Chromatin conformation governs T-cell receptor Jβ gene segment usage

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2012-09-10

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1073/pnas.1203916109PMID 22984176PMCID PMC3465372
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Chromatin topology and the regulation of antigen receptor assembly.

  2012cited by this paper
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  2012cited by this paper
• Developmentally controlled and tissue-specific expression of unrearranged VH gene segments. Cell. 1985. 40: 271-281.

  2012cited by this paper
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  2011cited by this paper
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  2011cited by this paper
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  2011cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2010cited by this paper
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  2009cited by this paper
• High-Throughput Sequencing of the Zebrafish Antibody Repertoire

  2009cited by this paper
• Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.

  2009influential reference
• rtracklayer: an R package for interfacing with genome browsers

  2009influential reference
• Next-generation DNA sequencing

  2008cited by this paper
• The molecular basis for public T-cell responses?

  2008cited by this paper
• Essential function for SWI-SNF chromatin-remodeling complexes in the promoter-directed assembly of Tcrb genes

  2007cited by this paper
• Reversible contraction by looping of the Tcra and Tcrb loci in rearranging thymocytes

  2007cited by this paper
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  2007cited by this paper
• Structural determinants of T-cell receptor bias in immunity

  2006cited by this paper
• Faculty Opinions recommendation of Activation of V(D)J recombination at the IgH chain JH locus occurs within a 6-kilobase chromatin domain and is associated with nucleosomal remodeling.

  2006influential reference
• Mechanism and control of V(D)J recombination at the immunoglobulin heavy chain locus.

  2006cited by this paper
• Dual binding modes for an HMG domain from human HMGB2 on DNA.

  2005influential reference
• IMGT®, the international ImMunoGeneTics information system®

  2004cited by this paper
• IMGT, the international ImMunoGeneTics information system®

  2004influential reference
• The V 17 + T Cell Repertoire : Skewed Jfl Usage after Thymic Selection ; Dissimilar CDR 3 s in CD 4 + Versus CD 8 + Cells

  2003influential reference
• A Functional Analysis of the Spacer of V(D)J Recombination Signal Sequences

  2003cited by this paper
• IMGT, the international ImMunoGeneTics information system®, http: //imgt.cines.fr: the reference in immunoinformatics

  2003cited by this paper
• Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling

  2003cited by this paper
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  2002cited by this paper
• Capturing Chromosome Conformation

  2002influential reference
• The shaping of the T cell repertoire.

  2001cited by this paper
• Protective Autoimmunity Is a Physiological Response to CNS Trauma

  2001cited by this paper
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  2001cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  1999cited by this paper
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  1999cited by this paper
• Nucleosome structure completely inhibits in vitro cleavage by the V(D)J recombinase

  1999influential reference
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  1998cited by this paper
• Individual variations in the murine T cell response to a specific peptide reflect variability in naive repertoires.

  1998cited by this paper
• Stimulation of V(D)J cleavage by high mobility group proteins

  1997cited by this paper
• Accessibility control of antigen-receptor variable-region gene assembly: role of cis-acting elements.

  1996influential reference
• Comparison of the J beta gene usage among different T cell receptor V beta families in spleens of C57BL/6 mice.

  1995cited by this paper
• Circulating T cell repertoire complexity in normal individuals and bone marrow recipients analyzed by CDR3 size spectratyping. Correlation with immune status.

  1994cited by this paper
• Comparison of the Jβ gene usage among different T cell receptor Vβ families in spleens of C57BL/6 mice

  1994cited by this paper
• Coding end sequence can markedly affect the initiation of V(D)J recombination.

  1993cited by this paper
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  1993cited by this paper
• The V beta 17+ T cell repertoire: skewed J beta usage after thymic selection; dissimilar CDR3s in CD4+ versus CD8+ cells

  1991cited by this paper
• Experiments in nonconvex optimization: Stochastic approximation with function smoothing and simulated annealing

  1990cited by this paper
• Generating functionology

  1990cited by this paper
• Molecular basis for the nonexpression of V beta 17 in some strains of mice.

  1988cited by this paper
• T-cell antigen receptor genes and T-cell recognition

  1988cited by this paper
• Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition

  1986cited by this paper
• Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences.@@@Elements of Applied Stochastic Processes, 2nd Edition.@@@Comparison Methods for Queues and Other Stochastic Models.@@@Parameter Estimation for Stochastic Processes.

  1986cited by this paper
• Handbook of stochastic methods for physics, chemistry and the natural sciences

  1986influential reference
• Developmentally controlled and tissue-specific expression of unrearranged VH gene segments.

  1985cited by this paper
• Identification of common molecular subsequences.

  1981influential reference

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