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 (VL–JL–CL) 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 (VL–JL–CL) 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 VL, JL and CL to have greater potential for immunoglobulin gene shuffling than traditionally studied mice and human models.
Highlights
Given definitive gene orders and accurate physical distances between Immunoglobulin light chain (IgL) gene segments are currently restricted to sequences annotated from BAC inserts, we identified a number of BAC clones screened to harbor IgL and had them prioritized for sequencing by the Sanger Institute
A total of 84 IgL gene segments were located in the zebrafish genome assembly Zv6 (Fig. 1)
Zebrafish IgL had previously been located to 3 separate chromosomes [25]
Summary
Because mouse Vl and Jl are in the same transcriptional polarity, VJ-rearrangement between the first and second clusters would result in a deletion of intervening Vl and Jl, thereby reducing the number of gene segments available for secondary rearrangements. This scenario appears to be avoided as the expressed mouse Vl repertoire demonstrates a strong bias to rearrange with Jl within a cluster and rearrangements that leapfrog between clusters appear to be extremely rare [1,2,3]
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