Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.

Journal Article (Journal Article)

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.

Full Text

Duke Authors

Cited Authors

  • Camp, JG; Frank, CL; Lickwar, CR; Guturu, H; Rube, T; Wenger, AM; Chen, J; Bejerano, G; Crawford, GE; Rawls, JF

Published Date

  • September 2014

Published In

Volume / Issue

  • 24 / 9

Start / End Page

  • 1504 - 1516

PubMed ID

  • 24963153

Pubmed Central ID

  • PMC4158762

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

Digital Object Identifier (DOI)

  • 10.1101/gr.165845.113


  • eng

Conference Location

  • United States