|Citation||Nègre, N., Brown, C.D., Ma, L., Bristow, C.A., Miller, S.W., Wagner, U., Kheradpour, P., Eaton, M.L., Loriaux, P., Sealfon, R., Li, Z., Ishii, H., Spokony, R.F., Chen, J., Hwang, L., Cheng, C., Auburn, R.P., Davis, M.B., Domanus, M., Shah, P.K., Morrison, C.A., Zieba, J., Suchy, S., Senderowicz, L., Victorsen, A., Bild, N.A., Grundstad, A.J., Hanley, D., MacAlpine, D.M., Mannervik, M., Venken, K., Bellen, H., White, R., Gerstein, M., Russell, S., Grossman, R.L., Ren, B., Posakony, J.W., Kellis, M., White, K.P. (2011). A cis-regulatory map of the Drosophila genome. Nature 471(7339): 527--531. (Export to RIS)|
|Publication Type||Research paper|
|PubMed 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-wide has successfully identified specific subtypes of regulatory elements. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II regulation and insulator elements; 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.|
|Supplementary material||DataS8: HOT regions. [FBrf0213505]
Supplementary Information. [FBrf0213507]
DataS7: Predicted TFBS. [FBrf0213603]
Supplementary Table 12 - HDAC associated PREs. [FBrf0214516]
Supplementary Table 13 - CBP embryo only enhancer predictions. [FBrf0214517]
|Personal communication to FlyBase||HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7).
Ma, 2011.6.8, HOT spots analysis (Data Set S8) and 41 TFBS GFF files (Data Set S7). [FBrf0213928]
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|Language of Publication||English|
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