title: Regulated large-scale nucleosome density patterns and precise nucleosome positioning correlate with V(D)J recombination.
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.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
authors.forename: Sandhya R
authors.initials: SR
authors.lastname: Pulivarthy
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
authors.forename: Mattia
authors.initials: M
authors.lastname: Lion
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114.
authors.forename: Guray
authors.initials: G
authors.lastname: Kuzu
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Biological Sciences, Wellesley College, Wellesley, MA 02481; Program in Biochemistry, Wellesley College, Wellesley, MA 02481.
authors.forename: Adam G W
authors.initials: AG
authors.lastname: Matthews
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Borowsky
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
authors.forename: John
authors.initials: J
authors.lastname: Morris
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Biological Science, Florida State University, Tallahassee, FL 32306.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Dennis
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; tolstorukov@molbio.mgh.harvard.edu oettinger@molbio.mgh.harvard.edu.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114; Department of Genetics, Harvard Medical School, Boston, MA 02115; tolstorukov@molbio.mgh.harvard.edu oettinger@molbio.mgh.harvard.edu.
authors.forename: Marjorie A
authors.initials: MA
authors.lastname: Oettinger
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D004268:DNA-Binding Proteins / Q000172:deficiency / Q000235:genetics; D057890:Epigenomics; D055786:Gene Knockout Techniques; D056426:Genetic Loci; D059014:High-Throughput Nucleotide Sequencing; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000235:genetics; D008214:Lymphocytes / Q000276:immunology / Q000378:metabolism; D051379:Mice; D018345:Mice, Knockout; D009707:Nucleosomes / Q000378:metabolism*; D009928:Organ Specificity; D054448:Precursor Cells, B-Lymphoid / Q000378:metabolism; D011485:Protein Binding; D016693:Receptors, Antigen, T-Cell, alpha-beta / Q000235:genetics; D060152:V(D)J Recombination
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D007143:Immunoglobulin Heavy Chains; D007135:Immunoglobulin Variable Region; D009707:Nucleosomes; C499308:Rag2 protein, mouse; D016693:Receptors, Antigen, T-Cell, alpha-beta
keywords: V(D)J recombination; chromatin; epigenetics; lymphocytes; nucleosome positioning