The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements

English version

Autoři: Augustin de Vanssay ^aff001; Amandine Touzeau ^aff001; Olivier Arnaiz ^aff002; Andrea Frapporti ^aff001; Jamie Phipps ^aff001; Sandra Duharcourt ^aff001
Působiště autorů: Université de Paris, Institut Jacques Monod, CNRS, Paris, France ^aff001; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France ^aff002
Vyšlo v časopise: The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements. PLoS Genet 16(7): e32767. doi:10.1371/journal.pgen.1008949
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008949

Souhrn

In Paramecium tetraurelia, a large proportion of the germline genome is reproducibly removed from the somatic genome after sexual events via a process involving small (s)RNA-directed heterochromatin formation and DNA excision and repair. How germline limited DNA sequences are specifically recognized in the context of chromatin remains elusive. Here, we use a reverse genetics approach to identify factors involved in programmed genome rearrangements. We have identified a P. tetraurelia homolog of the highly conserved histone chaperone Spt16 subunit of the FACT complex, Spt16-1, and show its expression is developmentally regulated. A functional GFP-Spt16-1 fusion protein localized exclusively in the nuclei where genome rearrangements take place. Gene silencing of Spt16-1 showed it is required for the elimination of all germline-limited sequences, for the survival of sexual progeny, and for the accumulation of internal eliminated sequence (ies)RNAs, an sRNA population produced when elimination occurs. Normal accumulation of 25 nt scanRNAs and deposition of silent histone marks H3K9me3 and H3K27me3 indicated that Spt16-1 does not regulate the scanRNA-directed heterochromatin pathway involved in the early steps of DNA elimination. We further show that Spt16-1 is required for the correct nuclear localization of the PiggyMac (Pgm) endonuclease, which generates the DNA double-strand breaks required for DNA elimination. Thus, Spt16-1 is essential for Pgm function during programmed genome rearrangements. We propose a model in which Spt16-1 mediates interactions between the excision machinery and chromatin, facilitating endonuclease access to DNA cleavage sites during genome rearrangements.

Klíčová slova:

DNA cleavage – DNA repair – Genomics – Histones – Chromatin – Paramecium – Protein domains – RNA interference

Zdroje

1. Hammond CM, Strømme CB, Huang H, Patel DJ, Groth A. Histone chaperone networks shaping chromatin function. Nat Rev Mol Cell Biol. 2017;18 : 141–158. doi: 10.1038/nrm.2016.159 28053344

2. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D. FACT, a factor that facilitates transcript elongation through nucleosomes. Cell. 1998;92 : 105–116. doi: 10.1016/s0092-8674(00)80903-4 9489704

3. Gurova K, Chang H-W, Valieva ME, Sandlesh P, Studitsky VM. Structure and function of the histone chaperone FACT–Resolving FACTual issues. Biochim Biophys Acta BBA—Gene Regul Mech. 2018;1861 : 892–904. doi: 10.1016/j.bbagrm.2018.07.008 30055319

4. Hondele M, Stuwe T, Hassler M, Halbach F, Bowman A, Zhang ET, et al. Structural basis of histone H2A-H2B recognition by the essential chaperone FACT. Nature. 2013;499 : 111–114. doi: 10.1038/nature12242 23698368

5. Hsieh F-K, Kulaeva OI, Patel SS, Dyer PN, Luger K, Reinberg D, et al. Histone chaperone FACT action during transcription through chromatin by RNA polymerase II. Proc Natl Acad Sci. 2013;110 : 7654–7659. doi: 10.1073/pnas.1222198110 23610384

6. Kemble DJ, McCullough LL, Whitby FG, Formosa T, Hill CP. FACT disrupts nucleosome structure by binding H2A-H2B with conserved peptide motifs. Mol Cell. 2015;60 : 294–306. doi: 10.1016/j.molcel.2015.09.008 26455391

7. Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, et al. FACT caught in the act of manipulating the nucleosome. Nature. 2019. doi: 10.1038/s41586-019-1820-0 31775157

8. Chen P, Dong L, Hu M, Wang Y-Z, Xiao X, Zhao Z, et al. Functions of FACT in Breaking the Nucleosome and Maintaining Its Integrity at the Single-Nucleosome Level. Mol Cell. 2018;71 : 284–293.e4. doi: 10.1016/j.molcel.2018.06.020 30029006

9. Tsunaka Y, Fujiwara Y, Oyama T, Hirose S, Morikawa K. Integrated molecular mechanism directing nucleosome reorganization by human FACT. Genes Dev. 2016;30 : 673–686. doi: 10.1101/gad.274183.115 26966247

10. Betermier M, Duharcourt S. Programmed Rearrangement in Ciliates: Paramecium. Microbiol Spectr. 2014;2. doi: 10.1128/microbiolspec.MDNA3-0035-2014 26104450

11. Guérin F, Arnaiz O, Boggetto N, Denby Wilkes C, Meyer E, Sperling L, et al. Flow cytometry sorting of nuclei enables the first global characterization of Paramecium germline DNA and transposable elements. BMC Genomics. 2017;18 : 327. doi: 10.1186/s12864-017-3713-7 28446146

12. Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury J-M, Wilkes CD, et al. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS genetics. 2012: e1002984. doi: 10.1371/journal.pgen.1002984 23071448

13. Baudry C, Malinsky S, Restituito M, Kapusta A, Rosa S, Meyer E, et al. PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia. Genes Dev. 2009;23 : 2478–83. doi: 10.1101/gad.547309 19884254

14. Bischerour J, Bhullar S, Denby Wilkes C, Régnier V, Mathy N, Dubois E, et al. Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. eLife. 2018;7: e37927. doi: 10.7554/eLife.37927 30223944

15. Kapusta A, Matsuda A, Marmignon A, Ku M, Silve A, Meyer E, et al. Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining. PLoS Genet. 2011;7: e1002049. doi: 10.1371/journal.pgen.1002049 21533177

16. Marmignon A, Bischerour J, Silve A, Fojcik C, Dubois E, Arnaiz O, et al. Ku-Mediated Coupling of DNA Cleavage and Repair during Programmed Genome Rearrangements in the Ciliate Paramecium tetraurelia. Copenhaver GP, editor. PLoS Genet. 2014;10: e1004552. doi: 10.1371/journal.pgen.1004552 25166013

17. Lepere G, Nowacki M, Serrano V, Gout JF, Guglielmi G, Duharcourt S, et al. Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia. Nucleic Acids Res. 2009;37 : 903–15. doi: 10.1093/nar/gkn1018 19103667

18. Sandoval PY, Swart EC, Arambasic M, Nowacki M. Functional Diversification of Dicer-like Proteins and Small RNAs Required for Genome Sculpting. Dev Cell. 2014;28 : 174–188. doi: 10.1016/j.devcel.2013.12.010 24439910

19. Lepere G, Betermier M, Meyer E, Duharcourt S. Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev. 2008;22 : 1501–12. doi: 10.1101/gad.473008 18519642

20. Furrer DI, Swart EC, Kraft MF, Sandoval PY, Nowacki M. Two Sets of Piwi Proteins Are Involved in Distinct sRNA Pathways Leading to Elimination of Germline-Specific DNA. Cell Rep. 2017;20 : 505–520. doi: 10.1016/j.celrep.2017.06.050 28700949

21. Bouhouche K, Gout JF, Kapusta A, Betermier M, Meyer E. Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. Nucleic Acids Res. 2011;39 : 4249–4264. doi: 10.1093/nar/gkq1283 21216825

22. Coyne RS, Lhuillier-Akakpo M, Duharcourt S. RNA-guided DNA rearrangements in ciliates: Is the best genome defence a good offence? Biol Cell. 2012;104 : 1–17. doi: 10.1111/boc.201100057 22352444

