Maternal SMARCA5 is required for major ZGA in mouse [NOME-seq]

Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood. We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages. Overall design: NOME-seq libraries were generated from Smarca5 Heterozygous 2 cell stage embryos (Smarca5 mat KO x WT male) (1 technincal replicates, containing embryos from multiple matings, pooled). Same type of libraries generated from WT 2 cell stage embryos in which SMARCA5 was degraded at the zygotic stage, using the TrimAway system (libraries generated at least 24 hours post-injection). The Trim Away embryos libraries are in 3 technical replicates (each replicate representing a different pool of injected embryos). The same samples were used to generate RNA-seq libraries (as part of the scNMT-seq protocol)