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[Preprint]. 2024 Nov 28:2024.11.26.625496. [Version 2] doi: 10.1101/2024.11.26.625496

Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins

Da Xu, Swen Besselink, Gokul N Ramadoss, Philip H Dierks, Justin P Lubin, Rithu K Pattali, Jinna I Brim, Anna E Christenson, Peter J Colias, Izaiah J Ornelas, Carolyn D Nguyen, Sarah E Chasins, Bruce R Conklin, James K Nuñez
PMCID: PMC11623636  PMID: 39651312

Abstract

Programmable epigenome editors modify gene expression in mammalian cells by altering the local chromatin environment at target loci without inducing DNA breaks. However, the large size of CRISPR-based epigenome editors poses a challenge to their broad use in biomedical research and as future therapies. Here, we present Robust ENveloped Delivery of Epigenome-editor Ribonucleoproteins (RENDER) for transiently delivering programmable epigenetic repressors (CRISPRi, DNMT3A-3L-dCas9, CRISPRoff) and activator (TET1-dCas9) as ribonucleoprotein complexes into human cells to modulate gene expression. After rational engineering, we show that RENDER induces durable epigenetic silencing of endogenous genes across various human cell types, including primary T cells. Additionally, we apply RENDER to epigenetically repress endogenous genes in human stem cell-derived neurons, including the reduction of the neurodegenerative disease associated V337M-mutated Tau protein. Together, our RENDER platform advances the delivery of CRISPR-based epigenome editors into human cells, broadening the use of epigenome editing in fundamental research and therapeutic applications.

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