HNF4A is required to specify glucocorticoid action in the liver
Description
The glucocorticoid receptor (GR) is a nuclear hormone receptor critical to the regulation of energy metabolism and the inflammatory response. The actions of GR are highly dependent on cell type and environmental context. Here, we demonstrate the necessity for liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver-specificity of GR action. In normal mouse liver, the HNF4 motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites found within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodelled, with both loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites leads to loss of GR binding at weak GRE motifs. GR binding and chromatin accessibility are gained at sites characterised by strong GRE motifs, which typically show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is further demonstrated by evidence of an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver. This Mendeley Data repository contains supportive data and code for our paper. Methods are described in the text. All experiments conducted on mouse (Mus musculus) liver, all processed data derived from raw sequencing data aligned to the mm10 genome. Differential GR binding analysis incorporated spike-in normalisation (spiked-in Drosophila melanogaster chromatin; reads aligned to dm6 genome). The "MACS2 GR ChIP-seq peaks, wildtype liver" folder contains the BED files for GR ChIP-seq peaks called in dexamethasone- or vehicle-treated mouse liver (Figures 1 & S1). The "Output of differential binding and differential expression analyses" folder contains the edgeR, stageR and csaw output, following the methods described in the text, using the code in the "Code for differential binding, differential accessibility and differential expression analyses" folder (Figures 2, 5, S3). The "HOMER motif discovery" folder contains screenshots of the output from HOMER (http://homer.ucsd.edu/homer/ngs/peakMotifs.html) motif discovery analysis of GR binding sites and sites of differential chromatin accessibility (Figures 1, S1, 2, 4). The "GIGGLE output" folder contains the output (csv) from GIGGLE analysis of GR binding sites, run through the Cistrome DB Toolkit portal (http://dbtoolkit.cistrome.org/) (Figure 3). The "Output of csaw differential accessibility analysis" folder contains the output from csaw analysis of ATAC-seq data (Figure 4).