Ambivalent chromatin logics of repetitive DNA in male germ cells and fertility – biCHLORE

Mammalian genomes are replete with repeated sequences of various origins. Some of these repeats are organized and function as genes, yet they need to be distinctively regulated from single-copy genes to limit excessive dosage and genomic instability. These coding repetitive sequences include clusters of multicopy genes, and transposable elements (TEs) that are dispersed throughout the genome. Although very different, these two repeat types share the male germline as a privileged expression niche, and are both involved in intragenomic conflicts that have profoundly shaped genome structure while compromising fertility in the short-term. Such common trajectory may imply a common regulatory mechanism. Indeed, we have recently discovered that TEs and multicopy genes share a non-canonical combination of antagonistic H3K4me3 and H3K9me3 marks during male germline development, which may attract the dual H3K4/K9me3 reader SPIN1. The biCHLORE project aims at testing the role played by this dual chromatin status as a universal signal to sense and regulate both TEs and multicopy genes, and its implication in male fertility, using the mouse model. We propose an original and structured program to 1) Decipher the dynamics and general chromatin configuration of dually marked H3K4/K9me3 repeats during male germline development, 2) Challenge the relationship between H3K4/K9me3 marks and the chromatin reader SPIN1 in vivo, and 3) Identify SPIN1 interactome and other H3K4/K9me3-associated proteins to highlight the mechanism of action of this novel chromatin pathway. To this end, we will use state-of-the art approaches spanning multimodal single-cell chromatin profiling, epigenomic editing and proteomics, and exploit our expertise in mouse genetics, reproductive biology and repeat-focused bioinformatics. This program has the potential to reveal a unifying mechanism of chromatin-based discrimination of repeated from non-repeated DNA, rooted into the genome of reproductive cells.