DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Postnatal Retrotransposon expression in spermatogenesis]
Silencing of young retrotransposons by Cytosine DNA methylation is essential for spermatogenesis. Failure to methylate retrotransposon promoters leads to their reactivation, meiotic catastrophe and infertility. How transposons become reactivated and why their reactivation follows spermatogenic developmental patterns remains unclear. Here, we show that specific retrotransposon families exhibit distinct expression patterns and chromatin landscapes throughout spermatogenesis when DNA methylation is absent from their promoters. We find a strong correlation between the loss of bivalent H3K4me3-H3K27me3 chromatin modifications and the  transition from low retrotransposon expression in spermatogonia to reactivation in meiotic spermatocytes. Using a combination of DNA pulldowns, mass spectrometry and chromatin profiling by CUT&Tag, we identify the DNA methylation-sensitive transcription factor NRF1 as a potential regulator of unmethylated retrotransposons in spermatogenesis. Germline conditional ablation of Nrf1 reduced the upregulation of IAPs in the absence of DNA methylation and rescued the accumulation of IAP-derived Pol protein to wild type germ cell levels. Our study demonstrates that a combination of chromatin modifications and a DNA methylation-sensitive TF regulates young retrotransposons upon loss of repressive DNA methylation in germ cells, suggesting these interactions may be a core strategy used by retrotransposons to proliferate in the germline after evading silencing by DNA methylation. Overall design: To get a comprehensive overview of the expression patterns of TEs after failure to silence by DNA methylation, we checked RNA expression of distinct germ cell stages wildtype and Dnmt3CKO/KO animals, where DNA methylation is absent at young retrotransposon promoters. To this end, we performed RNA-seq on sorted premeiotic (Spermatogonia, Spg) and meiotic (Spermatocytes, Spc) cells from wildtype and Dnmt3CKO/KO animals and characterized the transcriptional activity of retrotransposon families in response to the loss of promoter DNA methylation.