DNA methylation can alter CRISPR/Cas9 editing frequency and DNA repair outcome in a target‐specific manner

DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis

(2021) Zhenhui Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs

(2021) Yue Fei et al.   NUCLEIC ACIDS RESEARCH

Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

(2021) Ruben Schep et al.   MOLECULAR CELL

Structural basis of nucleosome transcription mediated by Chd1 and FACT

(2021) Lucas Farnung et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Are the current gRNA ranking prediction algorithms useful for genome editing in plants?

(2020) Fatima Naim et al.   PLoS One

CRISPR/Cas‐based precision genome editing via microhomology‐mediated end joining (MMEJ)

(2020) Tien Van Vu et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPResso2 provides accurate and rapid genome editing sequence analysis

(2019) Kendell Clement et al.   NATURE BIOTECHNOLOGY

Detailed insight into the dynamics of the initial phases of de novo RNA-directed DNA methylation in plant cells

(2019) Adéla Přibylová et al.   Epigenetics & Chromatin

Discovery of salicyl benzoate UDP‐glycosyltransferase, a central enzyme in poplar salicinoid phenolic glycoside biosynthesis

(2019) Christin Fellenberg et al.   PLANT JOURNAL

Further analysis of barley MORC1 using a highly efficient RNA-guided Cas9 gene-editing system

(2018) Neelendra Kumar et al.   PLANT BIOTECHNOLOGY JOURNAL

Activities and specificities of CRISPR-Cas9 and Cas12a nucleases for targeted mutagenesis in maize

(2018) Keunsub Lee et al.   PLANT BIOTECHNOLOGY JOURNAL

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles

(2018) Brenda R. Lemos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Survey of Validation Strategies for CRISPR-Cas9 Editing

(2018) Monica F. Sentmanat et al.   Scientific Reports

Review of CRISPR/Cas9 sgRNA Design Tools

(2018) Yingbo Cui et al.   Interdisciplinary Sciences-Computational Life Sciences

Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo

(2018) Robert M. Yarrington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants

(2018) Jianying Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

(2018) Eirini M. Kallimasioti-Pazi et al.   PLOS BIOLOGY

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

(2017) Hao Liu et al.   Molecular Plant

Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress

(2017) Chantal LeBlanc et al.   PLANT JOURNAL

Characterization of the interplay between DNA repair and CRISPR/Cas9-induced DNA lesions at an endogenous locus

(2017) Anne Bothmer et al.   Nature Communications

Efficient Targeted Genome Modification in Maize Using CRISPR/Cas9 System

(2016) Chao Feng et al.   Journal of Genetics and Genomics

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-freeArabidopsisplants

(2016) Douglas E. Pyott et al.   MOLECULAR PLANT PATHOLOGY

Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

Probing the impact of chromatin conformation on genome editing tools

(2016) Xiaoyu Chen et al.   NUCLEIC ACIDS RESEARCH

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

(2016) René M. Daer et al.   ACS Synthetic Biology

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Allele-specific locus binding and genome editing by CRISPR at the p16INK4a locus

(2016) Toshitsugu Fujita et al.   Scientific Reports

Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations

(2016) Zhicheng Zuo et al.   Scientific Reports

Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro

(2015) John M. Hinz et al.   BIOCHEMISTRY

Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage

(2015) Eric A. Josephs et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation within Transcribed Regions

(2015) Taiko K. To et al.   PLANT PHYSIOLOGY

Dynamics of CRISPR-Cas9 genome interrogation in living cells

(2015) Spencer C. Knight et al.   SCIENCE

Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway?

(2015) Agnel Sfeir et al.   TRENDS IN BIOCHEMICAL SCIENCES

A versatile reporter system for CRISPR-mediated chromosomal rearrangements

(2015) Yingxiang Li et al.   GENOME BIOLOGY

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

Transcript-RNA-templated DNA recombination and repair

(2014) Havva Keskin et al.   NATURE

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

(2014) Noe Fernandez-Pozo et al.   NUCLEIC ACIDS RESEARCH

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering inArabidopsis thaliana

(2014) Friedrich Fauser et al.   PLANT JOURNAL

Highly Efficient Genome Modifications Mediated by CRISPR/Cas9 in Drosophila

(2013) Z. Yu et al.   GENETICS

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9

(2013) Jian-Feng Li et al.   NATURE BIOTECHNOLOGY

Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease

(2013) Vladimir Nekrasov et al.   NATURE BIOTECHNOLOGY

Repair of Double-Strand Breaks by End Joining

(2013) K. K. Chiruvella et al.   Cold Spring Harbor Perspectives in Biology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

The requirement for recombination factors differs considerably between different pathways of homologous double-strand break repair in somatic plant cells

(2012) Nadine Roth et al.   PLANT JOURNAL

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

(2012) Devin Coleman-Derr et al.   PLoS Genetics