ArticleNature communications2022
Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Regional organization of nutrient absorption across the small intestine.Nature reviews. Gastroenterology & hepatology · 2026Review
- Depolymerizing F-actin accelerates the exit from pluripotency to enhance stem cell-derived islet differentiation.Nature communications · 2026Article
- Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors.bioRxiv : the preprint server for biology · 2025Article
- Embryonic Signaling Pathways Shape Colorectal Cancer Subtypes: Linking Gut Development to Tumor Biology.Pathophysiology : the official journal of the International Society for Pathophysiology · 2025Article
- Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.Evolutionary applications · 2025Article
- Advances and applications in single-cell and spatial genomics.Science China. Life sciences · 2025Review
- scBlood: A comprehensive single-cell accessible chromatin database of blood cells.Computational and structural biotechnology journal · 2024Article
- A statistical method for quantifying progenitor cells reveals incipient cell fate commitments.Nature methods · 2024Article
- Highlights of how single-cell analyses are illuminating differentiation and disease in the gastric corpus.American journal of physiology. Gastrointestinal and liver physiology · 2024Review
- Mapping Cell Atlases at the Single-Cell Level.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Advanced Progression for the Heterogeneity and Homeostasis of Intestinal Stem Cells.Stem cell reviews and reports · 2023Review
- iPSCs derived from esophageal atresia patients reveal SOX2 dysregulation at the anterior foregut stage.Disease models & mechanisms · 2022Article
- Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA.Nature communications · 2022Article
- Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions.Nature communications · 2022Article
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
Development of the gastrointestinal system occurs after gut tube closure, guided by spatial and temporal control of gene expression. However, it remains unclear what forces regulate these spatiotemporal gene expression patterns. Here we perform single-cell chromatin profiling of the primitive gut tube to reveal organ-specific chromatin patterns that reflect the anatomical patterns of distinct organs. We generate a comprehensive map of epigenomic changes throughout gut development, demonstrating that dynamic chromatin accessibility patterns associate with lineage-specific transcription factor binding events to regulate organ-specific gene expression. Additionally, we show that loss of Sox2 and Cdx2, foregut and hindgut lineage-specific transcription factors, respectively, leads to fate shifts in epigenomic patterns, linking transcription factor binding, chromatin accessibility, and lineage fate decisions in gut development. Notably, abnormal expression of Sox2 in the pancreas and intestine impairs lineage fate decisions in both development and adult homeostasis. Together, our findings define the chromatin and transcriptional mechanisms of organ identity and lineage plasticity in development and adult homeostasis.
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