Mapping and Analysis of Caenorhabditis elegans Transcription Factor Binding Specificities

The nematode Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been hampered by the fact that DNA binding motifs are known for only 71 (9%) of the estimated 763 high-confidence sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray (PBM) experiments on representatives of canonical TF families in the C. elegans TF repertoire, obtaining motifs for 129 distinct TFs. Moreover, we can infer motifs for 97 additional TFs that have DNA binding domains that are very similar to those already characterized, resulting in a total coverage of binding specificities for almost 40% of the C. elegans TF repertoire. These data highlight the diversification of binding motifs for the nuclear hormone receptor (NHR) and C2H2 zinc finger families, and reveal unexpected diversity of motifs for others, including the T-box and DM families. Enrichment of motifs in the promoters of functionally related genes is consistent with known biology in many cases, and also identifies putative new regulatory roles for poorly characterized TFs. The motifs are available at http:// http://cisbp.ccbr.utoronto.ca. Protein binding microarray (PBM) experiments were performed for a set of 129 diverse C. elegans transcription factors. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.