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The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome

Abstract

The male-specific lethal (MSL) complex upregulates the single male X chromosome to achieve dosage compensation in Drosophila melanogaster. We have proposed that MSL recognition of specific entry sites on the X is followed by local targeting of active genes marked by histone H3 trimethylation (H3K36me3). Here we analyze the role of the MSL3 chromodomain in the second targeting step. Using ChIP-chip analysis, we find that MSL3 chromodomain mutants retain binding to chromatin entry sites but show a clear disruption in the full pattern of MSL targeting in vivo, consistent with a loss of spreading. Furthermore, when compared to wild type, chromodomain mutants lack preferential affinity for nucleosomes containing H3K36me3 in vitro. Our results support a model in which activating complexes, similarly to their silencing counterparts, use the nucleosomal binding specificity of their respective chromodomains to spread from initiation sites to flanking chromatin.

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Figure 1: Characterization of MSL3 chromodomain mutants.
Figure 2: High-resolution ChIP-chip mapping of MSL3 mutant binding sites.
Figure 3: The MSL3 chromodomain is important for spreading.
Figure 4: MSL3 chromodomain mutants disrupt spreading in vivo.
Figure 5: Chromodomain mutants show loss of preference for H3K36me3-containing nucleosomes (Nuc).
Figure 6: A model for MSL3 chromodomain-dependent spreading.

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References

  1. Koonin, E.V., Zhou, S. & Lucchesi, J.C. The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 23, 4229–4233 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Marin, I. & Baker, B.S. Origin and evolution of the regulatory gene male-specific lethal-3. Mol. Biol. Evol. 17, 1240–1250 (2000).

    Article  CAS  PubMed  Google Scholar 

  3. Palmer, M.J., Richman, R., Richter, L. & Kuroda, M.I. Sex-specific regulation of the male-specific lethal-1 dosage compensation gene in Drosophila. Genes Dev. 8, 698–706 (1994).

    Article  CAS  PubMed  Google Scholar 

  4. Lyman, L.M., Copps, K., Rastelli, L., Kelley, R.L. & Kuroda, M.I. Drosophila Male-specific lethal-2 protein: structure/function analysis and dependence on MSL-1 for chromosome association. Genetics 147, 1743–1753 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Gu, W., Szauter, P. & Lucchesi, J.C. Targeting of MOF, a putative histone acetyl transferase, to the X chromosome of Drosophila melanogaster. Dev. Genet. 22, 56–64 (1998).

    Article  CAS  PubMed  Google Scholar 

  6. Demakova, O.V. et al. The MSL complex levels are critical for its correct targeting to the chromosomes in Drosophila melanogaster. Chromosoma 112, 103–115 (2003).

    Article  CAS  PubMed  Google Scholar 

  7. Alekseyenko, A.A., Larschan, E., Lai, W.R., Park, P.J. & Kuroda, M.I. High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev. 20, 848–857 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Larschan, E. et al. MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol. Cell 28, 121–133 (2007).

    Article  CAS  PubMed  Google Scholar 

  9. Bell, O. et al. Transcription-coupled methylation of histone H3 at lysine 36 regulates dosage compensation by enhancing recruitment of the MSL complex in Drosophila. Mol. Cell. Biol. 28, 3401–3409 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fagegaltier, D. & Baker, B.S. X chromosome sites autonomously recruit the dosage compensation complex in Drosophila males. PLoS Biol. 2, e341 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  11. Oh, H., Bone, J.R. & Kuroda, M.I. Multiple classes of MSL binding sites target dosage compensation to the X chromosome of Drosophila. Curr. Biol. 14, 481–487 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Dahlsveen, I.K., Gilfillan, G.D., Shelest, V.I., Lamm, R. & Becker, P.B. Targeting determinants of dosage compensation in Drosophila. PLoS Genet. 2, e5 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Gilfillan, G.D. et al. Cumulative contributions of weak DNA determinants to targeting the Drosophila dosage compensation complex. Nucleic Acids Res. 35, 3561–3572 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Kind, J. & Akhtar, A. Cotranscriptional recruitment of the dosage compensation complex to X-linked target genes. Genes Dev. 21, 2030–2040 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Muller, H.J. & Altenburg, E. The frequency of translocations produced by X-Rays in Drosophila. Genetics 15, 283–311 (1930).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Schotta, G., Ebert, A., Dorn, R. & Reuter, G. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 14, 67–75 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  18. Zhang, K., Mosch, K., Fischle, W. & Grewal, S.I.S. Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat. Struct. Mol. Biol. 15, 381–388 (2008).

    Article  CAS  PubMed  Google Scholar 

  19. Elgin, S.C. & Grewal, S.I. Heterochromatin: silence is golden. Curr. Biol. 13, R895–R898 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Schwartz, Y.B. & Pirrotta, V. Polycomb silencing mechanisms and the management of genomic programmes. Nat. Rev. Genet. 8, 9–22 (2007).

