A comparative epigenome analysis of gammaherpesviruses suggests cis-acting sequence features as critical mediators of rapid polycomb recruitment

English version

Autoři: Thomas Günther ^aff001; Jacqueline Fröhlich ^aff001; Christina Herrde ^aff001; Shinji Ohno ^aff002; Lia Burkhardt ^aff001; Heiko Adler ^aff002; Adam Grundhoff ^aff001
Působiště autorů: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany ^aff001; Comprehensive Pneumology Center, Research Unit Lung Repair and Regeneration, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Munich, Germany ^aff002; German Center of Lung Research (DZL), Giessen, Germany ^aff003
Vyšlo v časopise: A comparative epigenome analysis of gammaherpesviruses suggests cis-acting sequence features as critical mediators of rapid polycomb recruitment. PLoS Pathog 15(10): e32767. doi:10.1371/journal.ppat.1007838
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1007838

Souhrn

Latent Kaposi sarcoma-associated herpesvirus (KSHV) genomes rapidly acquire distinct patterns of the activating histone modification H3K4-me3 as well as repressive H3K27-me3 marks, a modification linked to transcriptional silencing by polycomb repressive complexes (PRC). Interestingly, PRCs have recently been reported to restrict viral gene expression in a number of other viral systems, suggesting they may play a broader role in controlling viral chromatin. If so, it is an intriguing possibility that latency establishment may result from viral subversion of polycomb-mediated host responses to exogenous DNA.

To investigate such scenarios we sought to establish whether rapid repression by PRC constitutes a general hallmark of herpesvirus latency. For this purpose, we performed a comparative epigenome analysis of KSHV and the related murine gammaherpesvirus 68 (MHV-68). We demonstrate that, while latently replicating MHV-68 genomes readily acquire distinct patterns of activation-associated histone modifications upon de novo infection, they fundamentally differ in their ability to efficiently attract H3K27-me3 marks. Statistical analyses of ChIP-seq data from in vitro infected cells as well as in vivo latency reservoirs furthermore suggest that, whereas KSHV rapidly attracts PRCs in a genome-wide manner, H3K27-me3 acquisition by MHV-68 genomes may require spreading from initial seed sites to which PRC are recruited as the result of an inefficient or stochastic recruitment, and that immune pressure may be needed to select for latency pools harboring PRC-silenced episomes in vivo.

Using co-infection experiments and recombinant viruses, we also show that KSHV’S ability to rapidly and efficiently acquire H3K27-me3 marks does not depend on the host cell environment or unique properties of the KSHV-encoded LANA protein, but rather requires specific cis-acting sequence features. We show that the non-canonical PRC1.1 component KDM2B, a factor which binds to unmethylated CpG motifs, is efficiently recruited to KSHV genomes, indicating that CpG island characteristics may constitute these features. In accord with the fact that, compared to MHV-68, KSHV genomes exhibit a fundamentally higher density of CpG motifs, we furthermore demonstrate efficient acquisition of H2AK119-ub by KSHV and H3K36-me2 by MHV-68 (but not vice versa), furthermore supporting the notion that KSHV genomes rapidly attract PRC1.1 complexes in a genome-wide fashion. Collectively, our results suggest that rapid PRC silencing is not a universal feature of viral latency, but that some viruses may rather have adopted distinct genomic features to specifically exploit default host pathways that repress epigenetically naive, CpG-rich DNA.

Klíčová slova:

Chromatin – DNA methylation – Comparative genomics – Histones – Mammalian genomics – Genome complexity – Viral persistence and latency – Kaposi's sarcoma-associated herpesvirus

Zdroje

1. Schulz TF, Cesarman E. Kaposi Sarcoma-associated Herpesvirus: mechanisms of oncogenesis. Curr Opin Virol. 2015;14:116–28. doi: 10.1016/j.coviro.2015.08.016 26431609.

2. Dittmer DP, Damania B. Kaposi sarcoma-associated herpesvirus: immunobiology, oncogenesis, and therapy. J Clin Invest. 2016;126(9):3165–75. doi: 10.1172/JCI84418 27584730.

3. Juillard F, Tan M, Li S, Kaye KM. Kaposi’s Sarcoma Herpesvirus Genome Persistence. Front Microbiol. 2016;7:1149. doi: 10.3389/fmicb.2016.01149 27570517.

4. Grundhoff A, Ganem D. Inefficient establishment of KSHV latency suggests an additional role for continued lytic replication in Kaposi sarcoma pathogenesis. J Clin Invest. 2004;113(1):124–36. Epub 2004/01/01. doi: 10.1172/JCI200417803 14702116.

