Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [ChIP-Seq]

In mammals, many retrotransposons are de-repressed during zygotic genome activation (ZGA). However, their functions in early development remain elusive largely due to the challenge to simultaneously manipulate thousands of retrotransposon insertions in embryos. Here, we employed epigenome editing to perturb long terminal repeat (LTR) MT2_Mm, a well-known ZGA and totipotency marker that exists in ~2667 insertions throughout the mouse genome. CRISPR interference (CRISPRi) robustly targeted and repressed 2485 (~93%) MT2_Mm insertions and 1090 (~55%) insertions of the closely related MT2C_Mm in 2-cell embryos. Remarkably, such perturbation caused down-regulation of hundreds of ZGA genes at 2C stage and embryonic arrest mostly at morula stage. Mechanistically, MT2_Mm/MT2C_Mm primarily served as alternative ZGA promoters activated by Obox proteins. Thus, through large-scale epigenome editing, we addressed to what extent MT2_Mm/MT2C_Mm regulates ZGA and preimplantation development. Our approach could be adapted to systematically perturb retrotransposons in other mammalian embryos as it doesn't require transgenic animals. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) data of dCas9 and HA in mouse embryonic stem cells. Control cells only express dCas9 whereas the treatment group express both dCas9 and MT2_Mm sgRNAs.