Transcriptional integration of separated and simultaneous microbial and nutritional signals by the intestinal epithelium

We performed RNA-seq, H3K27ac ChIP-seq, and HNF4a ChIP-seq on jejunal intestinal epithelial cells, which are primarily responsible for the absorption of fatty acids, in four conditions: Germ-free (GF), Germ-free plus high fat meal (GF+HFM), ex-GF colonized with a conventional microbiota for 2 weeks (Colonized, CV), and Colonized plus high fat meal (CV+HFM). We, for the first time, map genomewide HFM responsive regulatory regions in the intestine. We identify that in the absence of microbes the HNF4a transcriptional program supports a FAO program in enterocytes while suppressing a proliferation program. Generation and analysis of RNA-seq, H3K27ac ChIP-seq, and Hnf4a ChIP-seq from primary IECs isolated from the jejunum of Germ-Free (GF), Colonized (CV), Germ-Free+High Fat Meal (GF+HFM), and CV+HFM (Colonized+High Fat Meal) mice.