Binding of NF-κB to Nucleosomes: Effect of Translational Positioning, Nucleosome Remodeling and Linker Histone H1

Abstract

NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A–H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes.

Transcriptional Control of Inflammatory Responses

“…However, an initial report suggested the surprising notion that the nucleosome does not even minimally impair NF-kB binding (Angelov et al 2004). This apparent inconsistency was probably because of the experimental conditions used in these early experiments, which in fact relaxed octamer-DNA association and made underlying binding sites accessible to NF-kB (Lone et al 2013). Taken together, data are consistent with the notion that the DNAbinding mode of NF-kB makes it unable to contact sites associated with, and occluded by, nucleosomes.…”

Disruption of hSWI/SNF complexes in T cells by WAS mutations distinguishes X-linked thrombocytopenia from Wiskott-Aldrich syndrome

“…specific binding of NF-kB, 53 we propose that WASp through its effects on H2A-to-H2A.Z exchange facilitates NF-kB binding to gene promoters in T H 1 cells. Therefore, BRG1, whose enrichment at T H 1-gene promoters is unaffected, cannot substitute for the lost hBRM functions during T H 1 transcriptional-reprogramming.…”

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

“…For instance, binding sites for NF-κB, which controls the rapid induction of hundreds of inflammatory genes, showed their maximal relative enrichment in the higher deciles. Since NF-κB binding is greatly impaired by nucleosomes (Lone et al, 2013), the preferential inclusion of its binding sites within sequences that promote nucleosomal occupancy may provide the basis for a tight enforcement of its recruitment to regulatory sequences.…”