Genomic investigation of SREBP family transcription factors using ChIP-chip and ChIP-seq

Sterol regulatory element-binding protein (SREBP) family transcription factors control the expression of genes involved in lipid homeostasis and play critical roles in diet-related diseases. Although numerous studies have identified important lipogenic genes that are regulated by SREBPs, our understanding of the targets of SREBPs is incomplete and the role of SREBPs in other pathways is poorly understood. Furthermore, our understanding of the manner in which SREBPs regulate their target genes in combination with other transcriptional regulators is limited. To investigate these questions and gain additional insight into the functions of SREBPs, we have performed the first genome-wide studies of these factors by mapping their genomic binding sites using chromatin IP followed by either microarray analysis (ChIP-chip) or next-generation DNA sequencing (ChIP-seq).;Using ChIP-chip analysis in insulin-treated HepG2 cells, we have demonstrated that SREBP1 occupies the promoters of 1,141 genes involved in diverse biological pathways and identified a conserved DNA binding motif in SREBP1 target promoters. We have also shown that many SREBP1 target genes are transcriptionally activated by treatment with insulin and glucose using gene expression microarrays. Finally, by profiling the binding sites of NFY and SP1, we have demonstrated that SREBP1 regulates different classes of genes in a combinatorial manner with these key network partners.;In HepG2 cells subjected to cholesterol deprivation, we used Ch1P-seq to generate binding profiles for both SREBP1a and SREBP2 across the entire genome. Our results revealed that SREBP1a and SREBP2 localize to 1,164 and 815 genomic binding sites, respectively. Many sites are co-occupied by both factors, providing the first evidence that co-occupation by SREBP1a and SREBP2 is widespread in vivo. We also demonstrated that, in addition to promoters, SREBPs occupy a subset of predicted distal enhancer elements. Using the high-resolution binding data, we identified an enriched 10 bp DNA sequence motif corresponding to the sterol regulatory element (SRE), greatly expanding the number of these key elements annotated in the genome. In agreement with the binding data, gene expression analysis revealed that many SREBP-occupied genes are regulated by cholesterol levels. Our results provide novel insight into the genome-wide functions and regulatory circuitry of SREBPs and their role in human health and disease.