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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

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Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

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Figure 1: Chromatin annotation of the Drosophila melanogaster genome.
Figure 2: Visualization of spatial scales and organization using compact folding.
Figure 3: Chromatin patterns associated with transcriptionally active genes.
Figure 4: Signatures of TSSs within domains of Polycomb-mediated repression.
Figure 5: Chromatin signatures of regulatory elements identified by DNase I hypersensitivity.
Figure 6: Spatial arrangements of chromatin states associated with active transcription.

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Gene Expression Omnibus

Change history

  • 23 March 2011

    Author initials were corrected for T.K.C.


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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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Authors and Affiliations



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 to Gary H. Karpen or Peter J. Park.

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The authors declare no competing financial interests.

Additional information

The data are available from the modENCODE site ( 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).

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