title: Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER.
abstract: We analyzed 77 nonproductive and 574 productive human V(H)DJ(H) rearrangements with a newly developed program, JOINSOLVER. In the productive repertoire, the H chain complementarity determining region 3 (CDR3(H)) was significantly shorter (46.7 +/- 0.5 nucleotides) than in the nonproductive repertoire (53.8 +/- 1.9 nucleotides) because of the tendency to select rearrangements with less TdT activity and shorter D segments. Using criteria established by Monte Carlo simulations, D segments could be identified in 71.4% of nonproductive and 64.4% of productive rearrangements, with a mean of 17.6 +/- 0.7 and 14.6 +/- 0.2 retained germline nucleotides, respectively. Eight of 27 D segments were used more frequently than expected in the nonproductive repertoire, whereas 3 D segments were positively selected and 3 were negatively selected, indicating that both molecular mechanisms and selection biased the D segment usage. There was no bias for D segment reading frame (RF) use in the nonproductive repertoire, whereas negative selection of the RFs encoding stop codons and positive selection of RF2 that frequently encodes hydrophilic amino acids were noted in the productive repertoire. Except for serine, there was no consistent selection or expression of hydrophilic amino acids. A bias toward the pairing of 5' D segments with 3' J(H) segments was observed in the nonproductive but not the productive repertoire, whereas V(H) usage was random. Rearrangements using inverted D segments, DIR family segments, chromosome 15 D segments and multiple D segments were found infrequently. Analysis of the human CDR3(H) with JOINSOLVER has provided comprehensive information on the influences that shape this important Ag binding region of V(H) chains.
authors.affiliation: Repertoire Analysis Group, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: M Margarida
authors.initials: MM
authors.lastname: Souto-Carneiro
authors.forename: Nancy S
authors.initials: NS
authors.lastname: Longo
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Russ
authors.forename: Hong-wei
authors.initials: HW
authors.lastname: Sun
authors.forename: Peter E
authors.initials: PE
authors.lastname: Lipsky
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000032:analysis; D001483:Base Sequence; D022801:Complementarity Determining Regions / Q000032:analysis / Q000737:chemistry*; D004253:DNA Nucleotidylexotransferase / Q000378:metabolism; D015321:Gene Rearrangement; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry* / Q000235:genetics; D007133:Immunoglobulin Joining Region / Q000737:chemistry* / Q000235:genetics; D008969:Molecular Sequence Data; D009010:Monte Carlo Method
chemical_list: D000596:Amino Acids; D022801:Complementarity Determining Regions; D007143:Immunoglobulin Heavy Chains; D007133:Immunoglobulin Joining Region; D004253:DNA Nucleotidylexotransferase