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Chromatin proteins captured by ChIP–mass spectrometry are linked to dosage compensation in Drosophila

Nature Structural & Molecular Biology volume 20, pages 202209 (2013) | Download Citation

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.

Author information

Affiliations

  1. Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.

    • Charlotte I Wang
    • , Artyom A Alekseyenko
    • , Andrew EH Elia
    • , Andrey A Gorchakov
    • , Stephen J Elledge
    •  & Mitzi I Kuroda
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Charlotte I Wang
    • , Artyom A Alekseyenko
    • , Andrew EH Elia
    • , Andrey A Gorchakov
    • , Stephen J Elledge
    •  & Mitzi I Kuroda
  3. Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA.

    • Gary LeRoy
    • , Laura-Mae P Britton
    •  & Benjamin A Garcia
  4. Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA.

    • Andrew EH Elia
  5. Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, USA.

    • Andrew EH Elia
    •  & Stephen J Elledge
  6. Institute of Molecular and Cell Biology, Novosibirsk, Russia.

    • Andrey A Gorchakov
  7. Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.

    • Peter V Kharchenko
  8. Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Benjamin A Garcia

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Contributions

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.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Mitzi I Kuroda.

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DOI

https://doi.org/10.1038/nsmb.2477

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