Dataset Information

A cis-regulatory map of the Drosophila genome.

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.

SUBMITTER: Negre N

PROVIDER: S-EPMC3179250 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A cis-regulatory map of the Drosophila genome.

Nègre Nicolas N Brown Christopher D CD Ma Lijia L Bristow Christopher Aaron CA Miller Steven W SW Wagner Ulrich U Kheradpour Pouya P Eaton Matthew L ML Loriaux Paul P Sealfon Rachel R Li Zirong Z Ishii Haruhiko H Spokony Rebecca F RF Chen Jia J Hwang Lindsay L Cheng Chao C Auburn Richard P RP Davis Melissa B MB Domanus Marc M Shah Parantu K PK Morrison Carolyn A CA Zieba Jennifer J Suchy Sarah S Senderowicz Lionel L Victorsen Alec A Bild Nicholas A NA Grundstad A Jason AJ Hanley David D MacAlpine David M DM Mannervik Mattias M Venken Koen K Bellen Hugo H White Robert R Gerstein Mark M Russell Steven S Grossman Robert L RL Ren Bing B Posakony James W JW Kellis Manolis M White Kevin P KP

Nature 20110301 7339

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, comprehensi ...[more]

PMID: 21430782

Similar Datasets

Project description:While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. First, from the experimentally verified transcriptional regulatory networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis. We then applied a new comparative approach on five Shewanella genomes that allowed us to systematically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis. Sixty-four percent of the predicted motifs are conserved in at least three of the seven newly sequenced and distantly related Shewanella genomes. In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transcription units. Besides conservation in other genomes, 77 of these motifs are supported by at least one additional type of evidence, including matching to known transcription factor binding motifs and significant functional enrichment or expression coherence of the corresponding target genes. Using the same approach on a more focused gene set, 990 differentially expressed genes derived from published microarray data of S. oneidensis during exposure to metal ions, we identified 31 putative cis-regulatory motifs (16 with at least one type of additional supporting evidence) that are potentially involved in the process of metal reduction. The majority (18/31) of those motifs had been found in our whole-genome comparative approach, further demonstrating that such an approach is capable of uncovering a large fraction of the regulatory map of a genome even in the absence of experimental data. The integrated computational approach developed in this study provides a useful strategy to identify genome-wide cis-regulatory maps and a novel avenue to explore the regulatory pathways for particular biological processes in bacterial systems.

Dataset Information

A cis-regulatory map of the Drosophila genome.

Publications

A cis-regulatory map of the Drosophila genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets