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Genetics. 2018 Mar;208(3):937-949. doi: 10.1534/genetics.117.300657. Epub 2017 Dec 28.

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

Author information

1
Department of Genetics, Yale University, New Haven, Connecticut 06520.
2
Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637.
3
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195.
4
Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
5
Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520.
6
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520.
7
Department of Computer Science, Yale University, New Haven, Connecticut 06520.
8
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195 watersto@uw.edu.

Abstract

To develop a catalog of regulatory sites in two major model organisms, Drosophila melanogaster and Caenorhabditis elegans, the modERN (model organism Encyclopedia of Regulatory Networks) consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE (Model Organism ENCyclopedia Of DNA Elements), we now have data for 262 TFs identifying 1.23 M sites in the fly genome and 217 TFs identifying 0.67 M sites in the worm genome. Because sites from different TFs are often overlapping and tightly clustered, they fall into 91,011 and 59,150 regions in the fly and worm, respectively, and these binding sites span as little as 8.7 and 5.8 Mb in the two organisms. Clusters with large numbers of sites (so-called high occupancy target, or HOT regions) predominantly associate with broadly expressed genes, whereas clusters containing sites from just a few factors are associated with genes expressed in tissue-specific patterns. All of the strains expressing GFP-tagged TFs are available at the stock centers, and the chromatin immunoprecipitation sequencing data are available through the ENCODE Data Coordinating Center and also through a simple interface (http://epic.gs.washington.edu/modERN/) that facilitates rapid accessibility of processed data sets. These data will facilitate a vast number of scientific inquiries into the function of individual TFs in key developmental, metabolic, and defense and homeostatic regulatory pathways, as well as provide a broader perspective on how individual TFs work together in local networks and globally across the life spans of these two key model organisms.

KEYWORDS:

Caenorhabditis elegans; Drosophila; binding sites; regulation; transcription factors

PMID:
29284660
PMCID:
PMC5844342
DOI:
10.1534/genetics.117.300657
[Indexed for MEDLINE]
Free PMC Article

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