Optimized whole-genome CRISPR interference screens identify ARID1A-dependent growth regulators in human induced pluripotent stem cells

• DOI: 10.1016/j.stemcr.2023.03.008
• Publication Date: 2023-04-06T14:30:05Z
• Authors: Sunay Usluer; Pille Hallast; Luca Crepaldi; Yan Zhou; Katie Urgo; Cansu Dincer; Jing Su; Guillaume Noell; Kaur Alasoo; Omar El Garwany; Sebastian S. Gerety; Ben Newman; Oliver M. Dovey; Leopold Parts
• Keywords: DNA-Binding Proteins; 0301 basic medicine; 03 medical and health sciences; Genome; Induced Pluripotent Stem Cells; Humans; CRISPR-Cas Systems; Article; Transcription Factors

Perturbing expression is a powerful way to understand the role of individual genes, but can be challenging in important models. CRISPR-Cas screens human induced pluripotent stem cells (iPSCs) are limited efficiency due DNA break-induced stress, while less stressful silencing with an inactive Cas9 has been considered effective so far. Here, we developed dCas9-KRAB-MeCP2 fusion protein for screening iPSCs from multiple donors. We found 200 bp window around transcription start site polyclonal pools as using wild-type identifying essential much reduced cell numbers. Whole-genome identify ARID1A-dependent dosage sensitivity revealed PSMB2 gene, and enrichment proteasome genes among hits. This selective dependency was replicated inhibitor, indicating targetable drug-gene interaction. Many more plausible targets models efficiently identified our approach.