biostudies-literatureRosen BPNHGRI NIH HHSNCI NIH HHSU.S. Department of Health & Human Services | NIH | National Human Genome Research InstituteU.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)NIH HHSNIGMS NIH HHS8966https://www.ebi.ac.uk/biostudies/studies/S-EPMC11487130biostudies-literatureUnknown15(1)Pluripotent stem cells have remarkable self-renewal capacity: the ability to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into almost any cell type in the body. To investigate the interplay between these two aspects of self-renewal, we perform four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSCs and the dissolution of primed pluripotent identity during early differentiation. These screens distinguish genes with distinct roles in pluripotency regulation, including mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control pluripotent identity during early differentiation. We further identify a core set of genes controlling Nature communicationsParallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness.PMC11487130S10 OD030286P30 CA008748R01 HG012367UM1 HG012654T32 GM008539UM1HG012654U01HG012051U01 HG012051Cho HSGraff SYan JKale HTDamodaran JRYang DVerma NSidoli SKaplan SJHuangfu DLi QVRosen BPLiu DBeer MALuo RfalseParallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness.Pluripotent stem cells have remarkable self-renewal capacity: the ability to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into almost any cell type in the body. To investigate the interplay between these two aspects of self-renewal, we perform four parallel genome-scale CRISPR-Cas9 loss-of-function screens interrogating stem cell fitness in hPSCs and the dissolution of primed pluripotent identity during early differentiation. These screens distinguish genes with distinct roles in pluripotency regulation, including mitochondrial and metabolism regulators crucial for stem cell fitness, and chromatin regulators that control pluripotent identity during early differentiation. We further identify a core set of genes controlling 2024-01-01T00:00:00Z2024 Oct2026-07-15T13:09:19.438Z2025-04-04T14:37:30.033ZS-EPMC114871303941999410.1038/s41467-024-53284-4