title: Structure of nonhairpin coding-end DNA breaks in cells undergoing V(D)J recombination.
abstract: The V(D)J recombinase recognizes a pair of immunoglobulin or T-cell receptor gene segments flanked by recombination signal sequences and introduces double-strand breaks, generating two signal ends and two coding ends. Broken coding ends were initially identified as covalently closed hairpin DNA molecules. Before recombination, however, the hairpins must be opened and the ends must be modified by nuclease digestion and N-region addition. We have now analyzed nonhairpin coding ends associated with various immunoglobulin gene segments in cells undergoing V(D)J recombination. We found that these broken DNA ends have different nonrandom 5'-strand deletions which were characteristic for each locus examined. These deletions correlate well with the sequence characteristics of coding joints involving these gene segments. In addition, unlike broken signal ends, these nonhairpin coding-end V(D)J recombination reaction intermediates have 3' overhanging ends. We discuss the implications of these results for models of how sequence modifications occur during coding-joint formation.
authors.affiliation: Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. mss@welchlink.welch.jhu.edu
authors.forename: M S
authors.initials: MS
authors.lastname: Schlissel
mesh_terms: D000818:Animals; D001402:B-Lymphocytes / Q000737:chemistry*; D001483:Base Sequence; D001854:Bone Marrow Cells / Q000737:chemistry / Q000166:cytology; D002454:Cell Differentiation / Q000235:genetics; D002460:Cell Line; D003062:Codon / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D015322:Gene Rearrangement, B-Lymphocyte / Q000235:genetics*; D015329:Gene Rearrangement, T-Lymphocyte / Q000235:genetics*; D007143:Immunoglobulin Heavy Chains / Q000235:genetics; D007133:Immunoglobulin Joining Region / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000235:genetics; D051379:Mice; D008807:Mice, Inbred BALB C; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016133:Polymerase Chain Reaction / Q000379:methods; D011995:Recombination, Genetic; D013950:Thymus Gland / Q000737:chemistry / Q000166:cytology
chemical_list: D003062:Codon; D007143:Immunoglobulin Heavy Chains; D007133:Immunoglobulin Joining Region; D007135:Immunoglobulin Variable Region; D004247:DNA