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| Status |
Public on Nov 28, 2016 |
| Title |
Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes |
| Organism |
Mus musculus |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The gut microbiota impacts many aspects of host biology including immune function. One hypothesis is that microbial communities induce epigenetic changes with accompanying alterations in chromatin accessibility, providing a mechanism that allows a community to have sustained host effects even in the face of its structural or functional variation. We used ATAC-seq to define chromatin accessibility in predicted enhancer regions of intestinal αβ+ and γδ+ intraepithelial lymphocytes (IELs) purified from germ-free mice, their conventionally-raised (CONV-R) counterparts, and mice reared GF and then colonized with a CONV-R gut microbiota at the end of the suckling-weaning transition. Characterizing genes adjacent to traditional enhancers and super-enhancers revealed signaling networks, metabolic pathways, and enhancer-associated transcription factors affected by the microbiota. Our results support the notion that epigenetic modifications help define microbial community-affiliated functional features of host immune cell lineages.
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| Overall design |
We interrogated chromatin accessibility using ATAC-seq in four cell types derived from mice (CD4+ T cells, CD8+ T cells, αβ+ intraepithelial lymphocytes, and γδ+ intraepithelial lymphocytes), across three gut microbial colonization states (germ-free, conventionally-raised, and conventionalized).
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| Contributor(s) |
Gordon JI, Semenkovich NP |
| Citation(s) |
27911843 |
| Submission date |
Nov 08, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey Gordon |
| Organization name |
Washington University
|
| Department |
Center for Genome Sciences & Systems Biology
|
| Street address |
4515 McKinley Research Building
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (91)
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| Relations |
| BioProject |
PRJNA352791 |
| SRA |
SRP092893 |
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