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CRISPRoff epigenetic editing for programmable gene silencing in human cells without DNA breaks.

作者信息

Pattali Rithu K, Ornelas Izaiah J, Nguyen Carolyn D, Xu Da, Divekar Nikita S, Nuñez James K

机构信息

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.

Chan Zuckerberg Biohub San Francisco, San Francisco, California, USA.

出版信息

bioRxiv. 2024 Sep 17:2024.09.09.612111. doi: 10.1101/2024.09.09.612111.


DOI:10.1101/2024.09.09.612111
PMID:39345634
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11429707/
Abstract

The advent of CRISPR-based technologies has enabled the rapid advancement of programmable gene manipulation in cells, tissues, and whole organisms. An emerging platform for targeted gene perturbation is epigenetic editing, the direct editing of chemical modifications on DNA and histones that ultimately results in repression or activation of the targeted gene. In contrast to CRISPR nucleases, epigenetic editors modulate gene expression without inducing DNA breaks or altering the genomic sequence of host cells. Recently, we developed the CRISPRoff epigenetic editing technology that simultaneously establishes DNA methylation and repressive histone modifications at targeted gene promoters. Transient expression of CRISPRoff and the accompanying single guide RNAs in mammalian cells results in transcriptional repression of targeted genes that is memorized heritably by cells through cell division and differentiation. Here, we describe our protocol for the delivery of CRISPRoff through plasmid DNA transfection, as well as the delivery of CRISPRoff mRNA, into transformed human cell lines and primary immune cells. We also provide guidance on evaluating target gene silencing and highlight key considerations when utilizing CRISPRoff for gene perturbations. Our protocols are broadly applicable to other CRISPR-based epigenetic editing technologies, as programmable genome manipulation tools continue to evolve rapidly.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/80a9b9c8012d/nihpp-2024.09.09.612111v2-f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/87f3137398dc/nihpp-2024.09.09.612111v2-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/464b262faf81/nihpp-2024.09.09.612111v2-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/75e7deb004ab/nihpp-2024.09.09.612111v2-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/15318fa8f7f5/nihpp-2024.09.09.612111v2-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/af566e367ddc/nihpp-2024.09.09.612111v2-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/247d67973cd6/nihpp-2024.09.09.612111v2-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/a05b4bb69c74/nihpp-2024.09.09.612111v2-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/80a9b9c8012d/nihpp-2024.09.09.612111v2-f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/87f3137398dc/nihpp-2024.09.09.612111v2-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/464b262faf81/nihpp-2024.09.09.612111v2-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/75e7deb004ab/nihpp-2024.09.09.612111v2-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/15318fa8f7f5/nihpp-2024.09.09.612111v2-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/af566e367ddc/nihpp-2024.09.09.612111v2-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/247d67973cd6/nihpp-2024.09.09.612111v2-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/a05b4bb69c74/nihpp-2024.09.09.612111v2-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9977/11429707/80a9b9c8012d/nihpp-2024.09.09.612111v2-f0008.jpg

相似文献

[1]
CRISPRoff epigenetic editing for programmable gene silencing in human cells without DNA breaks.

bioRxiv. 2024-9-17

[2]
CRISPRoff epigenome editing for programmable gene silencing in human cell lines and primary T cells.

Methods Enzymol. 2025

[3]
Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.

Cell. 2021-4-29

[4]
Multiplexed epigenetic memory editing using CRISPRoff sensitizes glioblastoma to chemotherapy.

Neuro Oncol. 2025-7-30

[5]
Programmable epigenome editing by transient delivery of CRISPR epigenome editor ribonucleoproteins.

bioRxiv. 2024-11-28

[6]
Inheritable CRISPR based epigenetic modification in a fungus.

Microbiol Res. 2023-7

[7]
Epigenome Editing Durability Varies Widely Across Cardiovascular Disease Target Genes.

bioRxiv. 2023-5-17

[8]
Engineering a CRISPRoff Platform to Modulate Expression of Myeloid Cell Leukemia (MCL-1) in Committed Oligodendrocyte Neural Precursor Cells.

Bio Protoc. 2024-1-5

[9]
INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels.

Nucleic Acids Res. 2020-12-2

[10]
In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing.

J Vis Exp. 2023-5-5

本文引用的文献

[1]
Epigenome editing technologies for discovery and medicine.

Nat Biotechnol. 2024-8

[2]
Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor.

Science. 2024-6-28

[3]
Systematic epigenome editing captures the context-dependent instructive function of chromatin modifications.

Nat Genet. 2024-6

[4]
Durable and efficient gene silencing in vivo by hit-and-run epigenome editing.

Nature. 2024-3

[5]
CRISPR technologies for genome, epigenome and transcriptome editing.

Nat Rev Mol Cell Biol. 2024-6

[6]
Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control.

Nat Methods. 2023-11

[7]
Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.

Cell. 2023-10-12

[8]
Drug delivery systems for CRISPR-based genome editors.

Nat Rev Drug Discov. 2023-11

[9]
Genotoxic effects of base and prime editing in human hematopoietic stem cells.

Nat Biotechnol. 2024-6

[10]
The p53 challenge of hematopoietic stem cell gene editing.

Mol Ther Methods Clin Dev. 2023-6-12

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