen.1005674 26584049; PubMed Central PMCID: PMC4652862.
17. Liang Z, Liang F, Teng Y, Chen X, Liu J, Longerich S, et al. Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination. Cell Rep. 2019;26(3):564–72 e5. Epub 2019/01/17. doi: 10.1016/j.celrep.2018.12.084 30650351; PubMed Central PMCID: PMC6350941.
18. Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, et al. Replication stress induces accumulation of FANCD2 at central region of large fragile genes. Nucleic acids research. 2018;46(6):2932–44. Epub 2018/02/03. doi: 10.1093/nar/gky058 29394375; PubMed Central PMCID: PMC5888676.
19. Madireddy A, Kosiyatrakul ST, Boisvert RA, Herrera-Moyano E, Garcia-Rubio ML, Gerhardt J, et al. FANCD2 Facilitates Replication through Common Fragile Sites. Molecular cell. 2016;64(2):388–404. Epub 2016/10/22. doi: 10.1016/j.molcel.2016.09.017 27768874; PubMed Central PMCID: PMC5683400.
20. Schwab RA, Nieminuszczy J, Shah F, Langton J, Lopez Martinez D, Liang CC, et al. The Fanconi Anemia Pathway Maintains Genome Stability by Coordinating Replication and Transcription. Molecular cell. 2015;60(3):351–61. Epub 2015/11/26. doi: 10.1016/j.molcel.2015.09.012 26593718; PubMed Central PMCID: PMC4644232.
21. Sparmann A, van Lohuizen M. Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer. 2006;6(11):846–56. Epub 2006/10/25. doi: 10.1038/nrc1991 17060944.
22. Bentley ML, Corn JE, Dong KC, Phung Q, Cheung TK, Cochran AG. Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex. EMBO J. 2011;30(16):3285–97. Epub 2011/07/21. doi: 10.1038/emboj.2011.243 21772249; PubMed Central PMCID: PMC3160663.
23. Buchwald G, van der Stoop P, Weichenrieder O, Perrakis A, van Lohuizen M, Sixma TK. Structure and E3-ligase activity of the Ring-Ring complex of polycomb proteins Bmi1 and Ring1b. EMBO J. 2006;25(11):2465–74. Epub 2006/05/20. doi: 10.1038/sj.emboj.7601144 16710298; PubMed Central PMCID: PMC1478191.
24. Ismail IH, Andrin C, McDonald D, Hendzel MJ. BMI1-mediated histone ubiquitylation promotes DNA double-strand break repair. The Journal of cell biology. 2010;191(1):45–60. Epub 2010/10/06. doi: 10.1083/jcb.201003034 20921134; PubMed Central PMCID: PMC2953429.
25. Ginjala V, Nacerddine K, Kulkarni A, Oza J, Hill SJ, Yao M, et al. BMI1 is recruited to DNA breaks and contributes to DNA damage-induced H2A ubiquitination and repair. Molecular and cellular biology. 2011;31(10):1972–82. Epub 2011/03/09. doi: 10.1128/MCB.00981-10 21383063; PubMed Central PMCID: PMC3133356.
26. Nacerddine K, Beaudry JB, Ginjala V, Westerman B, Mattiroli F, Song JY, et al. Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. The Journal of clinical investigation. 2012;122(5):1920–32. Epub 2012/04/17. doi: 10.1172/JCI57477 22505453; PubMed Central PMCID: PMC3336972.
27. Ismail IH, Gagne JP, Caron MC, McDonald D, Xu Z, Masson JY, et al. CBX4-mediated SUMO modification regulates BMI1 recruitment at sites of DNA damage. Nucleic acids research. 2012;40(12):5497–510. Epub 2012/03/10. doi: 10.1093/nar/gks222 22402492; PubMed Central PMCID: PMC3384338.
28. Facchino S, Abdouh M, Chatoo W, Bernier G. BMI1 confers radioresistance to normal and cancerous neural stem cells through recruitment of the DNA damage response machinery. The Journal of neuroscience: the official journal of the Society for Neuroscience. 2010;30(30):10096–111. Epub 2010/07/30. doi: 10.1523/JNEUROSCI.1634-10.2010 20668194.
29. Rona G, Roberti D, Yin Y, Pagan JK, Homer H, Sassani E, et al. PARP1-dependent recruitment of the FBXL10-RNF68-RNF2 ubiquitin ligase to sites of DNA damage controls H2A.Z loading. Elife. 2018;7. Epub 2018/07/10. doi: 10.7554/eLife.38771 29985131; PubMed Central PMCID: PMC6037479.
30. Chagraoui J, Hebert J, Girard S, Sauvageau G. An anticlastogenic function for the Polycomb Group gene Bmi1. Proceedings of the National Academy of Sciences of the United States of America. 2011;108(13):5284–9. Epub 2011/03/16. doi: 10.1073/pnas.1014263108 21402923; PubMed Central PMCID: PMC3069154.
