Single embryo total RNA sequencing to map the effect of maternal SETDB1 on the 2-celll and 8-cell transcriptome

Embryos with maternal mutation of the H3K9 methyltransferase SETDB1 die before implantation. We tested the role of maternal SETDB1 in the timely processes of the preimplantation stage embryo. Using single embryo total RNA sequencing from 2-cell and 8-cell embryos, we found that maternal SETDB1 is required for switching off maternal transcripts by the 2-cell stage, minor ZGA transcripts by the 2-cell stage, and major ZGA transcripts by the 8-cell stage. By timely extinguishing of endogenous retroviruses, oocyte-specific ERVL-MaLRs, many oocyte-specific genes, MERVLs, MERVL LTR-driven chimeric transcripts and ZGA genes as well as KRAB ZF genes, maternal SETDB1 secures the proper transition from totipotency to pluripotency. Overall design: Setdb1 maternal mutant (Zp3Cre +) and control (Zp3Cre -) 2c and 8c stage mouse embryos were collected at 1.5 dpc and 2.5 dpc, respectively. Single embryo total RNA-seq was done using biological replicates.