Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

James K. Nuñez; Jin Chen; Greg C. Pommier; J. Zachery Cogan; Joseph M. Replogle; Carmen Adriaens; Gokul N. Ramadoss; Quanming Shi; King L. Hung; Avi J. Samelson; Angela N. Pogson; James Y.S. Kim; Amanda Chung; Manuel D. Leonetti; Howard Y. Chang; Martin Kampmann; Bradley E. Bernstein; Volker Hovestadt; Luke A. Gilbert; Jonathan S. Weissman

doi:10.1016/j.cell.2021.03.025

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

James K. Nuñez, Jin Chen, Greg C. Pommier, J. Zachery Cogan, Joseph M. Replogle, Carmen Adriaens, Gokul N. Ramadoss, Quanming Shi, King L. Hung, Avi J. Samelson, Angela N. Pogson, James Y.S. Kim, Amanda Chung, Manuel D. Leonetti, Howard Y. Chang, Martin Kampmann, Bradley E. Bernstein, Volker Hovestadt, Luke A. Gilbert, Jonathan S. Weissman

Research output: Contribution to journal › Article › peer-review

259 Scopus citations

Abstract

A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff—a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.

Original language	English (US)
Pages (from-to)	2503-2519.e17
Journal	Cell
Volume	184
Issue number	9
DOIs	https://doi.org/10.1016/j.cell.2021.03.025
State	Published - Apr 29 2021
Externally published	Yes

Keywords

CRISPR
DNA methylation
cell therapy
dCas9
epigenetics

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.cell.2021.03.025

Cite this

Nuñez, J. K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q., Hung, K. L., Samelson, A. J., Pogson, A. N., Kim, J. Y. S., Chung, A., Leonetti, M. D., Chang, H. Y., Kampmann, M., Bernstein, B. E., Hovestadt, V., Gilbert, L. A., & Weissman, J. S. (2021). Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell, 184(9), 2503-2519.e17. https://doi.org/10.1016/j.cell.2021.03.025

Nuñez, JK, Chen, J, Pommier, GC, Cogan, JZ, Replogle, JM, Adriaens, C, Ramadoss, GN, Shi, Q, Hung, KL, Samelson, AJ, Pogson, AN, Kim, JYS, Chung, A, Leonetti, MD, Chang, HY, Kampmann, M, Bernstein, BE, Hovestadt, V, Gilbert, LA & Weissman, JS 2021, 'Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing', Cell, vol. 184, no. 9, pp. 2503-2519.e17. https://doi.org/10.1016/j.cell.2021.03.025

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AU - Chung, Amanda

AU - Leonetti, Manuel D.

AU - Chang, Howard Y.

AU - Kampmann, Martin

AU - Bernstein, Bradley E.

AU - Hovestadt, Volker

AU - Gilbert, Luke A.

AU - Weissman, Jonathan S.

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Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

Abstract

Keywords

ASJC Scopus subject areas

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