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Series GSE129889 Query DataSets for GSE129889
Status Public on Jul 11, 2019
Title CRISPR adenine and cytosine base editors with reduced RNA off-target activities [ABE]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary CRISPR-guided DNA base editors enable the efficient installation of targeted single-nucleotide changes. Cytosine or adenine base editors (CBEs or ABEs), which are fusions of cytidine or adenosine deaminases to CRISPR-Cas nickases, can efficiently induce DNA C-to-T or A-to-G alterations in DNA, respectively.
We recently demonstrated that both the widely used CBE BE3 (harboring a rat APOBEC1 cytidine deaminase) and the optimized ABEmax editor can induce tens of thousands of guide RNA-independent, transcriptome-wide RNA base edits in human cells with high efficiencies. In addition, we showed the feasibility of creating SElective Curbing of Unwanted RNA Editing (SECURE)-BE3 variants that exhibit substantially reduced unwanted RNA editing activities while retaining robust and more precise on-target DNA editing. Here we describe structure-guided engineering of SECURE-ABE variants that not only possess reduced off-target RNA editing with comparable on-target DNA activities but are also the smallest Streptococcus pyogenes Cas9 (SpCas9) base editors described to date. In addition, we tested CBEs composed of cytidine deaminases other than APOBEC1 and found that human APOBEC3A (hA3A) cytidine deaminase CBE induces substantial transcriptome-wide RNA base edits with high efficiencies. By contrast, a previously described “enhanced” A3A (eA3A) cytidine deaminase CBE or a human activation-induced cytidine deaminase (hAID) CBE induce substantially reduced or near background levels of RNA edits. In sum, our work describes broadly useful SECURE-ABE and -CBE base editors and reinforces the importance of minimizing RNA editing activities of DNA base editors for research and therapeutic applications.
Overall design Overexpression of adenine base editors in HEK293T, GFP-based cell sorting and RNA-seq for evaluating the degree of off-target editing from ABEs.
Contributor(s) Grunewald J, Lareau C
Citation(s) 31477922
Submission date Apr 16, 2019
Last update date Oct 10, 2019
Contact name Caleb Lareau
Organization name Memorial Sloan Kettering
Street address 417 E 68th St, Zuckerman - ZRC 1132
City New York
State/province New York
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (48)
GSM3724217 HEK293T-NT-control-rep1
GSM3724218 HEK293T-NT-ABEmax-rep1
GSM3724219 HEK293T-NT-miniABEmax-rep1
This SubSeries is part of SuperSeries:
GSE129894 CRISPR adenine and cytosine base editors with reduced RNA off-target activities
BioProject PRJNA533094
SRA SRP192720

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE129889_ABE_SECURE_counts.tsv.gz 2.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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