ArticleProceedings of the National Academy of Sciences of the United States of America2015
New roles for DNA cytosine modification, eRNA, anchors, and superanchors in developing B cell progenitors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 64 citations in OpenAlex.
- A hierarchy of spatial confinements governs chromatin dynamics and genomic encounters.bioRxiv : the preprint server for biology · 2026Article
- Context-dependent regulation of IgH V(D)J recombination by cohesin-STAG1 and cohesin-STAG2.Nature communications · 2026Article
- Igh nuclear speckle association promotes V(D)J recombination.Nature communications · 2026Article
- IGF2BP3-mediated mBone research · 2025Article
- Exuberant long noncoding RNA expression may sculpt Igh locus topology.Frontiers in immunology · 2025Article
- Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- The Function of E2A in B-Cell Development.Advances in experimental medicine and biology · 2024Review
- Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes.Cell reports · 2023Article
- Enhancers associated with unstable RNAs are rare in plants.bioRxiv : the preprint server for biology · 2023Article
- Insight into the regulatory mechanism of dynamic chromatin 3D interactions during cardiomyocyte differentiation in human.Molecular therapy. Nucleic acids · 2023Article
- Contribution of the IGCR1 regulatory element and the 3'Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Profiling the epigenetic landscape of the antigen receptor repertoire: the missing epi-immunogenomics data.Nature methods · 2023Article
- An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation.Nature communications · 2023Article
- Roles of super enhancers and enhancer RNAs in skeletal muscle development and disease.Cell cycle (Georgetown, Tex.) · 2023Review
- Locus architecture and RAG scanning determine antibody diversity.Trends in immunology · 2023Review
- The role of chromatin loop extrusion in antibody diversification.Nature reviews. Immunology · 2022Review
- The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development.Nucleic acids research · 2022Article
- Review
- Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer.Oncogene · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
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Abstract
B-cell fate is orchestrated by a series of well-characterized developmental regulators. Here, we found that the onset of B-cell development was accompanied by large-scale changes in DNA cytosine modifications associated with promoters, enhancers, and anchors. These changes were tightly linked to alterations in transcription factor occupancy and nascent RNA (eRNA) transcription. We found that the prepro-B to the pro-B-cell transition was associated with a global exchange of DNA cytosine modifications for polycomb-mediated repression at CpG islands. Hypomethylated regions were found exclusively in the active/permissive compartment of the nucleus and were predominantly associated with regulatory elements or anchors that orchestrate the folding patterns of the genome. We identified superanchors, characterized by clusters of hypomethylated CCCTC-binding factor (CTCF)-bound elements, which were predominantly located at boundaries that define topological associated domains. A particularly prominent hypomethylated superanchor was positioned down-stream of the Ig heavy chain (Igh) locus. Analysis of global formaldehyde-cross-linking studies indicated that the Igh locus superanchor interacts with the VH region repertoire across vast genomic distances. We propose that the Igh locus superanchor sequesters the VH and DHJH regions into a spatial confined geometric environment to promote rapid first-passage times. Collectively, these studies demonstrate how, in developing B cells, DNA cytosine modifications associated with regulatory and architectural elements affect patterns of gene expression, folding patterns of the genome, and antigen receptor assembly.
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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.