The model organism C. elegans has many features that make it ideal for mapping functional elements encoded in its genome. We propose to build a genome-wide map of the binding sites for every C. elegans transcription factor. Moreover, over the course of this project, we will identify the exact localization of every transcription factor at single-cell resolution. These studies will be critical for deciphering the regulatory information housed in the genome to direct development and homeostasis. To maximize quality, speed, and comprehensiveness of the data collection, we have assembled a highly qualified team with extensive experience in performing the proposed goals, and developed a streamlined procedure for implementing these goals. First, we will make constructs in which each transcription factor is fused to a dual Myc-mCherry fluorescent tag. These constructs will be used to generate transgenic strains that express each tagged transcription factor at endogenous levels and locations. We will examine the temporal and spatial expression of each factor and determine its precise location using automated imaging techniques. Based on the optimal expression of each factor, we will perform genome-wide mapping of its binding sites in vivo using chromatin immunoprecipitation (ChIP) followed by hybridization to a microarray containing probes distributed across the entire genome. These binding data will be validated by multiple methods, including quantitative PCR of ChIP samples, expression analysis in transcription factor knockout strains, and mutational analysis of candidate binding sites in transgenic reporters. We will perform bioinformatic analysis to identify regulatory motifs and compare motifs between factors. All data generated from this project will be stored in a web-accessible in-house database for use by the scientific community, and incorporated into the modENCODE consortium database and Wormbase.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project--Cooperative Agreements (U01)
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Special Emphasis Panel (ZHG1-HGR-P (J3))
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Feingold, Elise A
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Stanford University
Schools of Medicine
United States
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Weicksel, Steven E; Mahadav, Assaf; Moyle, Mark et al. (2016) A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans. Development 143:3540-3548
Araya, Carlos L; Kawli, Trupti; Kundaje, Anshul et al. (2014) Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature 512:400-5
Dewey, Frederick E; Grove, Megan E; Pan, Cuiping et al. (2014) Clinical interpretation and implications of whole-genome sequencing. JAMA 311:1035-45
Boyle, Alan P; Araya, Carlos L; Brdlik, Cathleen et al. (2014) Comparative analysis of regulatory information and circuits across distant species. Nature 512:453-6
Kasper, Dionna M; Wang, Guilin; Gardner, Kathryn E et al. (2014) The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev Cell 31:145-58
Sarov, Mihail; Murray, John I; Schanze, Kristin et al. (2012) A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell 150:855-66
Niu, Wei; Lu, Zhi John; Zhong, Mei et al. (2011) Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res 21:245-54
Zhong, Mei; Niu, Wei; Lu, Zhi John et al. (2010) Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet 6:e1000848
Lei, Haiyan; Fukushige, Tetsunari; Niu, Wei et al. (2010) A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One 5:e15898