Abstract
X-chromosome dosage compensation by the MSL (male-specific lethal) complex is required in Drosophila melanogaster to increase gene expression from the single male X to equal that of both female X chromosomes. Instead of focusing solely on protein complexes released from DNA, here we used chromatin-interacting protein MS (ChIP-MS) to identify MSL interactions on cross-linked chromatin. We identified MSL-enriched histone modifications, including histone H4 Lys16 acetylation and histone H3 Lys36 methylation, and CG4747, a putative Lys36-trimethylated histone H3 (H3K36me3)-binding protein. CG4747 is associated with the bodies of active genes, coincident with H3K36me3, and is mislocalized in the Set2 mutant lacking H3K36me3. CG4747 loss of function in vivo results in partial mislocalization of the MSL complex to autosomes, and RNA interference experiments confirm that CG4747 and Set2 function together to facilitate targeting of the MSL complex to active genes, validating the ChIP-MS approach.
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Acknowledgements
We thank P. Kaiser (University of California, Irvine, Irvine, California, USA) for the HTB tag and insightful discussions. We thank G. Schotta (Ludwig-Maximilians Universität, Munich, Germany) for the pGS-mw[+] vector. The anti-Z4 antibody was a generous gift from H. Saumweber (Humboldt University, Berlin, Germany). We thank E. Gerace from the Moazed lab (Harvard Medical School, Boston, Massachusetts, USA) for providing the protocol for coupling IgG to magnetic beads. We thank the Bloomington Stock Center and TRiP at Harvard Medical School (NIH/NIGMS R01-GM084947) for providing fly stocks used in this study. We are grateful to M. Gelbart for support and expertise, E. Smith for technical assistance and A. Ciccia, B. Adamson and A. Plachetka for critical reading of the manuscript. This work was supported by grants from the US National Institutes of Health (NIH) to M.I.K. (GM45744 and GM101958), P.V.K. (K25AG037596) and S.J.E. (GM44664). A.E.H.E. is supported by fellowships from The Jane Coffin Childs Foundation and The American Society for Radiation Oncology. B.A.G. is supported by a US National Science Foundation Early Faculty CAREER award and NIH award number DP2OD007447 from the Office of the Director.
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C.I.W., A.A.A. and A.A.G. performed ChIP-MS experiments; A.E.H.E. performed LC-MS/MS to identify MSL-interacting proteins; G.L. and L.-M.P.B. performed quantitative MS of histone PTM; C.I.W. performed all other experiments; P.V.K. performed all bioinformatics analyses; S.J.E., B.A.G. and M.I.K. supervised analyses; C.I.W. and M.I.K. prepared the manuscript in consultation with all coauthors.
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Wang, C., Alekseyenko, A., LeRoy, G. et al. Chromatin proteins captured by ChIP–mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20, 202–209 (2013). https://doi.org/10.1038/nsmb.2477
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DOI: https://doi.org/10.1038/nsmb.2477
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