ArticleNucleic acids research2021
Chromatin regulatory dynamics of early human small intestinal development using a directed differentiation model.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 19 citations in OpenAlex.
- Mapping mesenchymal diversity in the human small intestine and organoids.Nature cell biology · 2026Article
- Human-mouse cross-species comparison identifies common and unique aspects of intestinal mesenchyme development.bioRxiv : the preprint server for biology · 2025Article
- Insights into Modeling Inflammatory Bowel Disease from Stem Cell Derived Intestinal Organoids.Stem cell reviews and reports · 2025Review
- Absence ofAmerican journal of physiology. Endocrinology and metabolism · 2024Article
- Integrative genome-scale analyses reveal post-transcriptional signatures of early human small intestinal development in a directed differentiation organoid model.BMC genomics · 2023Article
- Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors.Science advances · 2023Article
- Elucidation of HHEX in pancreatic endoderm differentiation using a human iPSC differentiation model.Scientific reports · 2023Article
- Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival.BMC genomics · 2022Article
- From Patient Material to New Discoveries: a Methodological Review and Guide for Intestinal Stem Cell Researchers.Stem cell reviews and reports · 2022Review
- From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.Science (New York, N.Y.) · 2022Article
- Multiomic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals novel markers of almost all major cell types.American journal of physiology. Gastrointestinal and liver physiology · 2021Article
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Authors and funding
9 authors at 4 institutions in 3 countries.
Funding
Abstract
The establishment of the small intestinal (SI) lineage during human embryogenesis ensures functional integrity of the intestine after birth. The chromatin dynamics that drive SI lineage formation and regional patterning in humans are essentially unknown. To fill this knowledge void, we apply a cutting-edge genomic technology to a state-of-the-art human model of early SI development. Specifically, we leverage chromatin run-on sequencing (ChRO-seq) to define the landscape of active promoters, enhancers and gene bodies across distinct stages of directed differentiation of human pluripotent stem cells into SI spheroids with regional specification. Through comprehensive ChRO-seq analysis we identify candidate stage-specific chromatin activity states, novel markers and enhancer hotspots during the directed differentiation. Moreover, we propose a detailed transcriptional network associated with SI lineage formation or regional patterning. Our ChRO-seq analyses uncover a previously undescribed pattern of enhancer activity and transcription at HOX gene loci underlying SI regional patterning. We also validated this unique HOX dynamics by the analysis of single cell RNA-seq data from human fetal SI. Overall, the results lead to a new proposed working model for the regulatory underpinnings of human SI development, thereby adding a novel dimension to the literature that has relied almost exclusively on non-human models.
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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.