Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
- J. Gray Camp1,
- Christopher L. Frank2,
- Colin R. Lickwar2,
- Harendra Guturu1,
- Tomas Rube1,
- Aaron M Wenger1,
- Jenny Chen1,
- Gill Bejerano1,
- Gregory E. Crawford2 and
- John F Rawls2,3
- ↵* Corresponding author; email: john.rawls{at}duke.edu
Abstract
Microbiota regulate intestinal physiology by modifying host gene expression along the length of the intestine but the underlying regulatory mechanisms remain unresolved. Transcriptional specificity occurs through interactions between transcription factors (TFs) and cis-regulatory regions (CRRs) characterized by nucleosome-depleted accessible chromatin. We profiled transcriptome and accessible chromatin landscapes in intestinal epithelial cells (IECs) from mice reared in the presence or absence of microbiota. We show that regional differences in gene transcription along the intestinal tract were accompanied by major alterations in chromatin accessibility. Surprisingly, we discovered that microbiota modify host gene transcription in IECs without significantly impacting the accessible chromatin landscape. Instead, microbiota regulation of host gene transcription might be achieved by differential expression of specific TFs and enrichment of their binding sites in nucleosome depleted CRRs near target genes. Our results suggest that the chromatin landscape in IECs is pre-programmed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs.
- Received August 29, 2013.
- Accepted June 6, 2014.
- Published by Cold Spring Harbor Laboratory Press
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