Database Commons

a catalog of worldwide biological databases

In order to develop a catalog of regulatory sites in two major model organisms, Drosophilia melanogaster and Caenorhabditis elegans, the modERN consortium has systematically assayed the binding sites of transcription factors (TFs). Combined with data produced by our predecessor, modENCODE, we now have data for 262 TFs identifying 1.23M sites in the fly genome and 217 TFs identifying 0.67M 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 Mb and 5.8 Mb in the two organisms. Clusters with large numbers of sites (so-called 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 ChIP-seq data are available through the ENCODE DCC, and also through a simple interface (http://epic.gs.washington.edu/modERN/) that facilitates rapid accessibility of processed datasets. These data will facilitate a vast number of scientific inquiries into the fuction of individual TFs in key developmental, metabolic, 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 lifespans of these two key model organisms.