ArticleCell genomics2024
Cell-type-specific loops linked to RNA polymerase II elongation in human neural differentiation.
Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Enhancer-dependent gene regulation in space, time, and malignancies.International journal of cancer · 2026Review
- 3D genome folding in epigenetic regulation and cellular memory.Trends in cell biology · 2026Review
- Engineering the Link: From Genome Interaction Maps to Functional Insight.Advanced biology · 2025Review
- Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons.bioRxiv : the preprint server for biology · 2025Article
- Learning induces persistent chromatin loops underlying robust gene expression during memory recall.bioRxiv : the preprint server for biology · 2025Article
- Revisiting models of enhancer-promoter communication in gene regulation.Genome research · 2025Review
- Genome structure mapping with high-resolution 3D genomics and deep learning.bioRxiv : the preprint server for biology · 2025Article
- Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity.bioRxiv : the preprint server for biology · 2025Article
- Transcriptional machinery as an architect of genome structure.Current opinion in structural biology · 2024Review
- The chromatin tapestry as a framework for neurodevelopment.Genome research · 2024Review
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5 authors.
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Abstract
DNA is folded into higher-order structures that shape and are shaped by genome function. The role of long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNA Pol II) during neural lineage commitment. We find thousands of loops decommissioned or gained de novo upon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitor cells (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNA Pol II initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops or promoter-promoter loops or when unlooped. Genes transitioning from repression to RNA Pol II initiation exhibit a slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNA Pol II-mediated elongation during neural cell fate transitions.
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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.