TERRA transcription destabilizes telomere integrity to initiate break-induced replication in human ALT cells

Abstract

Alternative Lengthening of Telomeres (ALT) is a Break-Induced Replication (BIR)-based mechanism elongating telomeres in a subset of human cancer cells. While the notion that spontaneous DNA damage at telomeres is required to initiate ALT, the molecular triggers of this physiological telomere instability are largely unknown. We previously proposed that the telomeric long noncoding RNA TERRA may represent one such trigger; however, given the lack of tools to suppress TERRA transcription in cells, our hypothesis remained speculative. We have developed Transcription Activator-Like Effectors able to rapidly inhibit TERRA transcription from multiple chromosome ends in an ALT cell line. TERRA transcription inhibition decreases marks of DNA replication stress and DNA damage at telomeres and impairs ALT activity and telomere length maintenance. We conclude that TERRA transcription actively destabilizes telomere integrity in ALT cells, thereby triggering BIR and promoting telomere elongation. Our data point to TERRA transcription manipulation as a potentially useful target for therapy.

References 53

1. 1.

   Azzalin CM, Lingner J. Telomere functions grounding on TERRA firma. Trends Cell Biol. 2015;25:29-36.

   Not in our library10.1016/j.tcb.2014.08.007

2. 2.

   Nergadze SG, et al. CpG-island promoters drive transcription of human telomeres. RNA. 2009;15:2186-2194.

   Not in our library10.1261/rna.1748309

3. 3.

   Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science. 2007;318:798-801.

   Not in our library10.1126/science.1147182

4. 4.

   Porro A, Feuerhahn S, Reichenbach P, Lingner J. Molecular dissection of telomeric repeat-containing RNA biogenesis unveils the presence of distinct and multiple regulatory pathways. Mol. Cell Biol. 2010;30:4808-4817.

   Not in our library10.1128/mcb.00460-10

5. 5.

   Moravec M, et al. TERRA promotes telomerase-mediated telomere elongation in Schizosaccharomyces pombe. EMBO Rep. 2016;17:999-1012.

   Not in our library10.15252/embr.201541708

6. 6.

   Cusanelli E, Romero CA, Chartrand P. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres. Mol. Cell. 2013;51:780-791.

   Not in our library10.1016/j.molcel.2013.08.029

7. 7.

   Chu HP, et al. TERRA RNA antagonizes ATRX and protects telomeres. Cell. 2017;170:86-101.

   Not in our library10.1016/j.cell.2017.06.017

8. 8.
   RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells · 2014

   No notice
9. 9.
   FANCM limits ALT activity by restricting telomeric replication stress induced by deregulated BLM and R-loops · 2019

   No notice
10. 10.

    Pfeiffer V, Crittin J, Grolimund L, Lingner J. The THO complex component Thp2 counteracts telomeric R-loops and telomere shortening. EMBO J. 2013;32:2861-2871.

    Not in our library10.1038/emboj.2013.217

11. 11.

    Balk B, et al. Telomeric RNA-DNA hybrids affect telomere-length dynamics and senescence. Nat. Struct. Mol. Biol. 2013;20:1199-1205.

    Not in our library10.1038/nsmb.2662

12. 12.

    Lee YW, Arora R, Wischnewski H, Azzalin CM. TRF1 participates in chromosome end protection by averting TRF2-dependent telomeric R loops. Nat. Struct. Mol. Biol. 2018;25:147-153.

    Not in our library10.1038/s41594-017-0021-5

13. 13.

    Deng Z, Norseen J, Wiedmer A, Riethman H, Lieberman PM. TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol. Cell. 2009;35:403-413.

    Not in our library10.1016/j.molcel.2009.06.025

14. 14.

    Feretzaki M, Renck Nunes P, Lingner J. Expression and differential regulation of human TERRA at several chromosome ends. RNA. 2019;25:1470-1480.

    Not in our library10.1261/rna.072322.119

15. 15.
    Alternative Lengthening of Telomeres is characterized by reduced compaction of telomeric chromatin · 2014

    No notice
16. 16.

    Arnoult N, Van Beneden A, Decottignies A. Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1alpha. Nat. Struct. Mol. Biol. 2012;19:948-956.

    Not in our library10.1038/nsmb.2364

17. 17.

    Sagie S, et al. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat. Commun. 2017;8:14015.

    Not in our library10.1038/ncomms14015

18. 18.

    Aguado J, et al. Inhibition of DNA damage response at telomeres improves the detrimental phenotypes of Hutchinson-Gilford Progeria syndrome. Nat. Commun. 2019;10:4990.

    Not in our library10.1038/s41467-019-13018-3

19. 19.

    Porro, A. et al. Functional characterization of the TERRA transcriptome at damaged telomeres. Nat. Commun.5, 5379 (2014).

    Not in our library10.1038/ncomms6379

20. 20.

    Deng Z, et al. A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection. EMBO J. 2012;31:4165-4178.

    Not in our library10.1038/emboj.2012.266

21. 21.

    Koskas S, et al. Heat shock factor 1 promotes TERRA transcription and telomere protection upon heat stress. Nucleic Acids Res. 2017;45:6321-6333.

    Not in our library10.1093/nar/gkx208

22. 22.

    Diman A, et al. Nuclear respiratory factor 1 and endurance exercise promote human telomere transcription. Sci. Adv. 2016;2:e1600031.

    Not in our library10.1126/sciadv.1600031

23. 23.
    TERRA recruitment of polycomb to telomeres is essential for histone trymethylation marks at telomeric heterochromatin · 2018

    No notice
24. 24.

