Exploration of retrotransposon deletion phenotype in pre-implantation mouse embryo development
Previous RNA-Seq analysis on mouse embryos revealed non-canonical mRNA splicing involving retrotransposon (RT) elements during pre-implantation development. The retrotransposon-element derived, non-canonical isoforms appear to be the dominant isoform in over 200 genes during critical stages of development. Specific retrotransposon-element knockout mice had been made to investigate possible developmental roles of the non-canonical gene regulation and protein expression. Preliminarily, heterozygous crosses between mice lacking a single retrotransposon fragment shows a statistically significant shift away from the expected mendelian ratio. In this project, through biochemical, histological and biostatics analysis, I aim to explore the phenotype associated with CRISPR-Cas9 deletion of the RT derived isoform of the nearby gene to explain the decrease in viability. This is one small step in the direction of understanding the role of retrotransposon, traditionally considered as “Junk DNA”, in embryo pre-implantation development.