SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin

Abstract

HP1 enrichment at pericentric heterochromatin is considered important for centromere function. Although HP1 binding to H3K9me3 can explain its accumulation at pericentric heterochromatin, how it is initially targeted there remains unclear. Here, in mouse cells, we reveal the presence of long nuclear noncoding transcripts corresponding to major satellite repeats at the periphery of pericentric heterochromatin. Furthermore, we find that major transcripts in the forward orientation specifically associate with SUMO-modified HP1 proteins. We identified this modification as SUMO-1 and mapped it in the hinge domain of HP1α. Notably, the hinge domain and its SUMOylation proved critical to promote the initial targeting of HP1α to pericentric domains using de novo localization assays, whereas they are dispensable for maintenance of HP1 domains. We propose that SUMO-HP1, through a specific association with major forward transcript, is guided at the pericentric heterochromatin domain to seed further HP1 localization.

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Figure 1: Strand-specific localization of centromeric RNAs.
Figure 2: SUMO-1–modified HP1α interacts specifically with forward major RNAs.
Figure 3: SUMOylation of HP1α occurs at its hinge domain in vitro.
Figure 4: SUMOylation of HP1α promotes its targeting and accumulation at pericentric heterochromatin.
Figure 5: The hinge domain is required for de novo localization of HP1α at pericentric heterochromatin.
Figure 6: Model for a de novo HP1α targeting to pericentric heterochromatin.

References

  1. 1

    Grewal, S.I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet. 8, 35–46 (2007).

    CAS  Article  Google Scholar 

  2. 2

    Guenatri, M., Bailly, D., Maison, C. & Almouzni, G. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. J. Cell Biol. 166, 493–505 (2004).

    CAS  Article  Google Scholar 

  3. 3

    Probst, A.V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol. 10, 192–206 (2009).

    CAS  Article  Google Scholar 

  4. 4

    Bannister, A.J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).

    CAS  Article  Google Scholar 

  5. 5

    Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001).

    CAS  Article  Google Scholar 

  6. 6

    Strahl, B.D. & Allis, C.D. The language of covalent histone modifications. Nature 403, 41–45 (2000).

    CAS  Google Scholar 

  7. 7

    Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 1074–1080 (2001).

    CAS  Article  Google Scholar 

  8. 8

    Peng, H., Ivanov, A.V., Oh, H.J., Lau, Y.F. & Rauscher, F.J. 3rd. Epigenetic gene silencing by the SRY protein is mediated by a KRAB-O protein which recruits the KAP1 co-repressor machinery. J. Biol. Chem. 284, 35670–35680 (2009).

    CAS  Article  Google Scholar 

  9. 9

    Quivy, J.P. et al. A CAF-1 dependent pool of HP1 during heterochromatin duplication. EMBO J. 23, 3516–3526 (2004).

    CAS  Article  Google Scholar 

  10. 10

    Lomberk, G., Bensi, D., Fernandez-Zapico, M.E. & Urrutia, R. Evidence for the existence of an HP1-mediated subcode within the histone code. Nat. Cell Biol. 8, 407–415 (2006).

    CAS  Article  Google Scholar 

  11. 11

    Maison, C. et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat. Genet. 30, 329–334 (2002).

    Article  Google Scholar 

  12. 12

    Muchardt, C. et al. Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha. EMBO Rep. 3, 975–981 (2002).

    CAS  Article  Google Scholar 

  13. 13

    Rudert, F., Bronner, S., Garnier, J.M. & Dolle, P. Transcripts from opposite strands of gamma satellite DNA are differentially expressed during mouse development. Mamm. Genome 6, 76–83 (1995).

    CAS  Article  Google Scholar 

  14. 14

    Lu, J. & Gilbert, D.M. Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. J. Cell Biol. 179, 411–421 (2007).

    CAS  Article  Google Scholar 

  15. 15

    Kalitsis, P. & Choo, K.H.A. Centromere DNA of higher eukaryotes. in The Centromere (ed. Choo, K.H.A.) 97–140 (Oxford University Press, New York, 1997).

  16. 16

    Heard, E. & Bickmore, W. The ins and outs of gene regulation and chromosome territory organisation. Curr. Opin. Cell Biol. 19, 311–316 (2007).

    CAS  Article  Google Scholar 

  17. 17

    Deng, Z., Norseen, J., Wiedmer, A., Riethman, H. & Lieberman, P.M. TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol. Cell 35, 403–413 (2009).

    CAS  Article  Google Scholar 

  18. 18

    Wang, Q., Zhang, Z., Blackwell, K. & Carmichael, G.G. Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr. Biol. 15, 384–391 (2005).

