[HTML][HTML] The NF-κB genomic landscape in lymphoblastoid B cells

B Zhao, LA Barrera, I Ersing, B Willox, SCS Schmidt… - Cell reports, 2014 - cell.com
B Zhao, LA Barrera, I Ersing, B Willox, SCS Schmidt, H Greenfeld, H Zhou, SB Mollo, TT Shi…
Cell reports, 2014cell.com
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 …
Summary
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.
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