Abstract
Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide1,2 has successfully identified specific subtypes of regulatory elements3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements4, chromatin states5, transcription factor binding sites6,7,8,9, RNA polymerase II regulation8 and insulator elements10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships.
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Acknowledgements
This work was supported by U01HG004264 from the National Human Genome Research Institute to K.P.W. and also funded by the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Human Genome Research Institute (NHGRI) or the National Institutes of Health (NIH). C.D.B. is supported by a Lilly-Life Sciences Research Foundation fellowship. C.A.B. is supported by a NIH NRSA postdoctoral fellowship. R.P.A. is in part supported by an Isaac Newton Trust award to R.W. P.L. was supported by a grant from the Department of Energy Computational Sciences Graduate Fellowship (DOE CSGF). M.E.L. and D.M.M. work was supported by NHGRI grant U01 HG004279. We thank the Functional Genomics Facility at the University of Chicago and the High-Throughput Genome Analysis Core at Argonne National Laboratory for processing of microarrays and of Illumina sequence. We thank T.-R. Li, J. D. Lambert, S. Rifkin, T. Herreman, C. Mason, L. Sun and Z. Gauhar for producing the developmental expression microarray data. We also thank the many members of the Drosophila community who contributed to this work by providing reagents. A complete list of community participants is included in the Supplementary Methods.
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N.N., L.S. and K.P.W. designed and produced modENCODE antibodies; N.N., Z.L., H.I., R.F.S., M.B.D., C.A.M., J.Z., S.S. and M.D. performed the ChIP-chip and ChIP-seq experiments; R.F.S., K.V., H.B. and A.V. produced the GFP-tagged transcription factor Drosophila lines; S.W.M., H.I., L.H. and R.P.A. performed the validation experiments of promoters, enhancers and insulators; N.N., P.K.S., N.A.B., A.J.G., D.H. and R.L.G. performed the primary analysis and organized the data of ChIP-chip and ChIP-seq experiments; N.N., C.D.B., L.M., C.A.B., U.W., P.K., M.L.E., P.L., R.S., J.C., C.C., P.K.S., D.M.M. and M.G. analysed the data; M.M. contributed to reagents; N.N., C.D.B., L.M., C.A.B., S.W.M., R.P.A., R.W., S.R., B.R., M.G., J.W.P., M.K. and K.P.W. wrote the paper; H.B., R.W., S.R. (silencer/insulator analysis), R.L.G. (informatics), B.R. (chromatin data and promoter validation), J.W.P. (enhancer/promoter validation), M.K. (data analysis) and K.P.W. (project director) supervised the work.
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Supplementary information
Supplementary Information
This file contains Supplementary Methods, additional references, Supplementary Tables 1, 2, 5, 9, 16 and legends for Tables 1-16 (see separate files for tables 3, 6-8 and 10-15) and Supplementary Figures and legends 1-28. (PDF 26217 kb)
Supplementary Table 3
Promoter validation results - see Supplementary Information file for full legend. (XLS 141 kb)
Supplementary Table 6
TSS class annotation at FDR 0.05 - see Supplementary Information file for full legend. (TXT 9092 kb)
Supplementary Table 7
TSS class annotation at FDR 0.1 - see Supplementary Information file for full legend (TXT 9092 kb)
Supplementary Table 8
Novel promoter prediction based on co-occurence of H3K4me3, PolII and RNA in embryos - see Supplementary Information file for full legend. (TXT 202 kb)
Supplementary Table 10
Insulators Class I - see Supplementary Information file for full legend. (TXT 106 kb)
Supplementary Table 11
Insulators Class II - see Supplementary Information file for full legend. (TXT 65 kb)
Supplementary Table 12
HDAC associated PREs - see Supplementary Information file for full legend. (TXT 16 kb)
Supplementary Table 13
CBP embryo only enhancer predictions - see Supplementary Information file for full legend. (TXT 2 kb)
Supplementary Table 14
TF driven clustering of CBP bound regions - see Supplementary Information file for full legend. (XLS 1278 kb)
Supplementary Table 15
Enrichment of CBP developmental stages within CBP clusters - see Supplementary Information file for full legend. (XLS 32 kb)
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Nègre, N., Brown, C., Ma, L. et al. A cis-regulatory map of the Drosophila genome. Nature 471, 527–531 (2011). https://doi.org/10.1038/nature09990
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DOI: https://doi.org/10.1038/nature09990
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