Profiling the transposable element landscape in a new wild mouse resource
In: Student Reports, Summer 2022, The Jackson Laboratory
Alexis Garretson, MS, Laura Blanco-Berdugo, MS, and Beth Dumont, Ph.D.
The classic inbred mouse strain, C57BL/6J (B6), has been used as a mouse model for decades, but lacks essential genetic diversity seen in the natural mouse population. The Nachman strains are inbred wild mouse strains derived to be more representative model organisms. The purpose of this project was to explore the transposable element (TE) landscape in the Nachman panel of wild mouse strains, and compare it to that of the B6 strain. Transposable elements are segments of the genome capable of mobilization and self replication and are important mechanisms for evolution. Using a TE identifying tool called DNA Pipe TE, we analyzed short-read sequencing data from several Nachman strains. We then compared those results to TEs identified in B6 samples. We found that within most TE families, the accumulation levels were highly similar. However, there were significantly fewer LINEs in both the Nachman strains analyzed. The LINE subfamilies responsible for large amounts of the variance between samples are associated with many human diseases, and are documented as the most recently active TEs in the B6 samples. Overall, this analysis yields important details on how transposable elements are characterized in this new mouse resource.
Kumar, Sirohi, "Profiling the transposable element landscape in a new wild mouse resource" (2022). Summer and Academic Year Student Reports. 2700.