CRISPRi Knockdown and Sequence Analysis of the BHIKHARI Family of Endogenous Retroviruses in Zebrafish

Abstract

Transposable Elements (TEs) are mobile, selfish genes that have, in some cases, been shown to provide functions for the host. A poorly characterized family of LTR retrotransposons, BHIKHARI (bik), has unusual early embryonic, cell-specific expression patterns in the zebrafish (Danio rerio). This led me to investigate their possible role in the development of the zebrafish embryo and their evolutionary history in related species. I present a successful CRISPRi knockdown experiment of bik-1, one of five subfamilies of bik, that shows evidence of the involvement of bik-1 in cell differentiation. Polymorphism analysis gave evidence that bik-1 may still be active in zebrafish while the other bik subfamilies may not be. Sequence analysis of the subfamilies suggests that all five may have arisen from a common element sometime after the divergence of the Danionella and Danio genera. Additionally, I characterize bik elements as members of the recently described Lokiretrovirus clade of retroelements.