title: 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.
authors: Institute for Genomics and Systems Biology, Department of Human Genetics, The University of Chicago, 900 East 57th Street, Chicago, Illinois 60637, USA.
authors: Nicolas
authors: N
authors: Nègre
authors: Christopher D
authors: CD
authors: Brown
authors: Lijia
authors: L
authors: Ma
authors: Christopher Aaron
authors: CA
authors: Bristow
authors: Steven W
authors: SW
authors: Miller
authors: Ulrich
authors: U
authors: Wagner
authors: Pouya
authors: P
authors: Kheradpour
authors: Matthew L
authors: ML
authors: Eaton
authors: Paul
authors: P
authors: Loriaux
authors: Rachel
authors: R
authors: Sealfon
authors: Zirong
authors: Z
authors: Li
authors: Haruhiko
authors: H
authors: Ishii
authors: Rebecca F
authors: RF
authors: Spokony
authors: Jia
authors: J
authors: Chen
authors: Lindsay
authors: L
authors: Hwang
authors: Chao
authors: C
authors: Cheng
authors: Richard P
authors: RP
authors: Auburn
authors: Melissa B
authors: MB
authors: Davis
authors: Marc
authors: M
authors: Domanus
authors: Parantu K
authors: PK
authors: Shah
authors: Carolyn A
authors: CA
authors: Morrison
authors: Jennifer
authors: J
authors: Zieba
authors: Sarah
authors: S
authors: Suchy
authors: Lionel
authors: L
authors: Senderowicz
authors: Alec
authors: A
authors: Victorsen
authors: Nicholas A
authors: NA
authors: Bild
authors: A Jason
authors: AJ
authors: Grundstad
authors: David
authors: D
authors: Hanley
authors: David M
authors: DM
authors: MacAlpine
authors: Mattias
authors: M
authors: Mannervik
authors: Koen
authors: K
authors: Venken
authors: Hugo
authors: H
authors: Bellen
authors: Robert
authors: R
authors: White
authors: Mark
authors: M
authors: Gerstein
authors: Steven
authors: S
authors: Russell
authors: Robert L
authors: RL
authors: Grossman
authors: Bing
authors: B
authors: Ren
authors: James W
authors: JW
authors: Posakony
authors: Manolis
authors: M
authors: Kellis
authors: Kevin P
authors: KP
authors: White
mesh_terms: D000818:Animals; D002843:Chromatin / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D004331:Drosophila melanogaster / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D006655:Histone Deacetylases / Q000378:metabolism; D038101:Insulator Elements / Q000235:genetics; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D015203:Reproducibility of Results; D037941:Silencer Elements, Transcriptional / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002843:Chromatin; D014157:Transcription Factors; D006655:Histone Deacetylases