Comprehensive analysis of the chromatin landscape in Drosophila melanogaster (original) (raw)

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Author initials were corrected for T.K.C.

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Acknowledgements

We thank our technicians D. Acevedo, S. Gadel, C. Kennedy, O.-K. Lee, S. Marchetti, S. Vong and M. Weaver, and Rutgers BRTC. We also thank our colleagues who donated antibodies: J. Kadonaga (H1), A. L. Greenleaf (RNA pol II), G. Reuter (SU(VAR)3-9), G. Cavalli (GAF) and I. F. Zhimulev/H. Saumweber (Chromator). The major support for this work came from the modENCODE grant U01HG004258 to G.H.K. (Principal Investigator) and S.C.R.E., M.I.K., P.J.P. and V.P. (co-Principal Investigators), administered under Department of Energy contract no. DE-AC02-05CH11231. Additional funding came from RC2 HG005639, U01 HG004279, R01 GM082798, R37 GM45744, RC1 HG005334, R01 GM071923, U54 HG004592 and NSF 0905968.

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Author notes

  1. Yuri B. Schwartz, Daniela Linder-Basso & Gregory Shanower
    Present address: Present addresses: Department of Molecular Biology, Umea University, 901 87 Umea, Sweden. (Y.B.S.); Department of Plant Biology and Pathology, SEBS, Rutgers University, New Brunswick, New Jersey 08901, USA (D.L.-B.); Department of Basic Sciences, The Commonwealth Medical College, Scranton, Pennsylvania 18510, USA (G.S.).,
  2. Gary H. Karpen and Peter J. Park: These authors contributed equally to this work.

Authors and Affiliations

  1. Center for Biomedical Informatics, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Peter V. Kharchenko, Michael Y. Tolstorukov, Lovelace J. Luquette, Ruibin Xi, Youngsook L. Jung, Richard W. Park, Eric P. Bishop & Peter J. Park
  2. Children’s Hospital Informatics Program, Boston, 02115, Massachusetts, USA
    Peter V. Kharchenko, Michael Y. Tolstorukov & Peter J. Park
  3. Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Boston, 02115, Massachusetts, USA
    Artyom A. Alekseyenko, Erica Larschan, Andrey A. Gorchakov, Annette Plachetka, Youngsook L. Jung, Mitzi I. Kuroda & Peter J. Park
  4. Department of Genetics, Harvard Medical School, Boston, 02115, Massachusetts, USA
    Artyom A. Alekseyenko, Erica Larschan, Andrey A. Gorchakov, Annette Plachetka & Mitzi I. Kuroda
  5. Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, 08854, New Jersey, USA
    Yuri B. Schwartz, Daniela Linder-Basso, Gregory Shanower & Vincenzo Pirrotta
  6. Department of Molecular and Cell Biology, and Department of Genome Dynamics, University of California at Berkeley, Lawrence Berkeley National Lab, Berkeley, 94720, California, USA
    Aki Minoda & Gary H. Karpen
  7. Department of Biology, Washington University in St Louis, St Louis, 63130, Missouri, USA
    Nicole C. Riddle, Tingting Gu & Sarah C. R. Elgin
  8. MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, 02139, Massachusetts, USA
    Jason Ernst & Manolis Kellis
  9. Broad Institute of MIT and Harvard, Cambridge, 02142, Massachusetts, USA
    Jason Ernst & Manolis Kellis
  10. Department of Genome Sciences, University of Washington, Seattle, 98195, Washington, USA
    Peter J. Sabo, Theresa K. Canfield, Richard Sandstrom, Robert E. Thurman & John A. Stamatoyannopoulos
  11. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, 02906, Rhode Island, USA
    Erica Larschan
  12. Graduate Program in Bioinformatics, Boston University, Boston, 02115, Massachusetts, USA
    Richard W. Park & Eric P. Bishop
  13. Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, 27710, North Carolina, USA
    David M. MacAlpine
  14. Department of Medicine, University of Washington, Seattle, 98195, Washington, USA
    John A. Stamatoyannopoulos

Authors

  1. Peter V. Kharchenko
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  2. Artyom A. Alekseyenko
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  3. Yuri B. Schwartz
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  4. Aki Minoda
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  5. Nicole C. Riddle
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  6. Jason Ernst
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  7. Peter J. Sabo
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  8. Erica Larschan
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  9. Andrey A. Gorchakov
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  10. Tingting Gu
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  11. Daniela Linder-Basso
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  12. Annette Plachetka
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  13. Gregory Shanower
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  14. Michael Y. Tolstorukov
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  15. Lovelace J. Luquette
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  16. Ruibin Xi
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  17. Youngsook L. Jung
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  18. Richard W. Park
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  19. Eric P. Bishop
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  20. Theresa K. Canfield
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  21. Richard Sandstrom
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  22. Robert E. Thurman
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  23. David M. MacAlpine
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  24. John A. Stamatoyannopoulos
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  25. Manolis Kellis
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  26. Sarah C. R. Elgin
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  27. Mitzi I. Kuroda
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  28. Vincenzo Pirrotta
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  29. Gary H. Karpen
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  30. Peter J. Park
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Contributions

P.V.K. performed most bioinformatic analysis. A.A.A., Y.B.S., A.M., N.C.R., E.L., A.A.G., T.G., D.L.-B., A.P. and G.S. generated data, directed by S.C.R.E., M.I.K., V.P. and G.H.K. The 30-state analysis was performed by J.E. and M.K., whereas M.Y.T., L.J.L., R.X., Y.L.J., R.W.P. and E.P.B. performed additional bioinformatic analysis. P.J.S., T.K.C., R.S., R.E.T. and J.A.S. generated and processed DHS data. D.M.M. helped with replication analysis. P.J.P. supervised all analysis. G.H.K. coordinated the entire project. P.V.K., G.H.K. and P.J.P. wrote the manuscript, with contributions from S.C.R.E., M.I.K., V.P., Y.B.S, N.C.R, A.A.A. and A.M.

Corresponding authors

Correspondence toGary H. Karpen or Peter J. Park.

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Competing interests

The authors declare no competing financial interests.

Additional information

The data are available from the modENCODE site (http://www.modencode.org). GRO-Seq data are available from Gene Expression Omnibus (GEO, GSE25321).

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Kharchenko, P., Alekseyenko, A., Schwartz, Y. et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.Nature 471, 480–485 (2011). https://doi.org/10.1038/nature09725

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