RT Journal
A1 Camp, J. Gray
A1 Frank, Christopher L.
A1 Lickwar, Colin R.
A1 Guturu, Harendra
A1 Rube, Tomas
A1 Wenger, Aaron M.
A1 Chen, Jenny
A1 Bejerano, Gill
A1 Crawford, Gregory E.
A1 Rawls, John F.
T1 Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape
JF Genome Research 
JO Genome Research 
YR 2014 
FD September 01 
VO 24 
IS 9 
SP 1504 
OP 1516 
DO 10.1101/gr.165845.113 
UL http://genome.cshlp.org/content/24/9/1504.abstract 
AB 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 preprogrammed by the host in a region-specific manner to permit responses to microbiota through binding of open CRRs by specific TFs.