Somatic retrotransposition in the developing rhesus macaque brain

Abstract

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 is poorly defined, and is 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 non-human primate L1s can similarly generate somatic insertions in the brain. Here we applied ~40× single-cell whole genome sequencing (scWGS), and retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and robustly 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 non-human primate, and allude to L1 mobility in the brain over the last 30 million years of human evolution.

LINE-1 retrotransposon activation intrinsic to interneuron development

“…Heritable L1 insertions principally arise in the early embryo and primordial germ cells 17–21 . Somatic L1 retrotransposition can occur in the brain, as first revealed by L1-EGFP retrotransposition reporter experiments 22–24 and later confirmed by single-neuron (NeuN + ) genomic analyses 4–7 . However, the key question remains of whether specific neuronal lineages are more permissive for somatic retrotransposition than others.…”

“…Our results do not however preclude other neuronal subtypes or brain regions from expressing L1 mRNAs and proteins, or supporting L1 retrotransposition. Engineered L1 reporter experiments have thus far generated data congruent with endogenous L1 mobility in the early embryo 18,19,21 , neurons 4–7,22,23,63 and cancer 14,64,65 . While we and others have mapped endogenous L1 retrotransposition events in human 4–6 and macaque 7 neurons, the composition of the L1 T F 3ʹUTR appears to severely impede such analyses in mouse 19,45,66 .…”

“…Engineered L1 reporter experiments have thus far generated data congruent with endogenous L1 mobility in the early embryo 18,19,21 , neurons 4–7,22,23,63 and cancer 14,64,65 . While we and others have mapped endogenous L1 retrotransposition events in human 4–6 and macaque 7 neurons, the composition of the L1 T F 3ʹUTR appears to severely impede such analyses in mouse 19,45,66 . A cL1 spa mouse model could in the future be used to evaluate mouse L1 mobilization in the PV + neuron lineage in vivo .…”

“…Developmental programs that activate these elements could, in principle, manifest in lineage-specific retrotransposition. Somatic LINE-1 (L1) retrotransposon insertions have been detected in human and non-human primate neurons 4–7 . It is however unknown whether L1 is mobile in only some neuronal lineages, or therein regulates neurodevelopmental genes.…”

Reactivation of an Endogenous retrovirus in Drosophila ovarian somatic tissue: from germline invasion to taming

“…If they do not, at least from time to time, they acquire mutations until there are no functional copies left and the ERV family dies out. Some ERVs gained cell and developmental stage specific expression [2][3][4][5][6][7] . ERVs that have acquired the capacity to be expressed exclusively in somatic cells must therefore maintain their ability to invade germ cells to survive.…”