DNA methylation-sensitive transcription factors and bivalency orchestrate transposon expression in the absence of DNA methylation [Chromatin landscape across spermatogenesis in wild type and Dnmt3C mutants]
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: Previous studies in mESCs suggest that in absence of DNA methylation, retrotransposon repression can be taken over by repressive histone modifications. To investigate if the developmental-like pattern of TE expression observed in Dnmt3C mutants correlates with the dynamics of the chromatin landscape in spermatogenesis, we performed CUT&Tag to profile key histone modifications in wild type (WT) and Dnmt3CKO/KO(KO) germ cells at three developmental stages: embryonic prospermatogonia (ProSpg), postnatal spermatogonia (Spg) and spermatocytes (Spc). We  profiled two active (H3K4me3, and H3K27ac) and three repressive (H3K9me2, H3K9me3, and H3K27me3) histone modifications.