The functional 3′-end of immunoglobulin heavy chain variable (IGHV) genes

Abstract

Inference of antibody gene repertoires using transcriptome data has emerged as an alternative approach to the complex process of sequencing of adaptive immune receptor germline gene loci. The diversity introduced during rearrangement of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes has however been identified as potentially affecting inference specificity. In this study, we have addressed this issue by analysing the nucleotide composition of unmutated human immunoglobulin heavy chains-encoding transcripts, focusing on the 3ö most bases of 47 IGHV germline genes. Although transcripts derived from some of the germline genes predominately incorporated the germline encoded base even at position 320, the last base of most IGHV genes, transcripts originating in other genes presented other nucleotides to the same extent at this position. In transcripts derived from two of the germline genes, IGHV3-13*01 and IGHV4-30-2*01, the predominating nucleotide (G) was in fact not that of the gene (A). Hence, we suggest that inference of IGHV genes should be limited to bases preceding nucleotide 320, as inference beyond this would jeopardize the specificity of the inference process. The different degree of incorporation of the final base of the IGHV gene directly influences the distribution of amino acids of the ascending strand of the third complementarity determining region of the heavy chain. Thereby it influences the nature of this specificity-determining part of the antibody population. In addition, we also present data that indicate the existence of a common so far un-recognized allelic variant of IGHV3-7 that carries an A318G difference in relation to IGHV3-7*02.

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 .…”

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution

“…Indeed, evolution that might affect the structure/flexibility of H chain V domain CDR3 ( 52 ), the loop created through the VDJ rearrangement process, provides interesting opportunities in terms of perfection of the paratope. For instance, we recently observed substantial germline-defined differences in the ability to incorporate the 3′-most nucleotide of the IGHV-encoding gene into the rearranged sequence ( 53 , 54 ). Many IGHV genes’ 3′-end has a sequence that it, if fully incorporated into the final product, would encode an acidic residue in position 107 of the ascending strand of CDR3.…”

“…Many IGHV genes’ 3′-end has a sequence that it, if fully incorporated into the final product, would encode an acidic residue in position 107 of the ascending strand of CDR3. These side chains display opportunities to establish polar interactions, for instance to the side chain of amino acid 40 (located immediately after CDR1), not available to residues (commonly glycine, alanine, or valine) that are incorporated in cases where the full length of the IGHV gene is not used ( 53 , 54 ). Importantly, the germline-encoded side chain of residue 40 is in many instances able to participate in polar interactions with a polar residue at position 107 in the ascending strand of H chain CDR3, and it holds capacity to be diversified (Figure S2 in Supplementary Material) ( 38 ).…”

Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains

“…This article present data of nucleotide composition in antibody heavy transcripts originating in 47 different immunoglobulin heavy chain variable (IGHV) germline genes/alleles ( Fig. 1 ) [1] . The data is limited to the three most 5′ codons (codon 105–107, according to IMGT numbering [5] ) that encode the sequence of the complementary determining region 3 (CDR3).…”

“…The nucleotide compositions of the corresponding 5′-ends of sequences encoding the CDR3 are presented for transcripts with an origin in 47 different IGHV alleles. These data have been used (Thörnqvist and Ohlin, 2018) [1] to demonstrate the extent of incorporation of the 3′ most bases of IGHV germline genes into rearranged immunoglobulin encoding sequences, and the extent whereby any difference in incorporation affects the specificity of inference of the 3′-end of IGHV genes from immunoglobulin-encoding transcripts. They have also been used to assess the effect of observed gene differences on the composition of the ascending strand of CDR3 associated to antibodies with an origin in different IGHV genes (Thörnqvist and Ohlin, 2018) [1].…”