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The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole-genome sequencing (scWGS), as well as retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and PCR-validated a somatic L1 insertion that generated target site duplications, carried a short 5 transduction, and was present in ∼7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30 million years of human evolution.

Structural Maintenance of Chromosomes, Hinge Domain containing 1 (Smchd1) is critical for the maintenance of X Chromosome Inactivation (XCI), and transcriptional repression at a subset of autosomal loci (Blewitt et al., 2008; Mould et al., 2013; Gendrel et al., 2013). Gain and loss of function mutations in SMCHD1 have been found to underlie Bosma arhinia micropthalmia syndrome (BAMS) and Facioscapulohumoral muscular dystrophy 2 (FSHD2), respectively - two distinct developmental disorders (Lemmers et al., 2012; Gordon et al., 2017; Shaw et al., 2017). Currently little is known about molecular mechanisms underlying the involvement of Smchd1 in transcriptional repression or disease. This project aimed to better understand how Smchd1 associates with and influences the chromatin. There has been growing evidence in the literature to suggest that Smchd1 and the non-coding RNA Xist might interact directly (Nozawa et al., 2013; Kelsey et al., 2015; Minajigi et al., 2015). We have previously shown that the hinge domain of Smchd1 binds synthetic DNA and RNA oligonucleotides in vitro (Chen et al., 2015). I was therefore interested in whether Smchd1 directly associates with endogenous nucleic acids, and whether such interactions could be important for Smchd1's localisation to the chromatin. To this end, I performed PAR-CLIP to determine whether Smchd1 binds endogenous RNAs genome-wide. I find Smchd1-RNA interactions to be non-specific, and are therefore unlikely to act as a targeting mechanism. I also find that while Smchd1 is dependent on Xist for its localisation to the Xi, this is not due to a direct protein-RNA interaction, but rather due to a dependency on the downstream HnrnpK-polycomb pathway. Evidence from our lab has suggested that Smchd1 may be involved in regulating higher order chromatin organisation (Chen et al., 2015). To investigate changes to the chromatin architecture in the absence of Smchd1, I have performed in-situ Hi-C and ATAC-seq in Smchd1 wild-type and de