ArticleProceedings of the National Academy of Sciences of the United States of America2016
Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 45 citations in OpenAlex.
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- The nonamer code for RAG-mediated recombination in vivo.Nucleic acids research · 2025Article
- Enhancers within the Ig V Gene Region Orchestrate Chromatin Topology and Regulate V Gene Rearrangement Frequency to Shape the B Cell Receptor Repertoire Specificities.Journal of immunology (Baltimore, Md. : 1950) · 2023Article
- Hindlimb unloading, a physiological model of microgravity, modifies the murine bone marrow IgM repertoire in a similar manner as aging but less strongly.Immunity & ageing : I & A · 2023Article
- Enhancer-instructed epigenetic landscape and chromatin compartmentalization dictate a primary antibody repertoire protective against specific bacterial pathogens.Nature immunology · 2023Article
- Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium.The EMBO journal · 2022Article
- RNA exosome drives early B cell development via noncoding RNA processing mechanisms.Science immunology · 2022Article
- Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome.Life (Basel, Switzerland) · 2022Article
- T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects.Journal of clinical immunology · 2022Article
- Individualized VDJ recombination predisposes the available Ig sequence space.Genome research · 2021Article
- IL-7R signaling activates widespread VCell reports · 2021Article
- Chromatin dynamics: Nucleosome occupancy and sensitivity as determinants of gene expression and cell fate.Journal of cancer biology · 2021Article
- BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics.BMC bioinformatics · 2020Article
- CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification.BMC bioinformatics · 2020Article
- Alterations in chromatin at antigen receptor loci define lineage progression during B lymphopoiesis.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Chemotherapy Curability in Leukemia, Lymphoma, Germ Cell Tumors and Gestational Malignancies: A Reflection of the Unique Physiology of Their Cells of Origin.Frontiers in genetics · 2020Article
- The murine IgH locus contains a distinct DNA sequence motif for the chromatin regulatory factor CTCF.The Journal of biological chemistry · 2019Article
- A new twist on V(D)J recombination.Nature structural & molecular biology · 2018Article
- LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.Bioinformatics (Oxford, England) · 2018Article
- Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression.BMC genomics · 2018Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
We show that the physical distribution of nucleosomes at antigen receptor loci is subject to regulated cell type-specific and lineage-specific positioning and correlates with the accessibility of these gene segments to recombination. At the Ig heavy chain locus (IgH), a nucleosome in pro-B cells is generally positioned over each IgH variable (VH) coding segment, directly adjacent to the recombination signal sequence (RSS), placing the RSS in a position accessible to the recombination activating gene (RAG) recombinase. These changes result in establishment of a specific chromatin organization at the RSS that facilitates accessibility of the genomic DNA for the RAG recombinase. In contrast, in mouse embryonic fibroblasts the coding segment is depleted of nucleosomes, which instead cover the RSS, thereby rendering it inaccessible. Pro-T cells exhibit a pattern intermediate between pro-B cells and mouse embryonic fibroblasts. We also find large-scale variations of nucleosome density over hundreds of kilobases, delineating chromosomal domains within IgH, in a cell type-dependent manner. These findings suggest that developmentally regulated changes in nucleosome location and occupancy, in addition to the known chromatin modifications, play a fundamental role in regulating V(D)J recombination. Nucleosome positioning-which has previously been observed to vary locally at individual enhancers and promoters-may be a more general mechanism by which cells can regulate the accessibility of the genome during development, at scales ranging from several hundred base pairs to many kilobases.
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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.