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

Publication ,  Journal Article
Camp, JG; Frank, CL; Lickwar, CR; Guturu, H; Rube, T; Wenger, AM; Chen, J; Bejerano, G; Crawford, GE; Rawls, JF
Published in: Genome Res
September 2014

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.

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Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

September 2014

Volume

24

Issue

9

Start / End Page

1504 / 1516

Location

United States

Related Subject Headings

  • Transcriptome
  • Transcription, Genetic
  • Transcription Factors
  • Promoter Regions, Genetic
  • Organ Specificity
  • Microbiota
  • Mice, Inbred C57BL
  • Mice
  • Intestinal Mucosa
  • Chromatin Assembly and Disassembly
 

Citation

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Camp, J. G., Frank, C. L., Lickwar, C. R., Guturu, H., Rube, T., Wenger, A. M., … Rawls, J. F. (2014). Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res, 24(9), 1504–1516. https://doi.org/10.1101/gr.165845.113
Camp, J Gray, Christopher L. Frank, Colin R. Lickwar, Harendra Guturu, Tomas Rube, Aaron M. Wenger, Jenny Chen, Gill Bejerano, Gregory E. Crawford, and John F. Rawls. “Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.Genome Res 24, no. 9 (September 2014): 1504–16. https://doi.org/10.1101/gr.165845.113.
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, et al. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 2014 Sep;24(9):1504–16.
Camp, J. Gray, et al. “Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.Genome Res, vol. 24, no. 9, Sept. 2014, pp. 1504–16. Pubmed, doi:10.1101/gr.165845.113.
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res. 2014 Sep;24(9):1504–1516.

Published In

Genome Res

DOI

EISSN

1549-5469

Publication Date

September 2014

Volume

24

Issue

9

Start / End Page

1504 / 1516

Location

United States

Related Subject Headings

  • Transcriptome
  • Transcription, Genetic
  • Transcription Factors
  • Promoter Regions, Genetic
  • Organ Specificity
  • Microbiota
  • Mice, Inbred C57BL
  • Mice
  • Intestinal Mucosa
  • Chromatin Assembly and Disassembly