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 pathway-mediated 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.

Keywords: ATAC-seq; chromatin; genome-editing; inflammation; interleukin-1.

Figure 1.

ATAC-seq identified peaks in IL-1-stimulated chondrocytes

Figure 2.

Correlation between differentially accessible chromatin regions and gene expression changes

Figure 3.

Effect of Cas9-mediated putative enhancer deletion on IL-1-induced gene expression

Figure 4.

Effect of enhancer-targetted Cas9-VPR on gene expression

Figure 5.

Enhancer activity of differentially accessible chromatin regions