5. Bechtel JT, Liang Y, Hvidding J, Ganem D. Host range of Kaposi’s sarcoma-associated herpesvirus in cultured cells. J Virol. 2003;77(11):6474–81. doi: 10.1128/JVI.77.11.6474-6481.2003 12743304.

6. Günther T, Grundhoff A. The epigenetic landscape of latent Kaposi sarcoma-associated herpesvirus genomes. PLoS Pathog. 2010;6(6):e1000935. Epub 2010/06/10. doi: 10.1371/journal.ppat.1000935 20532208.

7. Toth Z, Brulois K, Lee HR, Izumiya Y, Tepper C, Kung HJ, et al. Biphasic euchromatin-to-heterochromatin transition on the KSHV genome following de novo infection. PLoS Pathog. 2013;9(12):e1003813. doi: 10.1371/journal.ppat.1003813 24367262.

8. Günther T, Schreiner S, Dobner T, Tessmer U, Grundhoff A. Influence of ND10 components on epigenetic determinants of early KSHV latency establishment. PLoS Pathog. 2014;10(7):e1004274. Epub 2014/07/18. doi: 10.1371/journal.ppat.1004274 25033267.

9. Hilton IB, Simon JM, Lieb JD, Davis IJ, Damania B, Dittmer DP. The open chromatin landscape of Kaposi’s sarcoma-associated herpesvirus. J Virol. 2013;87(21):11831–42. doi: 10.1128/JVI.01685-13 23986576.

10. Sun R, Tan X, Wang X, Wang X, Yang L, Robertson ES, et al. Epigenetic Landscape of Kaposi’s Sarcoma-Associated Herpesvirus Genome in Classic Kaposi’s Sarcoma Tissues. PLoS Pathog. 2017;13(1):e1006167. doi: 10.1371/journal.ppat.1006167 28118409.

11. Toth Z, Maglinte DT, Lee SH, Lee HR, Wong LY, Brulois KF, et al. Epigenetic analysis of KSHV latent and lytic genomes. PLoS Pathog. 2010;6(7):e1001013. Epub 2010/07/28. doi: 10.1371/journal.ppat.1001013 20661424.

12. Hopcraft SE, Pattenden SG, James LI, Frye S, Dittmer DP, Damania B. Chromatin remodeling controls Kaposi’s sarcoma-associated herpesvirus reactivation from latency. PLoS Pathog. 2018;14(9):e1007267. doi: 10.1371/journal.ppat.1007267 30212584.

13. Toth Z, Papp B, Brulois K, Choi YJ, Gao SJ, Jung JU. LANA-Mediated Recruitment of Host Polycomb Repressive Complexes onto the KSHV Genome during De Novo Infection. PLoS Pathog. 2016;12(9):e1005878. doi: 10.1371/journal.ppat.1005878 27606464.

14. Marques S, Efstathiou S, Smith KG, Haury M, Simas JP. Selective gene expression of latent murine gammaherpesvirus 68 in B lymphocytes. J Virol. 2003;77(13):7308–18. Epub 2003/06/14. doi: 10.1128/JVI.77.13.7308-7318.2003 12805429.

15. Tarakanova VL, Suarez F, Tibbetts SA, Jacoby MA, Weck KE, Hess JL, et al. Murine gammaherpesvirus 68 infection is associated with lymphoproliferative disease and lymphoma in BALB beta2 microglobulin-deficient mice. J Virol. 2005;79(23):14668–79. Epub 2005/11/12. doi: 10.1128/JVI.79.23.14668-14679.2005 16282467.

16. Usherwood EJ, Stewart JP, Nash AA. Characterization of tumor cell lines derived from murine gammaherpesvirus-68-infected mice. J Virol. 1996;70(9):6516–8. Epub 1996/09/01. 8709292.

17. Gray KS, Allen RD 3rd, Farrell ML, Forrest JC, Speck SH. Alternatively initiated gene 50/RTA transcripts expressed during murine and human gammaherpesvirus reactivation from latency. J Virol. 2009;83(1):314–28. Epub 2008/10/31. doi: 10.1128/JVI.01444-08 18971285.

18. Yang Z, Tang H, Huang H, Deng H. RTA promoter demethylation and histone acetylation regulation of murine gammaherpesvirus 68 reactivation. PLoS One. 2009;4(2):e4556. Epub 2009/02/24. doi: 10.1371/journal.pone.0004556 19234612.

19. Martinez-Guzman D, Rickabaugh T, Wu TT, Brown H, Cole S, Song MJ, et al. Transcription program of murine gammaherpesvirus 68. J Virol. 2003;77(19):10488–503. Epub 2003/09/13. doi: 10.1128/JVI.77.19.10488-10503.2003 12970434.