    CAS  Article  Google Scholar 

  19. 19

    Kuroda, M.I., Kernan, M.J., Kreber, R., Ganetzky, B. & Baker, B.S. The maleless protein associates with the X chromosome to regulate dosage compensation in Drosophila. Cell 66, 935–947 (1991).

    CAS  Article  Google Scholar 

  20. 20

    Irvine, K., Stirling, R., Hume, D. & Kennedy, D. Rasputin, more promiscuous than ever: a review of G3BP. Int. J. Dev. Biol. 48, 1065–1077 (2004).

    CAS  Article  Google Scholar 

  21. 21

    Shin, J.A. et al. SUMO modification is involved in the maintenance of heterochromatin stability in fission yeast. Mol. Cell 19, 817–828 (2005).

    CAS  Article  Google Scholar 

  22. 22

    Aagaard, L. et al. Functional mammalian homologues of the Drosophila PEV- modifier Su(Var)3–9 encode centromere-associated proteins which complex with the heterochromatin component M31. EMBO J. 18, 1923–1938 (1999).

    CAS  Article  Google Scholar 

  23. 23

    Hay, R.T. SUMO: a history of modification. Mol. Cell 18, 1–12 (2005).

    CAS  Article  Google Scholar 

  24. 24

    Meulmeester, E. & Melchior, F. Cell biology: SUMO. Nature 452, 709–711 (2008).

    CAS  Article  Google Scholar 

  25. 25

    Park-Sarge, O.K. & Sarge, K.D. Detection of SUMOylated proteins. Methods Mol. Biol. 464, 255–265 (2009).

    Article  Google Scholar 

  26. 26

    Jakobs, A. et al. Ubc9 fusion-directed SUMOylation (UFDS): a method to analyze function of protein SUMOylation. Nat. Methods 4, 245–250 (2007).

    CAS  Article  Google Scholar 

  27. 27

    Peters, A.H. et al. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323–337 (2001).

    CAS  Article  Google Scholar 

  28. 28

    Loyola, A., Bonaldi, T., Roche, D., Imhof, A. & Almouzni, G. PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Mol. Cell 24, 309–316 (2006).

    CAS  Article  Google Scholar 

  29. 29

    Smothers, J.F. & Henikoff, S. The hinge and chromoshadow domain impart distinct targeting of HP1-like proteins. Mol. Cell. Biol. 21, 2555–2569 (2001).

    CAS  Article  Google Scholar 

  30. 30

    Kerscher, O. SUMO junction-what's your function? New insights through SUMO-interacting motifs. EMBO Rep. 8, 550–555 (2007).

    CAS  Article  Google Scholar 

  31. 31

    Ouyang, J., Shi, Y., Valin, A., Xuan, Y. & Gill, G. Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex. Mol. Cell 34, 145–154 (2009).

    CAS  Article  Google Scholar 

  32. 32

    Allshire, R.C. & Karpen, G.H. Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat. Rev. Genet. 9, 923–937 (2008).

    CAS  Article  Google Scholar 

  33. 33

    Moazed, D. Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009).

    CAS  Article  Google Scholar 

  34. 34

    Blankenship, J.T. & Wieschaus, E. Two new roles for the Drosophila AP patterning system in early morphogenesis. Development 128, 5129–5138 (2001).

    CAS  PubMed  Google Scholar 

  35. 35

    Kanellopoulou, C. et al. Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev. 19, 489–501 (2005).

    CAS  Article  Google Scholar 

  36. 36

    Murchison, E.P., Partridge, J.F., Tam, O.H., Cheloufi, S. & Hannon, G.J. Characterization of Dicer-deficient murine embryonic stem cells. Proc. Natl. Acad. Sci. USA 102, 12135–12140 (2005).

    CAS  Article  Google Scholar 

  37. 37

    Tsai, M.C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010).

    CAS  Article  Google Scholar 

  38. 38

    Savarese, F., Flahndorfer, K., Jaenisch, R., Busslinger, M. & Wutz, A. Hematopoietic precursor cells transiently reestablish permissiveness for X inactivation. Mol. Cell. Biol. 26, 7167–7177 (2006).

    CAS  Article  Google Scholar 

  39. 39

    Agrelo, R. et al. SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells. Dev. Cell 16, 507–516 (2009).

    CAS  Article  Google Scholar 

  40. 40

    Santos, F., Peters, A.H., Otte, A.P., Reik, W. & Dean, W. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev. Biol. 280, 225–236 (2005).

    CAS  Article  Google Scholar 

  41. 41

    Puschendorf, M. et al. PRC1 and Suv39h specify parental asymmetry at constitutive heterochromatin in early mouse embryos. Nat. Genet. 40, 411–420 (2008).

