DJ Pairing during VDJ Recombination Shows Positional Biases That Vary among Individuals with Differing IGHD Locus Immunogenotypes

Abstract

Human immunoglobulin heavy chain diversity is influenced by biases in the pairing of IGHD and IGHJ genes, but these biases have not been described in detail. We have used high throughput sequencing of VDJ rearrangements to explore DJ pairing biases in twenty-nine individuals. It was possible to infer three contrasting IGHD-IGHJ haplotypes in nine of these individuals, and two of these haplotypes include deletion polymorphisms involving multiple contiguous IGHD genes. We were therefore able to explore how the underlying genetic makeup of the heavy chain locus influences the formation of particular DJ pairs. Analysis of non-productive rearrangements demonstrates that 3′ IGHD genes tend to pair preferentially with 5′ IGHJ genes, while 5′ IGHD genes pair preferentially with 3′ IGHJ genes, and the relationship between IGHD gene pairing frequencies and IGHD gene position is a near linear one for each IGHJ gene. Striking differences are seen, however, in individuals who carry deletion polymorphisms in the D locus. The absence of different blocks of IGHD genes lead to increases in the utilization frequencies of just a handful of genes, and these genes have no clear positional relationships to the deleted genes. This suggests that pairing frequencies may be influenced by additional complex positional relationships that arise perhaps from chromatin structure. In contrast to IGHD gene usage, IGHJ gene usage is unaffected by the IGHD gene deletion polymorphisms. Such an outcome would be expected if the recombinase complex associates first with an IGHJ gene, before associating with an IGHD gene partner.

Data on haplotype-supported immunoglobulin germline gene inference

“…The frequencies of readily inferable [2] IGHD (Immunoglobulin heavy D-gene) genes used by the two haplotypes of five subjects are summarized (Table 4). Furthermore the data illustrate the effect of using a germline gene database that extends beyond codon 105 on gene inference (Fig.…”

A novel framework for characterizing genomic haplotype diversity in the human immunoglobulin heavy chain locus

“…Greater than 250 functional/ORF IGH gene segment alleles are curated in the IMmunoGeneTics Information System (IMGT) database 2 , and this number continues to increase [3][4][5][6][7][8][9][10] . The locus is enriched for single nucleotide variants (SNVs) and large structural variants (SVs) involving functional genes 3,[11][12][13][14][15][16][17][18] , at which allele frequencies are known to vary among human populations 4,18,19 .…”

“…While early studies uncovered associations to disease susceptibility within IGH, few links have been made by genome-wide association studies (GWAS) and whole genome sequencing (WGS) 20,22,23 . Moreover, little is known about the genetic regulation of the human Ab response, despite evidence that features of the Ab repertoire are heritable 12,19,[24][25][26][27][28][29] To define the role of IGH variation in Ab function and disease, all classes of variation must be resolved 3,12,15,19,29,30 . Although approaches have been developed for utilizing genomic or Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) data, variant calling and broad-scale haplotype inference are restricted primarily to coding regions 6,7,[16][17][18]31 .…”

Heavy Chain CDR 3 and Junctional Length Biases in Human Antibody Repertoires Associated with Heavy and Light Chain Germline Utilization

“…Haplotypes could potentially affect CDR H3 length distributions through differences in D germline composition and differential recombination frequencies of D or JH germlines of different lengths in different chromosomes (25). This, combined with differential recombination frequencies of VH alleles (26)(27)(28), may impact CDR H3 distributions associated with certain VH germlines.…”