New study reveals details across 20 diverse inbred mouse strains cellpressnews
The completion of the full “telomere-to-telomere” human genome last year emphasized that genome sequences that were previously thought to be “complete” were not, in fact, complete at all. Credit: The Jackson Laboratory
TEs are repetitive sequences that have moved to other locations in the genome, and the mobility of these sequences contribute greatly to genomic variation. Repetitive sequences frequently underlie the formation of structural variants - genomic differences resulting from duplications, insertions, deletions, and inversions. SVs are often missed when using short read sequencing but they can play important roles in genome dysregulation and disease.
For the work presented in"Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to, Dr. Beck selected a wide variety of commonly used strains, including the seven parental founders of the genetically diverse Collaborative Cross and Diversity Outbred mouse panels, six resultant CC strains with abnormalities of unknown genetic origin, and seven other commonly used strains with different genetic backgrounds.
While only a small number of TEs are still able to mobilize in human genomes, they are more mobile in mice. Because of this, Beck and her team focused on transposable element variants , which they found comprised nearly 40% of all SVs, with most being insertions. There are multiple kinds of TEVs, known as short versus long interspersed nuclear elements , which are predictably characterized by their size. LINEs were nearly twice as common as SINEs in the mouse genomes, 47% to 24%.
They also identified a previously undetected retroviral element insertion within a specific gene, Mutyh, a DNA repair gene associated with a known mutational signature in certain mouse strains. The underlying variant was unknown, but the team found that the insertion was associated with a significant decrease in Mutyh gene expression.
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