Epigenetic regulator function through mouse gastrulation

Development of a multicellular organism uses the same genetic code to generate a broad diversity of cell types, which is instructed by extracellular cues and orchestrated by transcriptional activators and repressors. While transcription factors establish cell identities according to the central dogma, a number of enzymes, which index and regulate chromatin, appear to perform essential functions as well. We optimized a versatile experimental and analytical approach that allows for rapid perturbation of genes and the recovery of high replicate powered phenotypic information. We applied this set-up to investigate a panel of epigenetic regulators that are essential for early gestation. Our comparative analysis approach enabled us to pinpoint affected genetic pathways and cell lineage-specific effects that distinguish even closely related regulators, such as polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Moreover, by incorporating additional epigenetic data, we were able to identify early aberrations that partially explain how certain developmental abnormalities emerge at the onset of gastrulation. Single-cell RNAseq data was collected on whole early mouse embryos generated using B6/CAST F1 sperm and B6D2F1 oocytes. Each experiment consists of 4-12 embryo replicates from developmental stages E6.5, 7.0, 7.5, 8.0, 8.5 for wild-type, of E8.5 for all epigenetic regulator knockouts (KOs) and for Eed KO additionally from E6.5 and 7.5. All scRNA-seq data was generated using the 10X Genomics single cell RNA sequencing platform. Sample titles with "a" or "b" represent distinct sets of cells sequenced from the same experiment. Additional epigenetic data was generated for E6.5 embryos generated by natural mating B6D2F1 females with B6D2F1 males for each KO and WT. Macroscopically dissected embryonic (epiblast) and extraembryonic (extraembryonic ectoderm) fractions were collected in pools of ~10 embryos per KO and whole-genome bisulfite sequencing data was generated using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences).