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

Genetics: A Periodical Record of Investigations Bearing on Heredity and Variation

article

Michelle M. Kudron¹  Alec Victorsen²  Louis Gevirtzman³  LaDeana W. Hillier³  William W. Fisher⁴  Dionne Vafeados³  Matt Kirkey²  Ann S. Hammonds⁴  Jeffery Gersch²  Haneen Ammouri²  Martha L. Wall²  Jennifer Moran²  David Steffen²  Matt Szynkarek²  Samantha Seabrook-Sturgis²  Nader Jameel²  Madhura Kadaba²  Jaeda Patton³  Robert Terrell³  Mitch Corson³  Timothy J. Durham³  Soo Park⁴  Swapna Samanta¹  Mei Han¹  Jinrui Xu⁵  Koon-Kiu Yan⁵  Susan E. Celniker⁴  Kevin P. White²  Lijia Ma²  Mark Gerstein⁵  Valerie Reinke¹  Robert H. Waterston³ 

[1] Department of Genetics,Yale University, New Haven, Connecticut 06520;Program in Computational Biology and Bioinformatics,Yale University, New Haven, Connecticut 06520;Department of Molecular Biophysics and Biochemistry,Yale University, New Haven, Connecticut 06520;Department of Computer Science, Yale University, New Haven, Connecticut 06520;Institute for Genomics and Systems Biology, Department of Human Genetics, University of Chicago, Illinois 60637;Department of Genome Sciences,University of Washington School of Medicine, Seattle, Washington 98195;Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California 94720

关键词: Drosophila;    Caenorhabditis elegans;    transcription factors;    binding sites;    regulation;   

DOI  :  10.1534/genetics.117.300657

学科分类：医学（综合）

来源: Genetics Society of America

【 摘 要 】

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.

【 授权许可】

CC BY