TNFα signalling primes chromatin for NF-κB binding and induces rapid and widespread nucleosome repositioning

Abstract

BackgroundThe rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signalling reshapes the chromatin landscape, in three-dimensional space and over time, to allow establishment of new transcriptional programs.ResultsUsing micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFα) - a proinflammatory cytokine that signals through nuclear factor kappa-B (NF-κB). Within 10 min, nucleosomes reposition at regions both proximal and distal to NF-κB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFα-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 min, widespread repositioning throughout megabase pair-long chromosomal segments, with consequential effects on three-dimensional structure (detected using chromosome conformation capture), is seen.ConclusionsWhilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFα-induced priming mechanism, mostly independent of NF-κB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0536-6) contains supplementary material, which is available to authorized users.

Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response

“…In human endothelial cells, proinflammatory stimulation is linked to both acute and chronic disorders (Libby et al 2011;Brown et al 2014), and we previously used these cells to characterize the dynamic clustering of NF-κB-regulated genes in 3D space , and global chromatin "priming" prior to NF-κB-dependent transcription (Diermeier et al 2014). Here, we study the still-elusive properties of how the new proinflammatory transcriptional program is integrated in the pre-existing one in 3D space and over time.…”

Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

“…While NF-B is not thought to be a 'pioneering factor', i.e. a transcription factor able to initiate chromatin remodelling, evidence does support a role for the factor in changing the nucleosome landscape at activated loci [33,34]. The second most enriched motif in IL-1 increased accessible regions was IRF1, interferon regulatory factor 1, a factor that increases with IL-1 stimulation [35].…”

Role of Dendritic Cell–Pathogen Interactions in the Immune Response to Pulmonary Cryptococcal Infection

“…Exciting new work from Diermeier et al has shown that TNF-α signaling directly changes chromatin structure around NF-κB-associated gene regions [191]. MAPK signaling has been shown to be required for IL-1β production in DCs [189] and MHCII expression in macrophages [192].…”