Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning

Scientific Reports
Aidan R O'BrienDenis C Bauer

Abstract

Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated "base editing" being limited to certain nucleotide changes, and only achievable within a small window around CRISPR-Cas target sites. The more versatile alternative, HDR (homology directed repair), has a 3-fold lower efficiency with known optimization factors being largely immutable in experiments. Here, we investigated the variable efficiency-governing factors on a novel mouse dataset using machine learning. We found the sequence composition of the single-stranded oligodeoxynucleotide (ssODN), i.e. the repair template, to be a governing factor. Furthermore, different regions of the ssODN have variable influence, which reflects the underlying mechanism of the repair process. Our model improves HDR efficiency by 83% compared to traditionally chosen targets. Using our findings, we developed CUNE (Computational Universal Nucleotide Editor), which enables users to identify and design the optimal targeting strategy using traditional base editing or - for-the-first-time - HDR-mediated nucleotide changes.

References

Oct 16, 2004·Molecular and Cellular Biology·Jeremy M StarkMaria Jasin
Jan 21, 2009·Cellular and Molecular Life Sciences : CMLS·B PardoA Aguilera
Sep 14, 2011·Annual Review of Genetics·Lorraine S Symington, Jean Gautier
Jan 5, 2013·Science·Le CongFeng Zhang
Jan 5, 2013·Science·Prashant MaliGeorge M Church
May 27, 2014·Bioinformatics·Aidan R O'Brien, Timothy L Bailey
Jun 24, 2014·Scientific Reports·Masafumi InuiShuji Takada
May 12, 2015·Nature Biotechnology·Junwei ShiChristopher R Vakoc
Jun 23, 2015·Nature·Benjamin P KleinstiverJ Keith Joung
Aug 17, 2016·Nature Reviews. Genetics·Euan A Ashley
Dec 12, 2017·Nature Reviews. Genetics·Nicholas J TimpsonJ Brent Richards
Jul 15, 2018·Nature Communications·Zhiquan LiuZhanjun Li
Sep 1, 2018·Molecular Therapy : the Journal of the American Society of Gene Therapy·Yanting ZengXingxu Huang
Oct 2, 2018·Communications Biology·Ke ZhengZheng-Fei Liu

Citations

Jul 23, 2019·The CRISPR Journal·Li XuRenzhi Han
Aug 7, 2020·Current Protocols in Molecular Biology·Kizhakke Mattada SathyanMichael J Guertin
Feb 20, 2021·Frontiers in Genetics·Iuri Viotti PerisseIrina A Polejaeva

Methods Mentioned

BETA
PCR

Related Concepts

Transfer Learning (machine activity)
Gene Editing
Metazoa
Nucleotide Excision Repair
Mice, Inbred C57BL
Mutation
Oligodeoxyribonucleotides
RNA, Guide
Mus domesticus
DNA Breaks, Double-Stranded

Related Feeds

CRISPR (general)

Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). CRISPR-Cas system enables the editing of genes to create or correct mutations. Discover the latest research on CRISPR here.

CRISPR Ribonucleases Deactivation

CRISPR-Cas system enables the editing of genes to create or correct mutations. This feed focuses on mechanisms that underlie deactivation of CRISPR ribonucleases. Here is the latest research.

CRISPR for Genome Editing

Genome editing technologies enable the editing of genes to create or correct mutations. Clustered regularly interspaced short palindromic repeats (CRISPR) are DNA sequences in the genome that are recognized and cleaved by CRISPR-associated proteins (Cas). Here is the latest research on the use of CRISPR-Cas system in gene editing.

Related Papers

Cranio : the Journal of Craniomandibular Practice
H Clifton Simmons
Seikagaku. The Journal of Japanese Biochemical Society
Tomomi Aida, Kohichi Tanaka
Canadian Medical Association Journal
R D Eaton
© 2021 Meta ULC. All rights reserved