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Abstract :
[en] Endogenous retrovirus (ERVs) is a component of mammalian genome, which records evolutionary fossils left over from ancient viral infections. Most ERVs have lost their mobilisation capacity due to mutational accumulation and inter-LTR recombination, but some ERVs are still transpositionally active in germlines in some species. By mining a dataset of whole-genome sequences for 131 extended cattle pedigrees, we identified 5 de novo transpositions (dnT) from same ERV subfamily. Thus, the ERV dnT rate (dnTR) can be roughly estimated at 1 new insertion every ~50 gametes, yet with major differences between individuals (as 3 from the 5 detected events occurred in the same animal). To allow us to quantify the inter-individual variation in dnTR, we modified a method (Pooled CRISPR Inverse PCR sequencing: PCIP-seq) initially developed to detect somatic retroviral insertions (Artesi et al, 2021). The features of this method: I) CRISPR-based; II) UMI-like; III) natural replicates; IV) NGS-based; enable the measurements on individual dnRT reproducible and robust. By applying this approach to sperm samples from a cohort of sire with similar age, dnTR was quantified in the range from 0.23 to 2.07 with an average of 1.2 per 100 gametes, which keeps in line with the rate assessed in pedigrees. Moreover, we applied this method to sperm samples of 9 sires sampling at two ages cross about 10 years, no significant inflation of dnTR observed with age. However, a fraction of dnT were identified in two ages, which means sperms with recurrent insertions originated from clone of same spermatogonial stem cell (SSC), indicating those transposition events have been occurred before or during SSC establishment. Intriguingly, dnRT of mature testis is at least one to two magnitude higher than rate of sperm with same age, speculating a process involving harsh checkpoint to filter out sperms with too many dnT to guard integrity of genetic transmission.