31. Sanchez A, De Vivo A, Uprety N, Kim J, Stevens SM Jr., Kee Y. BMI1-UBR5 axis regulates transcriptional repression at damaged chromatin. Proceedings of the National Academy of Sciences of the United States of America. 2016;113(40):11243–8. Epub 2016/09/21. doi: 10.1073/pnas.1610735113 27647897; PubMed Central PMCID: PMC5056041.
32. Ui A, Nagaura Y, Yasui A. Transcriptional elongation factor ENL phosphorylated by ATM recruits polycomb and switches off transcription for DSB repair. Molecular cell. 2015;58(3):468–82. Epub 2015/04/30. doi: 10.1016/j.molcel.2015.03.023 25921070.
33. Lukas C, Savic V, Bekker-Jensen S, Doil C, Neumann B, Pedersen RS, et al. 53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress. Nature cell biology. 2011;13(3):243–53. Epub 2011/02/15. doi: 10.1038/ncb2201 21317883.
34. Harrigan JA, Belotserkovskaya R, Coates J, Dimitrova DS, Polo SE, Bradshaw CR, et al. Replication stress induces 53BP1-containing OPT domains in G1 cells. The Journal of cell biology. 2011;193(1):97–108. Epub 2011/03/30. doi: 10.1083/jcb.201011083 21444690; PubMed Central PMCID: PMC3082192.
35. Yu DS, Cortez D. A role for CDK9-cyclin K in maintaining genome integrity. Cell Cycle. 2011;10(1):28–32. Epub 2011/01/05. doi: 10.4161/cc.10.1.14364 21200140; PubMed Central PMCID: PMC3048070.
36. Chan KL, Palmai-Pallag T, Ying S, Hickson ID. Replication stress induces sister-chromatid bridging at fragile site loci in mitosis. Nature cell biology. 2009;11(6):753–60. Epub 2009/05/26. doi: 10.1038/ncb1882 19465922.
37. Roy S, Luzwick JW, Schlacher K. SIRF: Quantitative in situ analysis of protein interactions at DNA replication forks. The Journal of cell biology. 2018;217(4):1521–36. Epub 2018/02/25. doi: 10.1083/jcb.201709121 29475976; PubMed Central PMCID: PMC5881507.
38. Kaushal S, Wollmuth CE, Das K, Hile SE, Regan SB, Barnes RP, et al. Sequence and Nuclease Requirements for Breakage and Healing of a Structure-Forming (AT)n Sequence within Fragile Site FRA16D. Cell Rep. 2019;27(4):1151–64 e5. Epub 2019/04/25. doi: 10.1016/j.celrep.2019.03.103 31018130; PubMed Central PMCID: PMC6506224.
39. Joo HY, Zhai L, Yang C, Nie S, Erdjument-Bromage H, Tempst P, et al. Regulation of cell cycle progression and gene expression by H2A deubiquitination. Nature. 2007;449(7165):1068–72. Epub 2007/10/05. doi: 10.1038/nature06256 17914355.
40. Gomez-Gonzalez B, Aguilera A. Transcription-mediated replication hindrance: a major driver of genome instability. Genes & development. 2019;33(15–16):1008–26. Epub 2019/05/28. doi: 10.1101/gad.324517.119 31123061; PubMed Central PMCID: PMC6672053.
41. Chen L, Chen JY, Zhang X, Gu Y, Xiao R, Shao C, et al. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Molecular cell. 2017;68(4):745–57 e5. Epub 2017/11/07. doi: 10.1016/j.molcel.2017.10.008 29104020; PubMed Central PMCID: PMC5957070.
42. Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, et al. Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability. Nucleic acids research. 2019. Epub 2019/06/11. doi: 10.1093/nar/gkz510 31180492.
43. Urban V, Dobrovolna J, Huhn D, Fryzelkova J, Bartek J, Janscak P. RECQ5 helicase promotes resolution of conflicts between replication and transcription in human cells. The Journal of cell biology. 2016;214(4):401–15. Epub 2016/08/10. doi: 10.1083/jcb.201507099 27502483; PubMed Central PMCID: PMC4987291.
44. Li M, Xu X, Chang CW, Zheng L, Shen B, Liu Y. SUMO2 conjugation of PCNA facilitates chromatin remodeling to resolve transcription-replication conflicts. Nat Commun. 2018;9(1):2706. Epub 2018/07/15. doi: 10.1038/s41467-018-05236-y 30006506; PubMed Central PMCID: PMC6045570.
45. Saponaro M, Kantidakis T, Mitter R, Kelly GP, Heron M, Williams H, et al. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell. 2014;157(5):1037–49. Epub 2014/05/20. doi: 10.1016/j.cell.2014.03.048 24836610; PubMed Central PMCID: PMC4032574.
