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Programmable Transcriptional Modulation with a Structured RNA-Mediated CRISPR-dCas9 Complex

  • Miao He
    Miao He
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Miao He
  • Xiang Zhou*
    Xiang Zhou
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    *Email: [email protected]
    More by Xiang Zhou
  • Zhigang Li
    Zhigang Li
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Zhigang Li
  • Xue Yin
    Xue Yin
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Xue Yin
  • Wenjie Han
    Wenjie Han
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Wenjie Han
  • Junxiang Zhou
    Junxiang Zhou
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
  • Xiaoyun Sun
    Xiaoyun Sun
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Xiaoyun Sun
  • Xiaoyu Liu
    Xiaoyu Liu
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    More by Xiaoyu Liu
  • Dongbao Yao*
    Dongbao Yao
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    *Email: [email protected]
    More by Dongbao Yao
  • , and 
  • Haojun Liang*
    Haojun Liang
    School of Chemistry and Materials Science, Department of Polymer Science and Engineering, iChEM (Collaborative Innovation Center of Chemistry for Energy Materials), University of Science and Technology of China, Hefei, Anhui 230026, China
    *Email: [email protected]
    More by Haojun Liang
Cite this: J. Am. Chem. Soc. 2022, 144, 28, 12690–12697
Publication Date (Web):July 6, 2022
https://doi.org/10.1021/jacs.2c02271
Copyright © 2022 American Chemical Society

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    Supporting Info (1)»

    Abstract

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    Multi-module dCas9 engineering systems have been developed for controllable transcriptional manipulation such as chemical- or light-induced systems. However, there is still a need for a separate module that can be used for internal control over the CRISPR-dCas9 system. Here, we describe a multi-module CRISPR-dCas9 system in which a separate structured RNA was applied as a programmable component that could control dCas9-based gene regulation and achieved a higher activation efficiency than dCas9-VPR that is traditionally used. By introducing a microRNA sensor, we generated a dCas9-based transcriptional regulation platform that responded to endogenous microRNAs and allowed controllable activation of endogenous genes. Moreover, we applied the platform to selectively identify HCT116 cells in a cell mixture. This work provides a flexible platform for efficient and controllable gene regulation based on CRISPR-dCas9.

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/jacs.2c02271.

    • Materials, experimental methods; supporting tables for sequences of guide RNA, bridge RNA, and primers for qRT-PCR; supporting figures for gene expression analysis of different complexes, secondary structure analyzed by NUPACK, characterization of the bridge RNA-mediated dCas9-based transcriptional activation complexes, comparison of different complexes with exchanged RNA binding protein, transcriptional activation with reverse bridge RNA, correlation between basal expression level and relative expression gain, bridge RNA-mediated dCas9 system for endogenous gene repression, fluorescence assay of different dCas9 fusion mutants with and without competitor tdMCP(V29I), microRNA activity assay, effect of the dCas9-tdMCP(V29I) dose and ratio to the tdMCP(V29I) on sensor performance, fluorescence microscope images and dot plots (PDF)

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    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 1 publications.

    1. Junxiang Zhou, Miao He, Xue Yin, Yue Yu, Dongbao Yao, Haojun Liang. Unexploited Performance of NLS in the dCas9-VPR-Mediated Transcriptional Activation. ACS Chemical Biology 2023, 18 (5) , 1246-1253. https://doi.org/10.1021/acschembio.3c00195

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