The genomic distribution and function of NFI and histone variant H2A.Z during Caenorhabditis elegans development

Development relies on precise spatial and temporal access of the transcription regulatory machinery to genomic information. Throughout development, transcription factors bind a discrete set of specific targets that cannot be predicted through sequence alone. Identification and access to regulatory elements is heavily influenced by the heterogeneous chromatin landscape that packages eukaryotic genomes. Local chromatin environments may specify a genomic index of sequence availability and genome function. To begin to examine this genomic index in development, I mapped the occupancy of a developmentally essential variant histone, H2A.Z, and a model transcription factor, NFI-1.;In one of the first utilizations of Chromatin ImmunoPrecipitation on genomic DNA microarrays (ChIP-chip) in C. elegans, I show that the histone variant H2A.Z occupies a subset of promoters that tend to be required for development and occupied by RNA Polymerase II. As in other metazoans, we show that C. elegans H2A.Z is required for proper development. H2A.Z identifies transcription start sites in both canonical genes and genes likely to be independently regulated within operons. Fewer sites of H2A.Z occupancy exist on the X chromosome, though the data suggests no direct role for H2A.Z in dosage compensation. Our data suggests H2A.Z plays a vital role in establishing or maintaining a specialized chromatin environment at developmental promoters.;We then mapped the in vivo binding of the animal-specific transcription factor, NFI. Despite a overabundance of the discovered binding motif in the genome, NFI binds few sites in vivo. There is little difference in the in vitro and in vivo sequence affinity of NFI. In vivo NFI sites have low nucleosome occupancy, suggesting that nucleosomes positioned at NFI binding sites may be susceptible to loss. C. elegans NFI targets are conserved, and 84% of the C. briggsae homologs have NFI promoter motifs. This study provides a basis for understanding NFI function and recruitment to a paucity of in vivo sites, despite an abundance of sequence motifs.;These studies present the first genome-wide maps of a chromatin component and transcription factor in C. elegans and provide a foundation for future studies of chromatin and transcription factor-genome interactions in a native developmental context.