Medaka vasa gene has an exonic enhancer for germline expression

Enhancers are DNA sequences that enhance gene transcription in a position- and orientation-independent manner. Many enhancers controlling somatic gene expression have been described. Enhancers controlling germline expression have remained rare. Here we report the identification of V35 as a first exonic germline enhancer in vertebrates. V35 constitutes the first 35bp of exon 1 of the medaka vasa gene. V35 is required for vasa promoter function and sufficient to increase transcriptional activity of a heterologous promoter by ~13 fold in either forward or reverse orientation. V35 contains CAGCAGCACGAG for two paired E box-like motifs. Upon incubation with nuclear extract from spermatogonial cells, V35 formed three DNA–protein complexes. We show that complex formation is inhibited partially by oligos containing an E box or E box-like motif but completely by V35 and oligos that contain overlapped E box and E box-like motifs. Most importantly, V35 is sufficient to drive transgene expression in germ cells of developing embryos. These results establish V35 as the first exonic germline enhancer in a lower vertebrate, and provide evidence for the importance of exonic sequences in controlling germ gene expression. •An exonic enhancer called V35 is present in the medaka vasa gene.•V35 is necessary and sufficient for transcriptional activity in vitro.•V35 forms DNA–protein complexes in EMSA.•V35 is sufficient to drive germline-specific expression in vivo.•We provide a first exonic enhancer for germline expression.