Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells

- NF-κB binds different chromosomes and chromosome regions with great differences.
- NF-κB binds intronic region with high preference.
- NF-κB binds a vast majority of target genes with multiple κB sites.
- NF-κB binds astonishing numbers of genes in the human genome.
- NF-κB binds more target genes through non-canonical κB sites.

This study characterized the genome-wide binding of NF-κB RelA with ChIP-Seq and explored its effects on the gene transcription with DNA microarray. It was found that NF-κB showed several significant binding characteristics, including the inter- and intra-chromosomal differential high-fold enrichment binding, the dominant intronic binding to vast majority of target genes through multiple ChIP-seq peaks and κB sites, extensively binding to large number of genes in the human genome, and binding its target genes more broadly through noncanonical κB sites than canonical κB sites. These in vivo genome-wide binding characteristics exerted effects on the transcription of its direct target genes in genome, reflecting some important traits of this protein which acts as a stimulatory transcription factor involving in many biological processes and responding to various internal and external stimuli.