Plant biotechnology journalMay 7, 2022

Genome-wide study shows ABE8e gene editor causes many off-target changes in rice

CRISPR Gene Editing Weekly Brief ↗PubMed ↗DOI ↗OA ↗

Updated Mar 30, 2026

Abstract

ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant.

Genome-wide of various Cas9 nucleases and base editors in rice have been examined.
Distinct off-target sites are preferred by Cas9 nucleases and base editors when using the same guide RNA.
SpRY editors generate additional, but minor, off-target mutations from newly created guide RNAs.
The preference of ABE8e for the TA motif is evident at both off-target and target sites.
from tissue culture significantly contributes to background mutations in edited plants.

Simplified

nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that Cas9 nuclease and base editors, when coupled with the same guide RNA (gRNA), prefer distinct gRNA-dependent off-target sites. De novo generated gRNAs by SpRY editors lead to additional, but insubstantial, off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. ABE8e's preference for the TA motif is also observed at the target sites. Finally, we investigate the timeline and mechanism of due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scale and mechanisms of off-target and background mutations occurring during PAM-relaxed genome editing in plants.

Key numbers

~500

Off-target A-to-G mutations per plant

Average number of A-to-G mutations induced by ABE8e in transgenic rice plants.

Full Text

We can’t show the full text here under this license.

View Full Text ↗

Funding

Competing interests

The authors declare no competing interests.

PubMed

Genome-wide study shows ABE8e gene editor causes many off-target changes in rice

Abstract

Key numbers

Full Text

Funding

Competing interests

You found one interesting study. We’ll send the next 7.

What Lands in Your Inbox Each Week:

Recent issues from the crispr gene editing brief

Abstract

Key numbers

Full Text

Funding

Competing interests

Related papers

You found one interesting study. We’ll send the next 7.

What Lands in Your Inbox Each Week:

Recent issues from the crispr gene editing brief