Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons
|Corresponding Author||Wu，Qianxin; Bassett，Andrew|
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.
NI Journal Papers
|ESI Research Field|
MOLECULAR BIOLOGY & GENETICS
Cited Times [WOS]:0
|Document Type||Journal Article|
|Department||Southern University of Science and Technology|
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.
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