Genomic Characterization of the Germline Marker vasa in a Species that Undergoes Programmed Genome Rearrangement

The sea lamprey, Petromyzon marinus, undergoes massive programmed genomic rearrangements early in development during the midblastula transition. During these rearrangements approximately 20% of the genome is deleted in somatic cells but is maintained in the germline. Our preliminary studies indicate that these genes are deleted in the somatic cells because misexpression would give rise to cancers and other developmental disorders. In order to better track genomically differentiated cell lineages in early embryogenesis, we cloned, sequenced, and characterized the lamprey homolog of the classical germline marker vasa. Vasa is essential in the development of germ cells in multiple species ranging from worms to humans, and presumably has the same function in lamprey. We used in situ hybridization to verify that the lamprey vasa homolog is specifically expressed in germ cell lineages. Analyses of the germline locus revealed novel aspects of the germline locus, specifically the introns have a reiterated repetitive structure with self-complementarity at the 5’ and 3’ intron boundaries. This unique intronic structure was not shared in the human homolog of the vasa gene, but is similar to sequence motifs (CA and GT dinucleotide repeats) that are enriched in the flanking regions of sequences that are targeted for elimination during programmed genome rearrangement. We speculate that this repetitive structure may be functionally related to the retention of germline specific DNAs and expression of germline specific genes.