    Article  CAS  PubMed  Google Scholar 

  21. Buscaino, A., Legube, G. & Akhtar, A. X-chromosome targeting and dosage compensation are mediated by distinct domains in MSL-3. EMBO Rep. 7, 531–538 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Zhang, P. et al. Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res. 34, 6621–6628 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Flanagan, J.F. et al. Molecular implications of evolutionary differences in CHD double chromodomains. J. Mol. Biol. 369, 334–342 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Groth, A.C., Fish, M., Nusse, R. & Calos, M.P. Construction of transgenic Drosophila by using the site-specific integrase from phage φC31. Genetics 166, 1775–1782 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Morales, V., Regnard, C., Izzo, A., Vetter, I. & Becker, P.B. The MRG domain mediates the functional integration of MSL3 into the dosage compensation complex. Mol. Cell. Biol. 25, 5947–5954 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lucchesi, J.C., Kelly, W.G. & Panning, B. Chromatin remodeling in dosage compensation. Annu. Rev. Genet. 39, 615–651 (2005).

    Article  CAS  PubMed  Google Scholar 

  27. Alekseyenko, A.A. et al. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134, 599–609 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28–36 (1994).

    CAS  PubMed  Google Scholar 

  29. Beermann, W. Chromomeres and genes. Results Probl. Cell Differ. 4, 1–33 (1972).

    Article  CAS  PubMed  Google Scholar 

  30. Carrozza, M.J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

    Article  CAS  PubMed  Google Scholar 

  31. Joshi, A.A. & Struhl, K. Eaf3 chromodomain interaction with methylated H3–K36 links histone deacetylation to Pol II elongation. Mol. Cell 20, 971–978 (2005).

    Article  CAS  PubMed  Google Scholar 

  32. Keogh, M.C. et al. Cotranscriptional Set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123, 593–605 (2005).

    Article  CAS  PubMed  Google Scholar 

  33. McDonel, P., Jans, J., Peterson, B.K. & Meyer, B.J. Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex. Nature 444, 614–618 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Ercan, S. et al. X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat. Genet. 39, 403–408 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Yokoyama, R., Pannuti, A., Ling, H., Smith, E.R. & Lucchesi, J.C. A plasmid model system shows that Drosophila dosage compensation depends on the global acetylation of histone H4 at lysine 16 and is not affected by depletion of common transcription elongation chromatin marks. Mol. Cell. Biol. 27, 7865–7870 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Nagel, A.C., Maier, D. & Preiss, A. Green fluorescent protein as a convenient and versatile marker for studies on functional genomics in Drosophila. Dev. Genes Evol. 212, 93–98 (2002).

    Article  CAS  PubMed  Google Scholar 

  37. Kelley, R.L. et al. Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98, 513–522 (1999).

    Article  CAS  PubMed  Google Scholar 

  38. Peng, S., Alekseyenko, A.A., Larschan, E., Kuroda, M.I. & Park, P.J. Normalization and experimental design for ChIP-chip data. BMC Bioinformatics 8, 219 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Li, B. et al. Combined action of PHD and chromo domains directs the Rpd3S HDAC to transcribed chromatin. Science 316, 1050–1054 (2007).

    Article  CAS  PubMed  Google Scholar 

  40. Li, B. et al. Preferential occupancy of histone variant H2AZ at inactive promoters influences local histone modifications and chromatin remodeling. Proc. Natl. Acad. Sci. USA 102, 18385–18390 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Li, B., Howe, L., Anderson, S., Yates, J.R. & Workman, J.L. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J. Biol. Chem. 278, 8897–8903 (2003).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Special thanks to A.A. Alekseyenko (Harvard-Partners Center for Genetics and Genomics) for important advice, discussions and protocols, S. Khorasanizadeh for discussions and to members of the Kuroda laboratory for critical comments on the manuscript, H. Oh (currently at Rutgers University), for a key fly stock, and J. Racine and A. Sarovschii for technical assistance and the Taplin Biological Mass Spectrometry Facility (Harvard Medical School) for peptide identification. This work was supported by the US National Institutes of Health (NIH; GM45744 to M.I.K. and GM67825 to P.J.P.). B.L. and J.L.W. were supported by GM47867 from the NIH and by funding from the Stowers Institute for Medical Research.

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Contributions

T.H.S. performed the mutagenesis, transgenic complementation, immunoprecipitations, ChIP-chip, purification of recombinant MSL3 and polytene-chromosome analyses; S.P. performed all bioinformatics analyses; B.L. performed the in vitro nucleosome binding assays; J.L.W., P.J.P. and M.I.K. supervised the analyses; T.H.S. and M.I.K. prepared the manuscript in consultation with all coauthors.

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Correspondence to Mitzi I Kuroda.

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Sural, T., Peng, S., Li, B. et al. The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nat Struct Mol Biol 15, 1318–1325 (2008). https://doi.org/10.1038/nsmb.1520

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