Targeted annotation of immunoglobulin light chain (IgL) genes in zebrafish from BAC clones reveals kappa-like recombining/deleting elements within IgL constant regions.

Genomic organization, composition, and microsynteny of immunoglobulin light chain (IgL) gene segments in the zebrafish were analyzed through the identification and annotation of overlapping BAC clone insert sequences and an Illumina de novo assembly. The resultant gap-free IgL annotation confirmed a number of previous conclusions about teleost IgL including: suites of (V(L)-J(L)-C(L)) clusters on multiple chromosomes; V(L) in the same or opposite transcriptional orientation as J(L) and C(L); and the apparent absence of lambda IgL in the zebrafish model. In addition, palindromic heptamers (CACAGTG or CACTGTG) within the 3' region of zebrafish C(L) were identified. In mammals, heptamers within J(κ)-C(κ) introns can recombine with downstream kappa deleting elements (Kde) to ablate C(κ) regions prior to rearrangements of V(λ)-J(λ) gene segments. The presence of palindromic heptamers within zebrafish C(L) is intriguing as their recombination with intact RSS might result in the deletion of a large portion of the C(L) thereby permanently silencing C(L) exons within the IgL locus. Given that bony fish have appreciably more C(L) spread over more chromosomes than mice and humans, it is plausible the presence of recombining sequences within C(L) may be tied to a need for heightened mechanisms to facilitate allelic exclusion or receptor editing. Collectively, with this report, gap-free annotations of the heavy and light chain Ig loci have now been completed for Danio rerio, the only teleost for which this has been accomplished, thereby strengthening the overall utility of zebrafish as a model organism for both comparative immunology and biomedical research.

Immunoglobulin light chain (IgL) genes in zebrafish: Genomic configurations and inversional rearrangements between (V(L)-J(L)-C(L)) gene clusters.

In mammals, Immunoglobulin light chain (IgL) are localized to two chromosomal regions (designated kappa and lambda). Here we report a genome-wide survey of IgL genes in the zebrafish revealing (V(L)-J(L)-C(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(L)-J(L)-C(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(L), J(L) and C(L) to have greater potential for immunoglobulin gene shuffling than traditionally studied mice and human models.