Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions

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dc.citation.firstpage7842
dc.citation.issueNumber14
dc.citation.journalTitleNucleic Acids Research
dc.citation.lastpage7855
dc.citation.volumeNumber50
dc.contributor.authorWang, Kaiyuan
dc.contributor.authorEscobar, Mario
dc.contributor.authorLi, Jing
dc.contributor.authorMahata, Barun
dc.contributor.authorGoell, Jacob
dc.contributor.authorShah, Spencer
dc.contributor.authorCluck, Madeleine
dc.contributor.authorHilton, Isaac B
dc.date.accessioned2022-09-08T14:40:03Z
dc.date.available2022-09-08T14:40:03Z
dc.date.issued2022
dc.description.abstractNuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer–promoter pairs. Here, we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as an activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer–promoter pairs. We find that these platforms display variable relative expression levels in different human cell types and that their transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs) and that this eRNA induction is positively correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to demonstrate that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that enhancer-mediated tracking and engagement of a downstream promoter can be synthetically driven by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.
dc.identifier.citationWang, Kaiyuan, Escobar, Mario, Li, Jing, et al.. "Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions." <i>Nucleic Acids Research,</i> 50, no. 14 (2022) Oxford University Press: 7842-7855. https://doi.org/10.1093/nar/gkac582.
dc.identifier.digitalgkac582
dc.identifier.doihttps://doi.org/10.1093/nar/gkac582
dc.identifier.urihttps://hdl.handle.net/1911/113196
dc.language.isoeng
dc.publisherOxford University Press
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleSystematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer–promoter interactions
dc.typeJournal article
dc.type.dcmiText
dc.type.publicationpublisher version
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