ArticleGenome research2014
Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
94 citing papers in PubMed, 1 synthesis or guideline pooled it, 166 citations in OpenAlex.
- Identification of host gene-microbiome associations in colorectal cancer patients using mendelian randomization.Journal of translational medicine · 2023Pooled it
- Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue.Physiological genomics · 2016Trial
- Microbial epigenetic regulation as a multilevel regulatory interface in host-microbe interactions.Gut microbes · 2026Review
- Host genotypes interact with microbial communities to modulate gene expression in the human intestine.medRxiv : the preprint server for health sciences · 2026Article
- Genomics of host-microbiome interactions in humans.Nature reviews. Genetics · 2026Review
- Article
- Intratumoral Microbiota Correlates with AP-2 Expression: A Pan-Cancer Map with Cohort-Specific Prognostic and Molecular Footprints.International journal of molecular sciences · 2025Article
- Host transcriptional responses to gut microbiome variation arising from urbanism.bioRxiv : the preprint server for biology · 2025Article
- A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma.Nature biomedical engineering · 2025Article
- Article
- Metagenome-guided culturomics for the targeted enrichment of gut microbes.Nature communications · 2025Article
- Covariation Between Microbiome Composition and Host Transcriptome in the Gut of WildEcology and evolution · 2025Article
- Early subclinical stages of the inflammatory bowel diseases: insights from human and animal studies.American journal of physiology. Gastrointestinal and liver physiology · 2025Review
- Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome.bioRxiv : the preprint server for biology · 2024Article
- Article
- Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.Scientific reports · 2024Article
- Article
- The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally.Cell reports · 2024Article
- Coping with extremes: the rumen transcriptome and microbiome co-regulate plateau adaptability of Xizang goat.BMC genomics · 2024Article
- Gut microbiota and interstitial cystitis: exploring the gut-bladder axis through mendelian randomization, biological annotation and bulk RNA sequencing.Frontiers in immunology · 2024Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 3 institutions in 1 country.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.