23. Duharcourt S, Lepere G, Meyer E. Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts. Trends Genet. 2009;25 : 344–50. doi: 10.1016/j.tig.2009.05.007 19596481

24. Lhuillier-Akakpo M, Frapporti A, Denby Wilkes C, Matelot M, Vervoort M, Sperling L, et al. Local effect of enhancer of zeste-like reveals cooperation of epigenetic and cis-acting determinants for zygotic genome rearrangements. PLoS Genet. 2014;10: e1004665. doi: 10.1371/journal.pgen.1004665 25254958

25. Frapporti A, Miró Pina C, Arnaiz O, Holoch D, Kawaguchi T, Humbert A, et al. The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium. Nat Commun. 2019;10 : 2710. doi: 10.1038/s41467-019-10648-5 31221974

26. Allen SE, Hug I, Pabian S, Rzeszutek I, Hoehener C, Nowacki M. Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs. Cell. 2017;168 : 990. doi: 10.1016/j.cell.2017.02.020 28283070

27. Piquet S, Le Parc F, Bai S-K, Chevallier O, Adam S, Polo SE. The Histone Chaperone FACT Coordinates H2A.X-Dependent Signaling and Repair of DNA Damage. Mol Cell. 2018 [cited 30 Oct 2018]. doi: 10.1016/j.molcel.2018.09.010 30344095

28. Arnaiz O, Meyer E, Sperling L. ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. Nucleic Acids Res. 2020;48: D599–D605. doi: 10.1093/nar/gkz948 31733062

29. Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature. 2006;444 : 171–8. doi: 10.1038/nature05230 17086204

30. VanDemark AP, Xin H, McCullough L, Rawlins R, Bentley S, Heroux A, et al. Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits. J Biol Chem. 2008;283 : 5058–5068. doi: 10.1074/jbc.M708682200 18089575

31. Arnaiz O, Dijk EV, Bétermier M, Lhuillier-Akakpo M, Vanssay A de, Duharcourt S, et al. Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression. BMC Genomics. 2017;18 : 483. doi: 10.1186/s12864-017-3887-z 28651633

32. Winkler DD, Muthurajan UM, Hieb AR, Luger K. Histone Chaperone FACT Coordinates Nucleosome Interaction through Multiple Synergistic Binding Events. J Biol Chem. 2011;286 : 41883–41892. doi: 10.1074/jbc.M111.301465 21969370

33. Galvani A, Sperling L. RNA interference by feeding in Paramecium. Trends Genet. 2002;18 : 11–2. doi: 10.1016/s0168-9525(01)02548-3 11750689

34. Berger JD. Nuclear differentiation and nucleic acid synthesis in well-fed exconjugants of Paramecium aurelia. Chromosoma. 1973;42 : 247–68. doi: 10.1007/BF00284774 4354261

35. Betermier M, Duharcourt S, Seitz H, Meyer E. Timing of developmentally programmed excision and circularization of Paramecium internal eliminated sequences. Mol Cell Biol. 2000;20 : 1553–61. doi: 10.1128/mcb.20.5.1553-1561.2000 10669733

36. Denby Wilkes C, Arnaiz O, Sperling L. ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. Bioinforma Oxf Engl. 2016;32 : 599–601. doi: 10.1093/bioinformatics/btv691 26589276

37. Duret L, Cohen J, Jubin C, Dessen P, Gout JF, Mousset S, et al. Analysis of sequence variability in the macronuclear DNA of Paramecium tetraurelia: a somatic view of the germline. Genome Res. 2008;18 : 585–96. doi: 10.1101/gr.074534.107 18256234

38. Gruchota J, Denby Wilkes C, Arnaiz O, Sperling L, Nowak JK. A meiosis-specific Spt5 homolog involved in non-coding transcription. Nucleic Acids Res. 2017; gkw1318. doi: 10.1093/nar/gkw1318 28053118

