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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 07, 2014 |
| Title |
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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 organization. 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.
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| Overall design |
mRNA and accessible chromatin (DNase-seq) profiles from colonic and ileal IECs were compared between conventionally-raised (CR), germ-free (GF), and conventionalized (CV) C57BL/6 mice.
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| Contributor(s) |
Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF |
| Citation(s) |
24963153 |
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| Submission date |
May 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher L Frank |
| E-mail(s) |
chris.frank21@gmail.com
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| Organization name |
Duke University
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| Lab |
Gregory Crawford
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| Street address |
101 Science Dr.
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (39)
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| Relations |
| BioProject |
PRJNA248410 |
| SRA |
SRP042206 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57919_RAW.tar |
18.4 Gb |
(http)(custom) |
TAR (of BIGWIG, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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