title: Partitioning of rearranged Ig genes by mutation analysis demonstrates D-D fusion and V gene replacement in the expressed human repertoire.
abstract: The accurate partitioning of Ig H chain V(H)DJ(H) junctions and L chain V(L)J(L) junctions is problematic. We have developed a statistical approach for the partitioning of such sequences, by analyzing the distribution of point mutations between a determined V gene segment and putative Ig regions. The establishment of objective criteria for the partitioning of sequences between V(H), D, and J(H) gene segments has allowed us to more carefully analyze intervening putative nontemplated (N) nucleotides. An analysis of 225 IgM H chain sequences, with five or fewer V mutations, led to the alignment of 199 sequences. Only 5.0% of sequences lacked N nucleotides at the V(H)D junction (N1), and 10.6% at the DJ(H) junction (N2). Long N regions (>9 nt) were seen in 20.6% of N1 regions and 17.1% of N2 regions. Using a statistical analysis based upon known features of N addition, and mutation analysis, two of these N regions aligned with D gene segments, and a third aligned with an inverted D gene segment. Nine additional sequences included possible alignments with a second D segment. Four of the remaining 40 long N1 regions included 5' sequences having six or more matches to V gene end motifs, which may be the result of V gene replacement. Such sequences were not seen in long N2 regions. The long N regions frequently seen in the expressed repertoire of human Ig gene rearrangements can therefore only partly be explained by V gene replacement and D-D fusion.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia. a.collins@unsw.edu.au
authors.forename: Andrew M
authors.initials: AM
authors.lastname: Collins
authors.forename: Masashi
authors.initials: M
authors.lastname: Ikutani
authors.forename: Daniela
authors.initials: D
authors.lastname: Puiu
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Buck
authors.forename: Aradhita
authors.initials: A
authors.lastname: Nadkarni
authors.forename: Bruno
authors.initials: B
authors.lastname: Gaeta
mesh_terms: D000916:Antibody Diversity / Q000235:genetics*; D003596:Cytosine / Q000378:metabolism; D004252:DNA Mutational Analysis / Q000379:methods*; D005786:Gene Expression Regulation / Q000276:immunology*; D015326:Gene Rearrangement, B-Lymphocyte, Heavy Chain; D005803:Genes, Immunoglobulin; D018095:Germ-Line Mutation; D006147:Guanine / Q000378:metabolism; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000096:biosynthesis / Q000235:genetics*; D007133:Immunoglobulin Joining Region / Q000096:biosynthesis / Q000235:genetics; D007075:Immunoglobulin M / Q000096:biosynthesis / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000096:biosynthesis / Q000235:genetics*; D009841:Oligonucleotides / Q000096:biosynthesis / Q000235:genetics; D017354:Point Mutation; D011336:Probability; D016415:Sequence Alignment / Q000379:methods
chemical_list: D007143:Immunoglobulin Heavy Chains; D007133:Immunoglobulin Joining Region; D007075:Immunoglobulin M; D007135:Immunoglobulin Variable Region; D009841:Oligonucleotides; D006147:Guanine; D003596:Cytosine