20. Laugesen A, Hojfeldt JW, Helin K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Mol Cell. 2019;74(1):8–18. doi: 10.1016/j.molcel.2019.03.011 30951652.

21. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics. 2009;25(15):1952–8. doi: 10.1093/bioinformatics/btp340 19505939.

22. Habison AC, de Miranda MP, Beauchemin C, Tan M, Cerqueira SA, Correia B, et al. Cross-species conservation of episome maintenance provides a basis for in vivo investigation of Kaposi’s sarcoma herpesvirus LANA. PLoS Pathog. 2017;13(9):e1006555. doi: 10.1371/journal.ppat.1006555 28910389.

23. Pires de Miranda M, Quendera AP, McVey CE, Kaye KM, Simas JP. In Vivo Persistence of Chimeric Virus after Substitution of the Kaposi’s Sarcoma-Associated Herpesvirus LANA DNA Binding Domain with That of Murid Herpesvirus 4. J Virol. 2018;92(21). doi: 10.1128/JVI.01251-18 30111565.

24. Gupta A, Oldenburg DG, Salinas E, White DW, Forrest JC. Murine Gammaherpesvirus 68 Expressing Kaposi Sarcoma-Associated Herpesvirus Latency-Associated Nuclear Antigen (LANA) Reveals both Functional Conservation and Divergence in LANA Homologs. J Virol. 2017;91(19). doi: 10.1128/JVI.00992-17 28747501.

25. Habison AC, Beauchemin C, Simas JP, Usherwood EJ, Kaye KM. Murine gammaherpesvirus 68 LANA acts on terminal repeat DNA to mediate episome persistence. J Virol. 2012;86(21):11863–76. doi: 10.1128/JVI.01656-12 22915819.

26. De Leo A, Deng Z, Vladimirova O, Chen HS, Dheekollu J, Calderon A, et al. LANA oligomeric architecture is essential for KSHV nuclear body formation and viral genome maintenance during latency. PLoS Pathog. 2019;15(1):e1007489. doi: 10.1371/journal.ppat.1007489 30682185.

27. Collins CM, Speck SH. Tracking murine gammaherpesvirus 68 infection of germinal center B cells in vivo. PLoS One. 2012;7(3):e33230. doi: 10.1371/journal.pone.0033230 22427999.

28. van Kruijsbergen I, Hontelez S, Veenstra GJ. Recruiting polycomb to chromatin. Int J Biochem Cell Biol. 2015;67:177–87. doi: 10.1016/j.biocel.2015.05.006 25982201.

29. He J, Kallin EM, Tsukada Y, Zhang Y. The H3K36 demethylase Jhdm1b/Kdm2b regulates cell proliferation and senescence through p15(Ink4b). Nat Struct Mol Biol. 2008;15(11):1169–75. doi: 10.1038/nsmb.1499 18836456.

30. Farcas AM, Blackledge NP, Sudbery I, Long HK, McGouran JF, Rose NR, et al. KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife. 2012;1:e00205. doi: 10.7554/eLife.00205 23256043.

31. Wu X, Johansen JV, Helin K. Fbxl10/Kdm2b recruits polycomb repressive complex 1 to CpG islands and regulates H2A ubiquitylation. Mol Cell. 2013;49(6):1134–46. doi: 10.1016/j.molcel.2013.01.016 23395003.

32. He J, Shen L, Wan M, Taranova O, Wu H, Zhang Y. Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes. Nat Cell Biol. 2013;15(4):373–84. doi: 10.1038/ncb2702 23502314.

33. Blackledge NP, Farcas AM, Kondo T, King HW, McGouran JF, Hanssen LL, et al. Variant PRC1 complex-dependent H2A ubiquitylation drives PRC2 recruitment and polycomb domain formation. Cell. 2014;157(6):1445–59. doi: 10.1016/j.cell.2014.05.004 24856970.

34. Streubel G, Watson A, Jammula SG, Scelfo A, Fitzpatrick DJ, Oliviero G, et al. The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells. Mol Cell. 2018;70(2):371–9 e5. doi: 10.1016/j.molcel.2018.02.027 29606589.

35. Schwartz YB, Pirrotta V. Ruled by ubiquitylation: a new order for polycomb recruitment. Cell Rep. 2014;8(2):321–5. doi: 10.1016/j.celrep.2014.07.001 25061856.

36. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, Kumar RM, et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell. 2006;125(2):301–13. doi: 10.1016/j.cell.2006.02.043 16630818.

37. Riising EM, Comet I, Leblanc B, Wu X, Johansen JV, Helin K. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol Cell. 2014;55(3):347–60. doi: 10.1016/j.molcel.2014.06.005 24999238.

