BIRTH OF POLYMORPHIC PIRNA CLUSTERS DRIVEN BY TRANSPOSABLE ELEMENT INSERTIONS IN THE MALE CATTLE GERMLINE

We aim at studying the two sides of the same coin: (i) one major line of host defense against the mobilization of transposable elements (TE): the PIWI-interacting RNA (piRNA) pathway and (ii) the activity of TE in the bovine germline. We previously demonstrated that several TE families are still active in present-day cattle breeds. These include endogenous retroviruses (ERV), long and short interspersed repeats (LINE and SINE) and processed pseudogenes. We have collected testes samples from sexually immature (pre-pachytene stage; n=100) and mature (pachytene stage; n=100) animals. From the host defense side, we are sequencing oxidized piRNA libraries, reads are mapped to the ARS-UCD1.2 bovine reference sequence and piRNA clusters are annotated using proTRAC (Rosenkranz & Zischler, 2012). From the TE side, we developed a bioinformatics tool to mine available whole genome sequences (WGS; n>1000) of the corresponding breeds to establish a catalog of polymorphic (unfixed) TE segregating in these breeds. Custom, array-based, genotyping assays, targeting insertion sites, are developed to directly genotype our testes collection. We will integrate piRNA and TE genotyping data to establish the degree of interplay between host defense and young TE to answer the following question: are unfixed piRNA clusters directly driven by recent TE insertions? Preliminary data on pre-pachytene testes with matched WGS, piRNA and mRNA sequences allowed us to indeed identify striking instances of births of new, allele-specific, polymorphic piRNA clusters derived from unfixed (i) ERVK, (ii) LINE1 and (iii) processed pseudogene intronic insertions. Latest results will be presented.