A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

• DOI: 10.1016/j.cels.2020.06.004
• Publication Date: 2020-07-06T14:36:02Z
• Authors: Celia Alda-Catalinas; Danila Bredikhin; Irene Hernando-He...; Fátima Santos; Oana Kubinyecz; Mélanie A. Eckers...; Oliver Stegle; Wolf Reik
• Keywords: 0301 basic medicine; 570; 03 medical and health sciences; Genome; Zygote; Humans; Clustered Regularly Interspaced Short Palindromic Repeats; Transcriptome; Article; Epigenesis, Genetic

Zygotic genome activation (ZGA) is an essential transcriptional event in embryonic development that coincides with extensive epigenetic reprogramming. Complex manipulation techniques and maternal stores of proteins preclude large-scale functional screens for ZGA regulators within early embryos. Here, we combined pooled CRISPR (CRISPRa) single-cell transcriptomics to identify ZGA-like transcription mouse stem cells, which serve as a tractable, vitro proxy Using multi-omics factor analysis (MOFA+) applied ∼200,000 transcriptomes comprising 230 CRISPRa perturbations, characterized molecular signatures uncovered 24 factors promote response. Follow-up assays validated top screen hits, including the DNA-binding protein Dppa2, chromatin remodeler Smarca5, Patz1, experiments revealed Smarca5's regulation dependent on Dppa2. Together, our transcriptomic profiling CRISPRa-perturbed cells provides both system-level insights into mechanisms orchestrate ZGA.