DNA-binding specificity and in vivo targets of Caenorhabditis elegans nuclear factor I.
The conserved nuclear factor I (NFI) family of transcription factors is unique to animals and essential for mammalian development. The Caenorhabditis elegans genome encodes a single NFI family member, whereas vertebrate genomes encode 4 distinct NFI protein subtypes (A, B, C, and X). NFI-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 NFI-1-bound loci in C. elegans. We first established NFI-1 DNA-binding specificity using an in vitro DNA-selection strategy. Analysis yielded a consensus motif of TTGGCA(N)(3)TGCCAA, which occurs 586 times in the genome, a 100-fold higher frequency than expected. We next asked which sites were occupied by NFI-1 in vivo by performing chromatin immunoprecipitation of NFI-1 followed by microarray hybridization. Only 55 genomic locations were identified, an unexpectedly small target set. In vivo NFI-1 binding sites tend to be upstream of genes involved in core cellular processes, such as chromatin remodeling, mRNA splicing, and translation. Remarkably, 59 out of 70 (84%) of the C. briggsae orthologs of the identified targets contain conserved NFI binding sites in their promoters. These experiments provide a foundation for understanding how NFI-1 is recruited to unexpectedly few in vivo sites to perform its developmental functions, despite a vast over-representation of its binding motif.
Whittle
Christina M
CM
Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
Lazakovitch
Elena
E
Gronostajski
Richard M
RM
Lieb
Jason D
JD
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000378:metabolism*; D016384:Consensus Sequence; D017124:Conserved Sequence; D018509:DNA, Helminth / Q000378:metabolism*; D017238:Genes, Helminth; D016678:Genome / Q000235:genetics; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D051839:NFI Transcription Factors / Q000737:chemistry / Q000378:metabolism*; D009707:Nucleosomes / Q000378:metabolism; D011485:Protein Binding; D017386:Sequence Homology, Amino Acid; D014714:Vertebrates
D029742:Caenorhabditis elegans Proteins; D018509:DNA, Helminth; D051839:NFI Transcription Factors; D009707:Nucleosomes; C543045:nfi-1 protein, C elegans