    Montero JJ, Lopez de Silanes I, Grana O, Blasco MA. Telomeric RNAs are essential to maintain telomeres. Nat. Commun. 2016;7:12534.

    Not in our library10.1038/ncomms12534

25. 25.

    Min, J., Wright, W. E. & Shay, J. W. Alternative lengthening of telomeres mediated by mitotic DNA synthesis engages break-induced replication processes. Mol. Cell Biol.37, e00226-17 (2017).

    Not in our library10.1128/mcb.00226-17

26. 26.

    Sobinoff AP, Pickett HA. Alternative lengthening of telomeres: DNA repair pathways converge. Trends Genet. 2017;33:921-932.

    Not in our library10.1016/j.tig.2017.09.003

27. 27.

    Dilley RL, et al. Break-induced telomere synthesis underlies alternative telomere maintenance. Nature. 2016;539:54-58.

    Not in our library10.1038/nature20099

28. 28.

    Roumelioti FM, et al. Alternative lengthening of human telomeres is a conservative DNA replication process with features of break-induced replication. EMBO Rep. 2016;17:1731-1737.

    Not in our library10.15252/embr.201643169

29. 29.

    Zhang JM, Yadav T, Ouyang J, Lan L, Zou L. Alternative lengthening of telomeres through two distinct break-induced replication pathways. Cell Rep. 2019;26:955-968.

    Not in our library10.1016/j.celrep.2018.12.102

30. 30.
    FANCM suppresses DNA replication stress at ALT telomeres by disrupting TERRA R-loops · 2019

    No notice
31. 31.
    The FANCM-BLM-TOP3A-RMI complex suppresses alternative lengthening of telomeres (ALT) · 2019

    Corrected
32. 32.

    Domingues-Silva B, Silva B, Azzalin CM. ALTernative functions for human FANCM at telomeres. Front. Mol. Biosci. 2019;6:84.

    Not in our library10.3389/fmolb.2019.00084

33. 33.

    Arora R, Azzalin CM. Telomere elongation chooses TERRA ALTernatives. RNA Biol. 2015;12:938-941.

    Not in our library10.1080/15476286.2015.1065374

34. 34.

    Mussolino C, Cathomen T. TALE nucleases: tailored genome engineering made easy. Curr. Opin. Biotechnol. 2012;23:644-650.

    Not in our library10.1016/j.copbio.2012.01.013

35. 35.

    Flynn RL, et al. Alternative lengthening of telomeres renders cancer cells hypersensitive to ATR inhibitors. Science. 2015;347:273-277.

    Not in our library10.1126/science.1257216

36. 36.

    Graf M, et al. Telomere length determines TERRA and R-loop regulation through the cell cycle. Cell. 2017;170:72-85.

    Not in our library10.1016/j.cell.2017.06.006

37. 37.

    Hu Y, et al. RNA-DNA hybrids support recombination-based telomere maintenance in fission yeast. Genetics. 2019;213:431-447.

    Not in our library10.1534/genetics.119.302606

38. 38.

    Garcia-Muse T, Aguilera A. R loops: from physiological to pathological roles. Cell. 2019;179:604-618.

    Not in our library10.1016/j.cell.2019.08.055

39. 39.

    Avogaro L, et al. Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells. RNA Biol. 2018;15:787-796.

    Not in our library10.1080/15476286.2018.1456300

40. 40.

    Sobinoff AP, et al. BLM and SLX4 play opposing roles in recombination-dependent replication at human telomeres. EMBO J. 2017;36:2907-2919.

    Not in our library10.15252/embj.201796889

41. 41.

    Verma P, et al. RAD52 and SLX4 act nonepistatically to ensure telomere stability during alternative telomere lengthening. Genes Dev. 2019;33:221-235.

    Not in our library10.1101/gad.319723.118

42. 42.

    Pepe A, West SC. MUS81-EME2 promotes replication fork restart. Cell Rep. 2014;7:1048-1055.

    Not in our library10.1016/j.celrep.2014.04.007

43. 43.

    Zeng S, et al. Telomere recombination requires the MUS81 endonuclease. Nat. Cell Biol. 2009;11:616-623.

    Not in our library10.1038/ncb1867

44. 44.

    Panier S, et al. SLX4IP antagonizes promiscuous BLM activity during ALT maintenance. Mol. Cell. 2019;76:27-43.

    Not in our library10.1016/j.molcel.2019.07.010

45. 45.

    Feretzaki, M. et al. RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature587, 303–308 (2020).

    Not in our library10.1038/s41586-020-2815-6

46. 46.

    Doyle EL, et al. TAL effector-nucleotide targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res. 2012;40:W117-W122.

    Not in our library10.1093/nar/gks608

47. 47.

    Stong N, et al. Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res. 2014;24:1039-1050.

    Not in our library10.1101/gr.166983.113

48. 48.

    Dobin A, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15-21.

    Not in our library10.1093/bioinformatics/bts635

49. 49.

    Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923-930.

    Not in our library10.1093/bioinformatics/btt656

50. 50.
    Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 · 2014

    No notice
51. 51.

    Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009;4:44-57.

    Not in our library10.1038/nprot.2008.211

52. 52.

    Ginestet C. ggplot2: Elegant graphics for data analysis. J. R. Stat. Soc. a Stat. 2011;174:245.

    Not in our library10.1111/j.1467-985x.2010.00676_9.x

53. 53.

    Walter W, Sanchez-Cabo F, Ricote M. GOplot: an R package for visually combining expression data with functional analysis. Bioinformatics. 2015;31:2912-2914.

    Not in our library10.1093/bioinformatics/btv300

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