title: Characterization of genome-wide binding of NF-κB in TNFα-stimulated HeLa cells.
abstract: 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.
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Xing
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.forename: Fei
authors.initials: F
authors.lastname: Zhou
authors.forename: Jinke
authors.initials: J
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000187:drug effects; D015894:Genome, Human; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016328:NF-kappa B / Q000378:metabolism*; D059372:Nucleotide Motifs; D011485:Protein Binding; D024363:Transcription Initiation Site; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology*
chemical_list: D016328:NF-kappa B; D014409:Tumor Necrosis Factor-alpha; D004247:DNA
keywords: 4-(2-hydroxyethyl) piperazine-1-ethanesulfonic acid; ChIP; ChIP in combination with DNA microarray; ChIP in combination with paired end tag; ChIP in combination with polymerase chain reaction; ChIP in combination with sequencing; ChIP-PCR; ChIP-PET; ChIP-Seq; ChIP-chip; DBP; DMEM; DNA binding profile; DTG; DTT; Dulbecco's Modified Eagle Medium; EDTA; EMSA-Seq; FBS; FC; FE; Genome-wide binding; HC-peak; HEPES; LPS; NF-κB; PCR; PIC; PMSF; TES; TNFα; TSS; chromatin immunoprecipitation; direct target genes; dithiothreitol; electrophoresis mobility shift assay in combination with sequencing; ethylenediaminetetraacetic acid; fetal bovine serum; fold change; fold enrichment; high-confidence peak; lipopolysaccharide; nuclear factor kappa B; phenylmethylsulfonyl fluoride; polymerase chain reaction; protease inhibitor cocktail; siRNA; small interfering RNA; transcription end site; transcription start site; tumor necrosis factor-alpha