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Genome Res DOI:10.1101/gr.168807.113

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.

Publication TypeJournal Article
Year of Publication2014
AuthorsSlattery, M, Ma, L, Spokony, RF, Arthur, RK, Kheradpour, P, Kundaje, A, Nègre, N, Crofts, A, Ptashkin, R, Zieba, J, Ostapenko, A, Suchy, S, Victorsen, A, Jameel, N, A Grundstad, J, Gao, W, Moran, JR, E Rehm, J, Grossman, RL, Kellis, M, White, KP
JournalGenome Res
Volume24
Issue7
Pages1224-35
Date Published2014 Jul
ISSN1549-5469
KeywordsAnimals, Base Sequence, Binding Sites, Chromatin, Cluster Analysis, Computational Biology, Drosophila melanogaster, Enhancer Elements, Genetic, Gene Expression Profiling, Gene Expression Regulation, Genome, Insect, Genomics, Nucleotide Motifs, Protein Binding, Regulatory Sequences, Nucleic Acid, Transcription Factors, Transcription, Genetic
Abstract

Annotation of regulatory elements and identification of the transcription-related factors (TRFs) targeting these elements are key steps in understanding how cells interpret their genetic blueprint and their environment during development, and how that process goes awry in the case of disease. One goal of the modENCODE (model organism ENCyclopedia of DNA Elements) Project is to survey a diverse sampling of TRFs, both DNA-binding and non-DNA-binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TRFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA regions with demonstrated enhancer activity. Regions of high TRF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TRF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. Together these data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.

URLhttp://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=24985916
DOI10.1101/gr.168807.113
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/24985916?dopt=Abstract

Alternate JournalGenome Res.
PubMed ID24985916
PubMed Central IDPMC4079976
Grant ListUL1 TR000430 / TR / NCATS NIH HHS / United States
R01 HG004037 / HG / NHGRI NIH HHS / United States
U01 HG004264 / HG / NHGRI NIH HHS / United States
U01HG004264 / HG / NHGRI NIH HHS / United States
T32 GM007197 / GM / NIGMS NIH HHS / United States