Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons

Wu，Qianxin1; Wu，Junjing1,3; Karim，Kaiser2; Chen，Xi1,4; Wang，Tengyao5; Iwama，Sho1; Carobbio，Stefania1,6,7; Keen，Peter1; Vidal-Puig，Antonio1,6,7; Kotter，Mark R.2; Bassett，Andrew1

2023-04-06

10.1016/j.molcel.2023.02.011

Molecular Cell   Impact Factor & Quartile

1097-2765

1097-4164

CRISPR activation (CRISPRa) is an important tool to perturb transcription, but its effectiveness varies between target genes. We employ human pluripotent stem cells with thousands of randomly integrated barcoded reporters to assess epigenetic features that influence CRISPRa efficacy. Basal expression levels are influenced by genomic context and dramatically change during differentiation to neurons. Gene activation by dCas9-VPR is successful in most genomic contexts, including developmentally repressed regions, and activation level is anti-correlated with basal gene expression, whereas dCas9-p300 is ineffective in stem cells. Certain chromatin states, such as bivalent chromatin, are particularly sensitive to dCas9-VPR, whereas constitutive heterochromatin is less responsive. We validate these rules at endogenous genes and show that activation of certain genes elicits a change in the stem cell transcriptome, sometimes showing features of differentiated cells. Our data provide rules to predict CRISPRa outcome and highlight its utility to screen for factors driving stem cell differentiation.

chromatin CRISPR activation CRISPRa epigenetic hiPSC iNeurons p300 single cell stem cells VPR

English

NI Journal Papers

Others

MOLECULAR BIOLOGY & GENETICS

2-s2.0-85151345784

Scopus

1.Wellcome Sanger Institute,Cambridge,Hinxton,CB10 1SA,United Kingdom
2.Department of Clinical Neurosciences,University of Cambridge,Cambridge,CB2 0QQ,United Kingdom
3.Institute of Animal Science and Veterinary Medicine,Hubei Academy of Agricultural Sciences,Wuhan,430064,China
4.Southern University of Science and Technology,Shenzhen,1088 Xueyuan Ave, Nanshanm Guangdong,518055,China
5.Department of Statistics,London School of Economics and Political Science,London,WC2B 4RR,United Kingdom
6.Metabolic Research Laboratories,Addenbrooke's Treatment Center,Institute of Metabolic Science,Addenbrooke's Hospital,University of Cambridge,Cambridge,United Kingdom
7.Centro de Investigacion Principe Felipe,Valencia,46012,Spain

Wu，Qianxin,Wu，Junjing,Karim，Kaiser,et al. Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons[J]. Molecular Cell,2023,83(7):1125-1139.e8.

Wu，Qianxin.,Wu，Junjing.,Karim，Kaiser.,Chen，Xi.,Wang，Tengyao.,...&Bassett，Andrew.(2023).Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons.Molecular Cell,83(7),1125-1139.e8.

Wu，Qianxin,et al."Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons".Molecular Cell 83.7(2023):1125-1139.e8.