Different modes of variation for each BG lineage suggest different functions

Abstract

Mammalian butyrophilins have various important functions, one for lipid binding but others as ligands for co-inhibition of αβ T cells or for stimulation of γδ T cells in the immune system. The chicken BG homologues are dimers, with extracellular immunoglobulin variable (V) domains joined by cysteines in the loop equivalent to complementarity-determining region 1 (CDR1). BG genes are found in three genomic locations: BG0 on chromosome 2, BG1 in the classical MHC (the BF-BL region) and many BG genes in the BG region just outside the MHC. Here, we show that BG0 is virtually monomorphic, suggesting housekeeping function(s) consonant with the ubiquitous tissue distribution. BG1 has allelic polymorphism but minimal sequence diversity, with the few polymorphic residues at the interface of the two V domains, suggesting that BG1 is recognized by receptors in a conserved fashion. Any phenotypic variation should be due to the intracellular region, with differential exon usage between alleles. BG genes in the BG region can generate diversity by exchange of sequence cassettes located in loops equivalent to CDR1 and CDR2, consonant with recognition of many ligands or antigens for immune defence. Unlike the mammalian butyrophilins, there are at least three modes by which BG genes evolve.

Functional Alleles of Chicken BG Genes, Members of the Butyrophilin Gene Family, in Peripheral T Cells

“…Throughout the length of the sequences, the dominantly expressed conceptual transcripts (as defined in the previous paragraph) from B15, B19, and B21 (BG8, BG9, and BG12 gene sequences from B12) are much more closely related with each other than with the dominantly expressed conceptual transcript from B2 (and the BG13 gene sequence) (Figures 3 and 5 ). The BG13 gene had already been seen to have an apparent gene conversion in exon 2 ( 25 ), but based on these latest data, we now consider the BG8-BG9-BG12 clade as having a type 2a cytoplasmic tail, with the BG13 (and other sequences such as BG3, BG4, and BG6) having a type 2b cytoplasmic tail (but not for the 3′UTR, which are nearly identical in all these sequences). Another surprise was the fact that many of the cDNA sequences isolated from line 6 1 (B2) are in fact identical (or very nearly so) to BG genes from the B12 haplotype (Figure 3 ), an unexpected finding for us since the B haplotype was originally defined by serology predominantly of the BG region.…”

“…Such intron read-through, a form of alternative splicing, was first noticed long ago in the cytoplasmic tails encoded by BG cDNAs ( 20 , 31 ). Some intron read-through seems to have become fixed, for example BG1 genes in which an active immunotyrosine inhibition motif (ITIM) is located in an exon bounded by two 21 nucleotide repeats ( 25 , 36 ). A bioinformatic analysis of the 14 BG genes of the B12 haplotype found many read-through introns that led to in-frame stop codons, but no additional signaling motifs were obvious in those introns that read through in-frame ( 24 ).…”

“…The SS forward (UC74) and TM reverse (UC76) primers (5′CTCCTGCCTTATCTCRTGGCTCTGCAC 3′and 5′CACAGCCAGAGCCACYKTCCAG 3′) to amplify the signal sequence to transmembrane region (Figure 1 ) have been described ( 24 ). The H forward (UC206) primer (5′TCCGCTCGAGCTCTCTYCTCCTACAG3′) has been described ( 25 ). The U reverse (UC650) primer (5′TAACACCCAAAGCAGTTTTCTNCC3′) was designed by inspection.…”

“…Comparison of alleles of BG loci was easy for the two singleton genes: a nearly monomorphic BG0 gene on chromosome 2 and the polymorphic BG1 gene in the BF-BL region on chromosome 16 ( 25 ). All other known BG genes are located head-to-tail in the BG region on chromosome 16, which renders them targets for apparent gene conversion (meaning that the polymorphism might be due to drift rather than selection) and also subject to unequal crossing-over (meaning that the CNV makes it hard to unequivocally identify orthologous alleles in different BG haplotypes) ( 24 , 25 ). To approach these problems, we have assumed that the genes from different haplotypes expressed in particular cell types could be considered alleles in a functional sense.…”

A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems

“…In addition, several other genes are located in the BF-BL region: a BG gene (BG1), a natural killer (NK) receptor gene and a potential ligand (BNK and Blec), the transcription factor RING3 (Brd2, found in every MHC carefully examined), the complement component C4, a structural gene tenascin and the enzyme steroid hydroxylase. BG1 and BNK are known to be highly polymorphic (Chattaway et al 2016, Hosomichi et al 2008, Rogers and Kaufman 2008.…”