Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation

Abstract

Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathwaymediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA, in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.

SIAH ubiquitin E3 ligases as modulators of inflammatory gene expression

“…The majority of proteins within this network of functional, physical and genetic interactions serve as inflammatory cytokines (including IL-1α and IL-6), signal transducers or transcription factors. The data are also consistent with a model suggesting that SIAH1/SIAH2 do not provide a contribution for upstream signaling cascades or basal gene expression and rather affect IL-1α-regulated gene expression, which is also under the control of several other regulatory circuitries [15,17,18,19]. Consistently, SIAH1 has been frequently identified as an interactor of transcription factors (RUNX1, RARα, KLF10 and STAT3), factors important for posttranscriptional gene regulation and also transcriptional co-regulators such as HIPK2 and the acetyl transferase CBP/p300 [4,24,25,26,27].…”

“…Inflammatory gene expression also requires the regulated activity of cofactors that are not relevant for cytosolic signaling and rather shape the chromatin compaction or transcription cycles of individual inflammatory target genes [ 15 , 17 , 18 , 19 , 20 ]. Thus, the lack of effect of SIAH1/2 suppression on the IL-1α-mediated upstream pathways does not pre-clude downstream effects of SIAH1/2 on gene expression.…”

Monitoring the Levels of Cellular NF-κB Activation States

“…Figure 6 B provides an example of ChIP-seq, ATAC-seq, and RNA-seq data derived from human epithelial carcinoma cells which were combined to reveal four regions of strong IL-1α-inducible p65 binding (three of which contain a predicted NF-κB motif) to the inducible enhancers and promoters of the prototypical NF-κB target gene CXCL8 ( IL8) [ 62 , 65 ]. Enhancers and promoters show already constitutively open and some inducible regions with increased chromatin accessibility based on ATAC-seq peaks, a transposase-based approach that yields information on chromatin accessibility [ 105 , 106 ].…”

The proximity-based protein interaction landscape of the transcription factor p65 NF-κB / RELA and its gene-regulatory logics

“…The pro-inflammatory cytokine interleukin-1 (IL-1) rapidly activates p65 / RELA in a broad range of cell types (Meier-Soelch et al, 2021). Numerous studies, including our own work, have shown the importance of p65 / RELA for the expression of IL-1-target genes, rendering this system an ideal model to study the dynamic p65 / RELA interactome (Barter et al, 2021;Jurida et al, 2015;Weiterer et al, 2020).…”