Impact of the gut microbiota on enhancer accessibility in gut intraepithelial lymphocytes

Nicholas P. Semenkovich, Joseph D. Planer, Philip P. Ahern, Nicholas W. Griffin, Charles Y. Lin, Jeffrey I. Gordon

Research output: Contribution to journalArticle

15 Scopus citations


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 Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to define chromatin accessibility in predicted enhancer regions of intestinal αβ+ and γδ+ intraepithelial lymphocytes purified from germ-free mice, their conventionally raised (CONV-R) counterparts, and mice reared germ free and then colonized with 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.

Original languageEnglish
Pages (from-to)14805-14810
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number51
StatePublished - Dec 20 2016


  • ATAC-seq
  • Enhancers of gut intraepithelial lymphocytes
  • Gnotobiotic mice
  • Gut microbiota-immune cell interactions
  • Transcription factors

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