Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells

The nuclear exosome targeting (NEXT) complex is responsible for recruiting RNA exosomes to degrade specific nuclear RNAs in mammalian cells. However, its function in mammalian development remains unknown. Here, we found that the depletion of a central factor of the NEXT complex, Zcchc8, resulted in mouse developmental defects, a shortened life span and infertility. Zcchc8-deficient embryonic stem cells (ESCs) exhibited proliferation abnormalities and reduced developmental potencies. Interestingly, we found that retrotransposon elements, especially LINE1 RNAs, are targeted and degraded by Zcchc8 in ESCs. We subsequently demonstrated that Zcchc8-depleted oocytes show defects in meiotic maturation and early embryo development. Moreover, the sustained expression of higher levels of LINE1 RNA was also detected in maternal Zcchc8-depleted oocytes and Zcchc8-deficient embryos, which can further increase chromatin accessibility. Collectively, our study uncovers the important role of Zcchc8 in the degradation of LINE1 transcripts in early embryos and ESCs at the posttranscriptional level. Nuclear RNA RIP seq of HA-Rbm7 and HA-Zcchc8 were done in ESCs using HA antibody, with 2 replicates for RIP and one for input. Small amount RNA seq of WT and Zcchc8 KO GV oocytes were done with 4 replicates respectively. Small amount RNA seq of WT and Zcchc8 knockdown embryos at 4 cell stage and blastocyst were done with 3 replicates for control and 2 replicates for knockdown embryos.Small amount RNA seq of WT and Zcchc8 knockout embryos at 4 cell stage and inner cell mass were done with 3-4 replicates for each sample. rRNA free total RNA seq were done for control, KO, overexpression of Zcchc8 in KO ESCs with 2 replicates each. Total RNA half-life test of control and Zcchc8 KO ESCs using Actinomycin D treatment, with 2 replicates each time point. ATAC-seq was done for WT and Zcchc8 KO ESCs with 2 replicates.