CRISPR-Cas immunity, DNA repair and genome stability

The Biology of CRISPR-Cas: Backward and Forward

(2018) Frank Hille et al.   CELL

DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity

(2018) Rajat Gupta et al.   CELL

Repair of DNA double-strand breaks by mammalian alternative end-joining pathways

(2018) Annahita Sallmyr et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Homologous recombination and the repair of DNA double-strand breaks

(2018) William Douglass Wright et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microhomology-mediated end joining: Good, bad and ugly

(2018) Ja-Hwan Seol et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells

(2018) Harveer Dev et al.   NATURE CELL BIOLOGY

CRISPR–Cas9 genome editing in human cells occurs via the Fanconi anemia pathway

(2018) Chris D. Richardson et al.   NATURE GENETICS

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair

(2018) M. Charpentier et al.   Nature Communications

Microhomology-assisted scarless genome editing in human iPSCs

(2018) Shin-Il Kim et al.   Nature Communications

Development of versatile non-homologous end joining-based knock-in module for genome editing

(2018) Shun Sawatsubashi et al.   Scientific Reports

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing

(2018) Daan C. Swarts et al.   Wiley Interdisciplinary Reviews-RNA

53BP1 cooperation with the REV7–shieldin complex underpins DNA structure-specific NHEJ

(2018) Hind Ghezraoui et al.   NATURE

The shieldin complex mediates 53BP1-dependent DNA repair

(2018) Sylvie M. Noordermeer et al.   NATURE

Erratum: Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

CRISPR–Cas adaptation in Escherichia coli requires RecBCD helicase but not nuclease activity, is independent of homologous recombination, and is antagonized by 5′ ssDNA exonucleases

(2018) Marin Radovčić et al.   NUCLEIC ACIDS RESEARCH

DNA replication roadblocks caused by Cascade interference complexes are alleviated by RecG DNA repair helicase

(2018) Tom Killelea et al.   RNA Biology

CRISPR-Cas guides the future of genetic engineering

(2018) Gavin J. Knott et al.   SCIENCE

Enhancing CRISPR/Cas9-mediated homology-directed repair in mammalian cells by expressing Saccharomyces cerevisiae Rad52

(2017) Simin Shao et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

CRISPR-Cas: Adapting to change

(2017) Simon A. Jackson et al.   SCIENCE

Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks

(2017) Fei Song et al.   Molecular Therapy-Nucleic Acids

Establishment of expanded and streamlined pipeline of PITCh knock-in – a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO

(2017) Kazuki Nakamae et al.   Bioengineered

Small molecules enhance CRISPR/Cas9-mediated homology-directed genome editing in primary cells

(2017) Guoling Li et al.   Scientific Reports

The democratization of gene editing: Insights from site-specific cleavage and double-strand break repair

(2016) Maria Jasin et al.   DNA REPAIR

Noncanonical views of homology-directed DNA repair

(2016) Priyanka Verma et al.   GENES & DEVELOPMENT

Adaptation in CRISPR-Cas Systems

(2016) Samuel H. Sternberg et al.   MOLECULAR CELL

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

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

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

Molecular recordings by directed CRISPR spacer acquisition

(2016) Seth L. Shipman et al.   SCIENCE

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

(2016) Prarthana Mohanraju et al.   SCIENCE

Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells

(2016) M. A. DeWitt et al.   Science Translational Medicine

Repair Pathway Choices and Consequences at the Double-Strand Break

(2016) Raphael Ceccaldi et al.   TRENDS IN CELL BIOLOGY

CRISPaint allows modular base-specific gene tagging using a ligase-4-dependent mechanism

(2016) Jonathan L. Schmid-Burgk et al.   Nature Communications

Non-homologous DNA increases gene disruption efficiency by altering DNA repair outcomes

(2016) C. D. Richardson et al.   Nature Communications

Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases

(2016) Jean-Baptiste Renaud et al.   Cell Reports

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining

(2015) Takeshi Maruyama et al.   NATURE BIOTECHNOLOGY

Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells

(2015) Van Trung Chu et al.   NATURE BIOTECHNOLOGY

MMEJ-assisted gene knock-in using TALENs and CRISPR-Cas9 with the PITCh systems

(2015) Tetsushi Sakuma et al.   Nature Protocols

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Different genome stability proteins underpin primed and naïve adaptation inE. coliCRISPR-Cas immunity

(2015) Ivana Ivančić-Baće et al.   NUCLEIC ACIDS RESEARCH

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

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

Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

(2015) Marius Rutkauskas et al.   Cell Reports

Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing

(2015) Francis Robert et al.   Genome Medicine

Mitosis Inhibits DNA Double-Strand Break Repair to Guard Against Telomere Fusions

(2014) A. Orthwein et al.   SCIENCE

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

DNA repair mechanisms in dividing and non-dividing cells

(2013) Teruaki Iyama et al.   DNA REPAIR

HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis

(2013) Carrie A. Adelman et al.   NATURE

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells

(2013) L. N. Truong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Repair of Strand Breaks by Homologous Recombination

(2013) M. Jasin et al.   Cold Spring Harbor Perspectives in Biology

Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs

(2013) Kei-ichi Takata et al.   Nature Communications

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

Obligate Ligation-Gated Recombination (ObLiGaRe): Custom-designed nuclease-mediated targeted integration through nonhomologous end joining

(2012) M. Maresca et al.   GENOME RESEARCH

RecFOR Proteins Target RecA Protein to a DNA Gap with Either DNA or RNA at the 5′ Terminus

(2012) Katsumi Morimatsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3

(2012) Edze R. Westra et al.   MOLECULAR CELL

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) M. Jinek et al.   SCIENCE

Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system

(2012) Kirill A. Datsenko et al.   Nature Communications

Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system

(2011) Tomas Sinkunas et al.   EMBO JOURNAL

High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

(2011) Fuqiang Chen et al.   NATURE METHODS

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

(2011) Matthijs M Jore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

(2008) M. S. Dillingham et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Regulation of DNA repair throughout the cell cycle

(2008) Dana Branzei et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY