Journal article

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

Celia Alda-Catalinas, Danila Bredikhin, Irene Hernando-Herraez, Fatima Santos, Oana Kubinyecz, Melanie A Eckersley-Maslin, Oliver Stegle, Wolf Reik

CELL SYSTEMS | CELL PRESS | Published : 2020

Abstract

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 activation (CRISPRa) with single-cell transcriptomics to identify regulators of ZGA-like transcription in mouse embryonic stem cells, which serve as a tractable, in vitro proxy of early mouse embryos. Using multi-omics factor analysis (MOFA+) applied to ∼200,000 single-cell transcriptomes comprising 230 CRISPRa perturbations, we characterized molecular signatures of ZGA..

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Grants

Awarded by UK Research and Innovation (UKRI)


Awarded by Marie Sklodowska-Curie Individual Fellowship


Awarded by BBSRC Discovery fellowship


Awarded by BBSRC


Awarded by Wellcome Trust


Awarded by EU (ERC )


Funding Acknowledgements

The authors thank all members of the Reik and Stegle laboratories for helpful discussions. We also thank Laura Benson for technical assistance; Mario Iurlaro for helpful discussions on Smarca5; Paul Datlinger for advice on CROPseq lentiviral preparation; Felix Krueger and the bioinformatics facility from the Babraham Institute for processing sequencing data and assistance with repeat mapping; Lia Chappell for training in 10x Genomics library preparation; Anne Segonds-Pinchon for statistical advice; the sequencing facilities at Babraham Institute, Sanger Institute, and CRUK in Cambridge for high-throughput library preparation and sequencing; and the flow cytometry facility at the Babraham Institute for cell sorting. Smarca5 (Snf2h) KO ESCs were a kind gift from Dirk Sch_ubeler. Lenti sgRNA(MS2)_puro backbone (Addgene 73795), lenti dCAS-VP64_Blast (Addgene 61425), and lenti MS2-P65-HSF1_Hygro (Addgene 61426) were a gift from Feng Zhang. pMD2.G (Addgene 12259) and psPAX2 (Addgene 12260) were a gift from Didier Trono. C.A.-C. was supported by a postgraduate award by UK Research and Innovation (UKRI, 1645504). D.B is supported by a Darwin Trust fellowship. I.H.-H. is supported by a Marie Sklodowska-Curie Individual Fellowship (751439). M.A.E.-M. is supported by a BBSRC Discovery fellowship (BB/T009713/1). Research in the Reik lab is supported by BBSRC (BBS/E/B/000C0422) and Wellcome Trust (105031/Z/14/Z; 210754/Z/18/Z). Research in the Stegle lab is supported by core funding from EMBL, the BMBF, the Volkswagen Foundation, and the EU (ERC project DECODE 810296).