46. Bravo M, Nicolini F, Starowicz K, Barroso S, Cales C, Aguilera A, et al. Polycomb RING1A- and RING1B-dependent histone H2A monoubiquitylation at pericentromeric regions promotes S-phase progression. J Cell Sci. 2015;128(19):3660–71. Epub 2015/08/15. doi: 10.1242/jcs.173021 26272920.
47. Klusmann I, Wohlberedt K, Magerhans A, Teloni F, Korbel JO, Altmeyer M, et al. Chromatin modifiers Mdm2 and RNF2 prevent RNA:DNA hybrids that impair DNA replication. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(48):E11311–E20. Epub 2018/11/11. doi: 10.1073/pnas.1809592115 30413623; PubMed Central PMCID: PMC6275510.
48. Lang KS, Hall AN, Merrikh CN, Ragheb M, Tabakh H, Pollock AJ, et al. Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis. Cell. 2017;170(4):787–99 e18. Epub 2017/08/13. doi: 10.1016/j.cell.2017.07.044 28802046; PubMed Central PMCID: PMC5630229.
49. Lin X, Wei F, Whyte P, Tang D. BMI1 reduces ATR activation and signalling caused by hydroxyurea. Oncotarget. 2017;8(52):89707–21. Epub 2017/11/23. doi: 10.18632/oncotarget.21111 29163782; PubMed Central PMCID: PMC5685703.
50. Okamoto Y, Abe M, Itaya A, Tomida J, Ishiai M, Takaori-Kondo A, et al. FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress. FEBS J. 2019;286(1):139–50. Epub 2018/11/16. doi: 10.1111/febs.14700 30431240.
51. Howlett NG, Taniguchi T, Durkin SG, D'Andrea AD, Glover TW. The Fanconi anemia pathway is required for the DNA replication stress response and for the regulation of common fragile site stability. Hum Mol Genet. 2005;14(5):693–701. Epub 2005/01/22. doi: 10.1093/hmg/ddi065 15661754.
52. Nguyen DT, Voon HPJ, Xella B, Scott C, Clynes D, Babbs C, et al. The chromatin remodelling factor ATRX suppresses R-loops in transcribed telomeric repeats. EMBO Rep. 2017;18(6):914–28. Epub 2017/05/11. doi: 10.15252/embr.201643078 28487353; PubMed Central PMCID: PMC5452009.
53. Yeo JE, Lee EH, Hendrickson EA, Sobeck A. CtIP mediates replication fork recovery in a FANCD2-regulated manner. Hum Mol Genet. 2014;23(14):3695–705. Epub 2014/02/22. doi: 10.1093/hmg/ddu078 24556218; PubMed Central PMCID: PMC4065146.
54. Makharashvili N, Arora S, Yin Y, Fu Q, Wen X, Lee JH, et al. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. Elife. 2018;7. Epub 2018/12/14. doi: 10.7554/eLife.42733 30523780; PubMed Central PMCID: PMC6296784.
55. Chen YH, Jones MJ, Yin Y, Crist SB, Colnaghi L, Sims RJ, 3rd, et al. ATR-mediated phosphorylation of FANCI regulates dormant origin firing in response to replication stress. Molecular cell. 2015;58(2):323–38. Epub 2015/04/07. doi: 10.1016/j.molcel.2015.02.031 25843623; PubMed Central PMCID: PMC4408929.
56. van der Lugt NM, Domen J, Linders K, van Roon M, Robanus-Maandag E, te Riele H, et al. Posterior transformation, neurological abnormalities, and severe hematopoietic defects in mice with a targeted deletion of the bmi-1 proto-oncogene. Genes & development. 1994;8(7):757–69. Epub 1994/04/01. doi: 10.1101/gad.8.7.757 7926765.
57. Lu R, Wang Q, Han Y, Li J, Yang XJ, Miao D. Parathyroid hormone administration improves bone marrow microenvironment and partially rescues haematopoietic defects in Bmi1-null mice. PLoS One. 2014;9(4):e93864. Epub 2014/04/08. doi: 10.1371/journal.pone.0093864 24705625; PubMed Central PMCID: PMC3976339.
58. Tang J, Cho NW, Cui G, Manion EM, Shanbhag NM, Botuyan MV, et al. Acetylation limits 53BP1 association with damaged chromatin to promote homologous recombination. Nat Struct Mol Biol. 2013;20(3):317–25. Epub 2013/02/05. doi: 10.1038/nsmb.2499 23377543; PubMed Central PMCID: PMC3594358.
59. Tonzi P, Yin Y, Lee CWT, Rothenberg E, Huang TT. Translesion polymerase kappa-dependent DNA synthesis underlies replication fork recovery. Elife. 2018;7. Epub 2018/11/14. doi: 10.7554/eLife.41426 30422114; PubMed Central PMCID: PMC6251625.
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