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Live (epi)genomic battle between unfixed transposable elements and their cognate piRNA clusters in cattle testes
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International audience. Transposable elements (TE) can affect genomic stability, gene function and trigger deleterious mutations. PIWI-interacting small RNAs (piRNAs) are known as important soldiers standing in the arms race against TE mobilization in the germline. We previously demonstrated that several TE families are still active in present-day cattle breeds, including endogenous retroviruses (ERV), long and short interspersed repeats (LINE and SINE) and pseudogenes. We have collected testes samples from sexually immature (9 neonate; 100 juvenile = pre-pachytene stage) and mature (100 adult = pachytene stage) animals. piRNA and mRNA libraries were built for a subset of animals with different ages and reads were mapped to the ARS-UCD1.2 bovine reference. From the TE side, we established a catalogue of polymorphic (unfixed) ERV, LINE and processed pseudogenes in cattle, mining whole-genome sequencing data available from different breeds (n>1000). Intersecting piRNA data with our catalogue of TE insertions, we observed higher expression of piRNAs nearby ERVs, LINE and pseudogenes in pre-pachytene animals compared to pachytene animals. Combining TE insertion genotypes with the piRNA normalised counts, we detected polymorphic piRNA clusters directly driven by recent TE insertions. For all the three TE classes, manual inspection allowed us to indeed identify striking instances of births of new, allele-specific (cis), polymorphic piRNA clusters. Especially for pseudogenes, we identified polymorphic insertions driving piRNA clusters putatively affecting the corresponding parent gene expression in trans. We are performing an eQTL study based on TE genotypes and testis mRNA data to investigate the putative effect of polymorphic piRNA clusters on gene expression. Latest results will be presented.
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