Abstract Our project seeks to identify the regulatory elements recognized by essentially all of transcription factors (TFs) in the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Transcription factors (TFs) play key roles in diverse aspects of development and physiology. A catalog of sites where transcription factors bind (regulatory sequences) is perhaps only second in importance to a catalog of genes in understanding how a genome specifies an organism. First as part of modENCODE and over the past grant cycle as the independent modern program, we will have generated about 800 ChIP-seq profiles (440 worm, 380 fly) for more than 600 transcription factors (280 worm, 340 fly). Building on this progress in this proposal we seek: 1) to complete an initial catalog of binding sites for all transcription factors in both D. melanogaster and C. elegans; 2) to validate these sites through measuring the impact of transcription factor loss on the expression of genes; 3) to integrate binding sites and gene expression profiles both with one another and with other available information to develop models of gene expression and gene regulatory networks. All of the strain resources and data will be made publicly available on a timely basis throughout the project. These catalogs will represent the first comprehensive description of the TF binding sites in any metazoan and will provide a context for understanding the catalog of TF binding sites that will emerge from ENCODE.