Immunoglobulin light chain (IgL) genes in zebrafish: Genomic configurations and inversional rearrangements between (V[subscript L]–J[subscript L–C[subscript L) gene clusters

Abstract

In mammals, Immunoglobulin light chain (IgL) are localized to two chromosomal regions (designated κ and λ). Here we report a genome-wide survey of IgL genes in the zebrafish revealing (V[subscript L]–J[subscript L]–C[subscript L]) clusters spanning 5 separate chromosomes. To elucidate IgL loci present in the zebrafish genome assembly (Zv6), conventional sequence similarity searches and a novel scanning approach based on recombination signal sequence (RSS) motifs were applied. RT-PCR with zebrafish cDNA was used to confirm annotations, evaluate VJ-rearrangement possibilities and show that each chromosomal locus is expressed. In contrast to other vertebrates in which IgL exon usage has been studied, inversional rearrangement between (V[subscript L]–J[subscript L]–C[subscript L]) clusters were found. Inter-cluster rearrangements may convey a selective advantage for editing self-reactive receptors and poise zebrafish by virtue of their extensive numbers of V[subscript L], J[subscript L] and C[subscript L] to have greater potential for immunoglobulin gene shuffling than traditionally studied mice and human models.