38. Perino M, van Mierlo G, Karemaker ID, van Genesen S, Vermeulen M, Marks H, et al. MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding. Nat Genet. 2018;50(7):1002–10. doi: 10.1038/s41588-018-0134-8 29808031.

39. Li H, Liefke R, Jiang J, Kurland JV, Tian W, Deng P, et al. Polycomb-like proteins link the PRC2 complex to CpG islands. Nature. 2017;549(7671):287–91. doi: 10.1038/nature23881 28869966.

40. Choi J, Bachmann AL, Tauscher K, Benda C, Fierz B, Muller J. DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation. Nat Struct Mol Biol. 2017;24(12):1039–47. doi: 10.1038/nsmb.3488 29058710.

41. Thakur NN, El-Gogo S, Steer B, Freimuller K, Waha A, Adler H. A gammaherpesviral internal repeat contributes to latency amplification. PLoS One. 2007;2(8):e733. doi: 10.1371/journal.pone.0000733 17710133.

42. Vargas-Ayala RC, Jay A, Manara F, Maroui MA, Hernandez-Vargas H, Diederichs A, et al. Interplay between the epigenetic enzyme lysine (K)-specific demethylase 2B and Epstein-Barr virus infection. J Virol. 2019. doi: 10.1128/JVI.00273-19 30996097.

43. Renne R, Zhong W, Herndier B, McGrath M, Abbey N, Kedes D, et al. Lytic growth of Kaposi’s sarcoma-associated herpesvirus (human herpesvirus 8) in culture. Nat Med. 1996;2(3):342–6. Epub 1996/03/01. doi: 10.1038/nm0396-342 8612236.

44. Weber K, Bartsch U, Stocking C, Fehse B. A multicolor panel of novel lentiviral "gene ontology" (LeGO) vectors for functional gene analysis. Mol Ther. 2008;16(4):698–706. doi: 10.1038/mt.2008.6 18362927.

45. Adler H, Messerle M, Wagner M, Koszinowski UH. Cloning and mutagenesis of the murine gammaherpesvirus 68 genome as an infectious bacterial artificial chromosome. J Virol. 2000;74(15):6964–74. Epub 2000/07/11. doi: 10.1128/jvi.74.15.6964-6974.2000 10888635.

46. Brulois KF, Chang H, Lee AS, Ensser A, Wong LY, Toth Z, et al. Construction and manipulation of a new Kaposi’s sarcoma-associated herpesvirus bacterial artificial chromosome clone. J Virol. 2012;86(18):9708–20. doi: 10.1128/JVI.01019-12 22740391.

47. Tischer BK, Smith GA, Osterrieder N. En passant mutagenesis: a two step markerless red recombination system. Methods Mol Biol. 2010;634:421–30. doi: 10.1007/978-1-60761-652-8_30 20677001.

48. Myoung J, Ganem D. Generation of a doxycycline-inducible KSHV producer cell line of endothelial origin: maintenance of tight latency with efficient reactivation upon induction. J Virol Methods. 2011;174(1–2):12–21. doi: 10.1016/j.jviromet.2011.03.012 21419799.

49. Paden CR, Forrest JC, Tibbetts SA, Speck SH. Unbiased mutagenesis of MHV68 LANA reveals a DNA-binding domain required for LANA function in vitro and in vivo. PLoS Pathog. 2012;8(9):e1002906. doi: 10.1371/journal.ppat.1002906 22969427.

50. Skene PJ, Henikoff S. A simple method for generating high-resolution maps of genome-wide protein binding. Elife. 2015;4:e09225. doi: 10.7554/eLife.09225 26079792.

51. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009/03/06. doi: 10.1186/gb-2009-10-3-r25 19261174.

52. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92. Epub 2012/04/21. doi: 10.1093/bib/bbs017 22517427.

53. Lerdrup M, Johansen JV, Agrawal-Singh S, Hansen K. An interactive environment for agile analysis and visualization of ChIP-sequencing data. Nat Struct Mol Biol. 2016;23(4):349–57. doi: 10.1038/nsmb.3180 26926434.

54. Stovner EB, Saetrom P. epic2 efficiently finds diffuse domains in ChIP-seq data. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz232 30923821.

55. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. doi: 10.1093/bioinformatics/bts635 23104886.

56. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–30. doi: 10.1093/bioinformatics/btt656 24227677.

57. Cheng BY, Zhi J, Santana A, Khan S, Salinas E, Forrest JC, et al. Tiled microarray identification of novel viral transcript structures and distinct transcriptional profiles during two modes of productive murine gammaherpesvirus 68 infection. J Virol. 2012;86(8):4340–57. Epub 2012/02/10. doi: 10.1128/JVI.05892-11 22318145.