Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha (Mouse ChIP-seq, RNA-seq, and DNase-seq)

We profiled transcriptome and chromatin landscapes in jejunal mouse intestinal epithelial cells (IECs) from mice reared in the absence (Germ Free or GF) or presence (Conventionalized or CV) of microbiota. We show that microbiota colonization results in changes in histone modifications at hundreds of enhancers that are associated with microbiota-regulated genes. Furthermore, we show that microbiota colonization is associated with a drastic genome-wide reduction in Hnf4a and Hnf4g binding. Generation and analysis of RNA-seq, DNase-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, Hnf4a ChIP-seq, and Hnf4g ChIP-seq datasets from primary IECs isolated from the jejunum of GF and CV mice.