| Abstrakt: |
The conserved nuclear factor I (NFl) family of transcription factors is unique to animals and essential for mammalian development The Caenothabditis elegans genome encodes a single NFl family member, whereas vertebrate genomes encode 4 distinct NFl protein subtypes (A. B, C, and X). NFl-1-deficient worms exhibit abnormalities, including reduced lifespan, defects in movement and pharyngeal pumping, and delayed egg-laying. To explore the functional basis of these phenotypes, we sought to comprehensively identify NFl-1-bound loci in C elegans. We first established NFl-1 DNA-binding specificity using an in vitro DNA-selection strategy. Analysis yielded a consensus motif of TTGGCA(NhTGCCAA, which occurs 586 times in the genome, a 100-fold higher frequency than expected. We next asked which sites were occupied by NFl-1 in vivo by performing chromatin immunoprecipitation of NFl-1 followed by microarray hybridization. Only 55 genomic locations were identified, an unexpectedly small target set. In vivo NFl-1 binding sites tend to be upstream of genes involved in core cellular processes, such as chromatin remodeling, mRNA splicing, and translation. Remark- ably, 59 out of 70 (84%) of the C briggsae orthologs of the identified targets contain conserved NFl binding sites in their promoters. These experiments provide a foundation for understanding how NFl-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif. [ABSTRACT FROM AUTHOR] |