    CAS  Article  Google Scholar 

  42. 42

    Probst, A.V. et al. A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev. Cell 19, 625–638 (2010).

    CAS  Article  Google Scholar 

  43. 43

    Haaf, T. & Ward, D.C. Higher order nuclear structure in mammalian sperm revealed by in situ hybridization and extended chromatin fibers. Exp. Cell Res. 219, 604–611 (1995).

    CAS  Article  Google Scholar 

  44. 44

    Mayer, R. et al. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol. 6, 44 (2005).

    Article  Google Scholar 

  45. 45

    Terranova, R., Sauer, S., Merkenschlager, M. & Fisher, A.G. The reorganisation of constitutive heterochromatin in differentiating muscle requires HDAC activity. Exp. Cell Res. 310, 344–356 (2005).

    CAS  Article  Google Scholar 

  46. 46

    Hajkova, P. et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877–881 (2008).

    CAS  Article  Google Scholar 

  47. 47

    Solovei, I. et al. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137, 356–368 (2009).

    CAS  Article  Google Scholar 

  48. 48

    Narita, M. et al. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113, 703–716 (2003).

    CAS  Article  Google Scholar 

  49. 49

    Nielsen, A.L. et al. Heterochromatin formation in mammalian cells: interaction between histones and HP1 proteins. Mol. Cell 7, 729–739 (2001).

    CAS  Article  Google Scholar 

  50. 50

    Dodson, R.E. & Shapiro, D.J. Vigilin, a ubiquitous protein with 14 K homology domains, is the estrogen-inducible vitellogenin mRNA 3′-untranslated region-binding protein. J. Biol. Chem. 272, 12249–12252 (1997).

    CAS  Article  Google Scholar 

  51. 51

    Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003).

    CAS  Article  Google Scholar 

  52. 52

    Martini, E., Roche, D.M., Marheineke, K., Verreault, A. & Almouzni, G. Recruitment of phosphorylated chromatin assembly factor 1 to chromatin after UV irradiation of human cells. J. Cell Biol. 143, 563–575 (1998).

    CAS  Article  Google Scholar 

  53. 53

    Fevrier, B. et al. Cells release prions in association with exosomes. Proc. Natl. Acad. Sci. USA 101, 9683–9688 (2004).

    CAS  Article  Google Scholar 

  54. 54

    Poullet, P., Carpentier, S. & Barillot, E. myProMS, a web server for management and validation of mass spectrometry-based proteomic data. Proteomics 7, 2553–2556 (2007).

    CAS  Article  Google Scholar 

  55. 55

    Matic, I. et al. In vivo identification of human small ubiquitin-like modifier polymerization sites by high accuracy mass spectrometry and an in vitro to in vivo strategy. Mol. Cell. Proteomics 7, 132–144 (2008).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank A. Bird, D. Shapiro, R. Hay, T. Jenuwein, R. Losson and J. Seeler for constructs and reagents. We thank W. Faigle for mass spectrometry support, G. Cappello for helpful discussions, A. Cook for critical reading and P. Le Baccon at the Curie Imaging Platform. G.A.'s laboratory is funded by la Ligue Nationale contre le Cancer (Equipe labellisée la Ligue), Curie Programme Incitatif et Collaboratif (PIC) Programs, the European Network of Excellence Epigenome (LSHG-CT-2004-503433), ACI-2007-Cancéropôle IdF 'Breast cancer and Epigenetics', Agence Nationale de la Recherche (ANR) 'EcenS' ANR-09-BLAN-0257-01, INCa 'GepiG', European Research Council (ERC) Advanced Grant 2009-AdG-20090506, and D.L.'s laboratory was funded by le Cancéropôle Ile-de-France and l'INCA.

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C.M., J.-P.Q. and G.A. conceived and designed the experiments. C.M., D.B. and J.-P.Q. performed most of the experiments. D.R. and I.V. performed immuno-DNA FISH and immuno-RNA FISH. A.V.P. performed RNA FISH. F.D., B.L. and D.L. performed and analyzed mass spectrometry data using samples prepared by R.M.d.O. and they wrote together the corresponding parts. C.M. generated all figures. C.M., J.-P.Q. and G.A. analyzed the data. C.M. and G.A. wrote the paper. All authors contributed to final editing of the manuscript.

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Correspondence to Jean-Pierre Quivy or Geneviève Almouzni.

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Maison, C., Bailly, D., Roche, D. et al. SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin. Nat Genet 43, 220–227 (2011). https://doi.org/10.1038/ng.765

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