ArticlePLoS biology2017
Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells.
Article in PLoS biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 134 citations in OpenAlex.
- Article
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- Rank-dependent control of tuft and BEST4 cell development in the intestine.Nature communications · 2026Article
- Prenatal and postnatal effects of gestational immune activation on synaptic and neurodevelopmental pathways via epigenetic mechanisms.Translational psychiatry · 2026Article
- Comparative transcriptomics reveal the common anteroposterior molecular blueprint of adult bilaterian guts.PLoS biology · 2026Article
- TheMicrobiology and molecular biology reviews : MMBR · 2025Review
- Article
- Novel and unscrutinized immune entities of the zebrafish gut.FEBS letters · 2025Review
- Identification of intestinal enteroendocrine cell subtypes and their associated hormones in zebrafish.PLoS biology · 2025Article
- The mouse neonatal small intestine is regionally specialized for protein absorption and transepithelial transport.Development (Cambridge, England) · 2025Article
- Beyond Rodents: Alternative Animal Models in Colorectal Cancer Research.International journal of molecular sciences · 2025Review
- Aging Reduces Intestinal Stem Cell Activity in Killifish and Intermittent Fasting Reverses Intestinal Gene Expression Patterns.Aging cell · 2025Article
- Recent evolution of the developing human intestine affects metabolic and barrier functions.Science (New York, N.Y.) · 2025Article
- Review
- Article
- Zebrafish as a model for human epithelial pathology.Laboratory animal research · 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
- Utilizing Zebrafish Embryos for Replication of Tulane Virus: A Human Norovirus Surrogate.Food and environmental virology · 2024Article
- The Future Exploring of Gut Microbiome-Immunity Interactions: From In Vivo/Vitro Models to In Silico Innovations.Microorganisms · 2024Review
- Metabolic disrupting chemicals in the intestine: the need for biologically relevant models: Zebrafish: what can we learn from this small environment-sensitive fish?FEBS open bio · 2024Review
12 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology.
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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.