title: The restricted DH gene reading frame usage in the expressed human antibody repertoire is selected based upon its amino acid content.
abstract: The Ab repertoire is not uniform. Some variable, diversity, and joining genes are used more frequently than others. Nonuniform usage can result from the rearrangement process, or from selection. To study how the Ab repertoire is selected, we analyzed one part of diversity generation that cannot be driven by the rearrangement mechanism: the reading frame usage of DH genes. We have used two high-throughput sequencing methodologies, multiple subjects and advanced algorithms to measure the DH reading frame usage in the human Ab repertoire. In most DH genes, a single reading frame is used predominantly, and inverted reading frames are practically never observed. The choice of a single DH reading frame is not limited to a single position of the DH gene. Rather, each DH gene participates in rearrangements of differing CDR3 lengths, restricted to multiples of three. In nonproductive rearrangements, there is practically no reading frame bias, but there is still a striking absence of inversions. Biases in DH reading frame usage are more pronounced, but also exhibit greater interindividual variation, in IgG(+) and IgA(+) than in IgM(+) B cells. These results suggest that there are two developmental checkpoints of DH reading frame selection. The first occurs during VDJ recombination, when inverted DH genes are usually avoided. The second checkpoint occurs after rearrangement, once the BCR is expressed. The second checkpoint implies that DH reading frames are subjected to differential selection. Following these checkpoints, clonal selection induces a host-specific DH reading frame usage bias.
authors: Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel.
authors: Jennifer
authors: J
authors: Benichou
authors: Jacob
authors: J
authors: Glanville
authors: Eline T Luning
authors: ET
authors: Prak
authors: Roy
authors: R
authors: Azran
authors: Tracy C
authors: TC
authors: Kuo
authors: Jaume
authors: J
authors: Pons
authors: Cindy
authors: C
authors: Desmarais
authors: Lea
authors: L
authors: Tsaban
authors: Yoram
authors: Y
authors: Louzoun
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D000916:Antibody Diversity / Q000235:genetics*; D016175:B-Lymphocyte Subsets / Q000378:metabolism; D001483:Base Sequence; D018388:Codon, Terminator; D022801:Complementarity Determining Regions / Q000737:chemistry / Q000235:genetics*; D005260:Female; D015870:Gene Expression; D015321:Gene Rearrangement; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007070:Immunoglobulin A / Q000235:genetics / Q000378:metabolism; D007074:Immunoglobulin G / Q000235:genetics / Q000378:metabolism; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry / Q000235:genetics*; D007133:Immunoglobulin Joining Region / Q000737:chemistry / Q000235:genetics; D007075:Immunoglobulin M / Q000235:genetics / Q000378:metabolism; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000235:genetics; D008297:Male; D008875:Middle Aged; D016364:Reading Frames; D015203:Reproducibility of Results; D060152:V(D)J Recombination; D055815:Young Adult
chemical_list: D018388:Codon, Terminator; D022801:Complementarity Determining Regions; D007070:Immunoglobulin A; D007074:Immunoglobulin G; D007143:Immunoglobulin Heavy Chains; D007133:Immunoglobulin Joining Region; D007075:Immunoglobulin M; D007135:Immunoglobulin Variable Region
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