CRISPRi Knockdown and Sequence Analysis of the BHIKHARI Family of Endogenous Retroviruses in Zebrafish
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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.
CRISPRi; transposon; transposable element; endogenous retrovirus; zebrafish
dissertation or thesis