ArticleNature communications2023
Regulation of CTCF loop formation during pancreatic cell differentiation.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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Who cites it
20 citing papers in PubMed, 17 citations in OpenAlex.
- CTCF delimits a DNA methylation transition at the intergenic region between the embryonic and adult α-globin genes.Epigenetics · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.Genome biology · 2026Article
- Jointly-hic: joint decomposition of contact frequency maps captures salient features of genome architecture across tissues and development.Genome biology · 2026Article
- Genomic-microbial coevolution in human development: chromosome 2 fusion, and human accelerated regions.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Review
- Impaired cohesin loading disrupts pancreatic differentiation by Polycomb-driven chromatin rewiring and loop collapse.Communications biology · 2026Article
- TF-loop: deciphering the transcription factor regulatory language for CTCF-mediated chromatin loop based on BERT.Briefings in bioinformatics · 2026Article
- UnionLoops: a workflow for calling chromatin loops across related Hi-C datasets with improved specificity, precision, and sensitivity.bioRxiv : the preprint server for biology · 2026Article
- Article
- CTCF-RNA interactions orchestrate cell-specific chromatin loop organization.Science advances · 2025Article
- Single-cell multiomics analysis reveals CTCF as a key regulator of lung morphogenesis and progenitor maintenance.Nature communications · 2025Article
- CTCF binding landscape is shaped by the epigenetic state of the N-terminal nucleosome in relation to CTCF motif orientation.Nucleic acids research · 2025Article
- Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans.Nature communications · 2025Article
- Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.Communications biology · 2025Article
- Spatially defined microenvironment for engineering organoids.Biophysics reviews · 2024Review
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.NAR genomics and bioinformatics · 2024Article
- The chromatin tapestry as a framework for neurodevelopment.Genome research · 2024Review
- Deciphering the Landscape of GATA-Mediated Transcriptional Regulation in Gastric Cancer.Antioxidants (Basel, Switzerland) · 2024Article
- Mechanistic drivers of chromatin organization into compartments.Current opinion in genetics & development · 2024Review
- HiCrayon reveals distinct layers of multi-state 3D chromatin organization.bioRxiv : the preprint server for biology · 2024Article
- Application and challenge of pancreatic organoids in therapeutic research.Frontiers in pharmacology · 2024Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Transcription reprogramming during cell differentiation involves targeting enhancers to genes responsible for establishment of cell fates. To understand the contribution of CTCF-mediated chromatin organization to cell lineage commitment, we analyzed 3D chromatin architecture during the differentiation of human embryonic stem cells into pancreatic islet organoids. We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of H3K9me3 to H3K9me2, demethylation of DNA, recruitment of pioneer factors, and positioning of nucleosomes flanking the new CTCF sites. Existing CTCF sites not involved in loop formation become functional loop anchors via the establishment of new cohesin loading sites containing NIPBL and YY1 at sites between the new anchors. In both cases, formation of new CTCF loops leads to strengthening of enhancer promoter interactions and increased transcription of genes adjacent to loop anchors. These results suggest an important role for CTCF and cohesin in controlling gene expression during cell differentiation.
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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 Socratic graph.