39. Dubois E, Mathy N, Régnier V, Bischerour J, Baudry C, Trouslard R, et al. Multimerization properties of PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements. Nucleic Acids Res. 2017;45 : 3204–3216. doi: 10.1093/nar/gkw1359 28104713

40. Maliszewska-Olejniczak K, Gruchota J, Gromadka R, Denby Wilkes C, Arnaiz O, Mathy N, et al. TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements. PLoS Genet. 2015;11: e1005383. doi: 10.1371/journal.pgen.1005383 26177014

41. Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, et al. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017;547 : 236–240. doi: 10.1038/nature22822 28636604

42. Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH. Phase separation drives heterochromatin domain formation. Nature. 2017;547 : 241–245. doi: 10.1038/nature22989 28636597

43. Sand-Dejmek J, Adelmant G, Sobhian B, Calkins AS, Marto J, Iglehart DJ, et al. Concordant and opposite roles of DNA-PK and the “facilitator of chromatin transcription” (FACT) in DNA repair, apoptosis and necrosis after cisplatin. Mol Cancer. 2011;10 : 74. doi: 10.1186/1476-4598-10-74 21679440

44. Abello A, Régnier V, Arnaiz O, Bars RL, Bétermier M, Bischerour J. Functional diversification of Paramecium Ku80 paralogs safeguards genome integrity during precise programmed DNA elimination. PLOS Genet. 2020;16: e1008723. doi: 10.1371/journal.pgen.1008723 32298257

45. Yang J, Zhang X, Feng J, Leng H, Li S, Xiao J, et al. The Histone Chaperone FACT Contributes to DNA Replication-Coupled Nucleosome Assembly. Cell Rep. 2016;14 : 1128–1141. doi: 10.1016/j.celrep.2015.12.096 26804921

46. Lejeune E, Bortfeld M, White SA, Pidoux AL, Ekwall K, Allshire RC, et al. The chromatin-remodeling factor FACT contributes to centromeric heterochromatin independently of RNAi. Curr Biol CB. 2007;17 : 1219–1224. doi: 10.1016/j.cub.2007.06.028 17614284

47. Ashraf K, Nabeel-Shah S, Garg J, Saettone A, Derynck J, Gingras A-C, et al. Proteomic analysis of histones H2A/H2B and variant Hv1 in Tetrahymena thermophila reveals an ancient network of chaperones. Mol Biol Evol. [cited 28 Mar 2019]. doi: 10.1093/molbev/msz039 30796450

48. Keck KM, Pemberton LF. Histone chaperones link histone nuclear import and chromatin assembly. Biochim Biophys Acta BBA—Gene Regul Mech. 2012;1819 : 277–289. doi: 10.1016/j.bbagrm.2011.09.007 22015777

49. Beisson J, Betermier M, Bre MH, Cohen J, Duharcourt S, Duret L, et al. Maintaining clonal Paramecium tetraurelia cell lines of controlled age through daily reisolation. Cold Spring Harb Protoc. 2010;2010: pdb prot5361. doi: 10.1101/pdb.prot5361 20150120

50. Garnier O, Serrano V, Duharcourt S, Meyer E. RNA-mediated programming of developmental genome rearrangements in Paramecium tetraurelia. Mol Cell Biol. 2004;24 : 7370–9. doi: 10.1128/MCB.24.17.7370-7379.2004 15314149

51. Beisson J, Betermier M, Bre MH, Cohen J, Duharcourt S, Duret L, et al. Mass culture of Paramecium tetraurelia. Cold Spring Harb Protoc. 2010;2010: pdb prot5362. doi: 10.1101/pdb.prot5362 20150121

52. Hoffmann C, Neumann H. In Vivo Mapping of FACT–Histone Interactions Identifies a Role of Pob3 C-terminus in H2A–H2B Binding. ACS Chem Biol. 2015;10 : 2753–2763. doi: 10.1021/acschembio.5b00493 26414936

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