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Zhao, Bo; Barrera, Luis A.; Ersing, Ina; Willox, Bradford; Schmidt, Stefanie C.S.; Greenfeld, Hannah; Zhou, Hufeng; Mollo, Sarah B.; Shi, Tommy T.; Takasaki, Kaoru; Jiang, Sizun; Cahir-McFarland, Ellen; Kellis, Manolis; Bulyk, Martha L.; Kieff, Elliott; Gewurz, Benjamin E.
Cell reports, 09/2014, Letnik: 8, Številka: 5Journal Article
The nuclear factor κB (NF-κΒ) subunits RelA, RelB, cRel, p50, and p52 are each critical for B cell development and function. To systematically characterize their responses to canonical and noncanonical NF-κB pathway activity, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analysis in lymphoblastoid B cell lines (LCLs). We found a complex NF-κB-binding landscape, which did not readily reflect the two NF-κB pathway paradigms. Instead, 10 subunit-binding patterns were observed at promoters and 11 at enhancers. Nearly one-third of NF-κB-binding sites lacked κB motifs and were instead enriched for alternative motifs. The oncogenic forkhead box protein FOXM1 co-occupied nearly half of NF-κB-binding sites and was identified in protein complexes with NF-κB on DNA. FOXM1 knockdown decreased NF-κB target gene expression and ultimately induced apoptosis, highlighting FOXM1 as a synthetic lethal target in B cell malignancy. These studies provide a resource for understanding mechanisms that underlie NF-κB nuclear activity and highlight opportunities for selective NF-κB blockade. Display omitted •A complex NF-κB genomic landscape results from activation of both NF-κB pathways•Ten promoter and 11 enhancer NF-κB subunit-binding patterns are observed•One-third of NF-κB sites lack a κB motif and are enriched for other motifs•FOXM1 is recruited to half of κB sites and forms a complex with NF-κB on DNA ChIP-seq analysis of the five NF-κB subunits reveals a complex NF-κB-binding landscape in B cells, where the canonical and noncanonical NF-κB pathways are persistently active. Zhao et al. identify 10 promoter and 11 enhancer subunit-binding profiles, absence of κB motifs at one-third of these sites, alternative motifs enriched at sites that lack κB motifs, frequent recruitment of FOXM1 to NF-κB sites, and an important role for FOXM1 as an NF-κB coactivator.
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