CRISPR Cpf1 proteins: structure, function and implications for genome editing

Knockout rat models mimicking human atherosclerosis created by Cpf1-mediated gene targeting

(2019) Jong Geol Lee et al.   Scientific Reports

Multiple Chemical Inducible Tal Effectors for Genome Editing and Transcription Activation

(2018) Chen Zhao et al.   ACS Chemical Biology

Structural insights into the apo-structure of Cpf1 protein from Francisella novicida

(2018) Kyungjin Min et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Generation of the Adenovirus Vector-Mediated CRISPR/Cpf1 System and the Application for Primary Human Hepatocytes Prepared from Humanized Mice with Chimeric Liver

(2018) Tomohito Tsukamoto et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Cpf1-assisted efficient genomic integration of in vivo assembled DNA parts in Saccharomyces cerevisiae

(2018) Zhen-Hai Li et al.   BIOTECHNOLOGY LETTERS

Engineering CRISPR/Cpf1 with tRNA promotes genome editing capability in mammalian systems

(2018) Han Wu et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

New Developments in CRISPR Technology: Improvements in Specificity and Efficiency

(2018) Fatemeh Safari et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Delivering CRISPR: a review of the challenges and approaches

(2018) Christopher A. Lino et al.   DRUG DELIVERY

CRISPR and personalized Treg therapy: new insights into the treatment of rheumatoid arthritis

(2018) Fatemeh Safari et al.   IMMUNOPHARMACOLOGY AND IMMUNOTOXICOLOGY

Bidirectional Degradation of DNA Cleavage Products Catalyzed by CRISPR/Cas9

(2018) Anthony A. Stephenson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Gene repression via multiplex gRNA strategy in Y. lipolytica

(2018) Jin-lai Zhang et al.   Microbial Cell Factories

Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system

(2018) Jun Sun et al.   Microbial Cell Factories

Engineering Introns to Express RNA Guides for Cas9- and Cpf1-Mediated Multiplex Genome Editing

(2018) Dan Ding et al.   Molecular Plant

Expanding the Scope of CRISPR/Cpf1-Mediated Genome Editing in Rice

(2018) Shaoya Li et al.   Molecular Plant

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

(2018) Hui Kwon Kim et al.   NATURE BIOTECHNOLOGY

Membrane permeabilizing amphiphilic peptide delivers recombinant transcription factor and CRISPR-Cas9/Cpf1 ribonucleoproteins in hard-to-modify cells

(2018) Thomas Del’Guidice et al.   PLoS One

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

(2018) Janice S. Chen et al.   SCIENCE

Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion

(2018) Ryan D. Chow et al.   Nature Communications

Targeting repair pathways with small molecules increases precise genome editing in pluripotent stem cells

(2018) Stephan Riesenberg et al.   Nature Communications

Small molecules promote CRISPR-Cpf1-mediated genome editing in human pluripotent stem cells

(2018) Xiaojie Ma et al.   Nature Communications

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

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

CRISPR-Cas12a-assisted nucleic acid detection

(2018) Shi-Yuan Li et al.   Cell Discovery

Genetic editing and interrogation with Cpf1 and caged truncated pre-tRNA-like crRNA in mammalian cells

(2018) Xuhua Zhang et al.   Cell Discovery

Nanoparticle delivery of CRISPR into the brain rescues a mouse model of fragile X syndrome from exaggerated repetitive behaviours

(2018) Bumwhee Lee et al.   Nature Biomedical Engineering

Critical Micrornas in Lung Cancer: Recent Advances and Potential Applications

(2018) Habib Zarredar et al.   Anti-Cancer Agents in Medicinal Chemistry

CRISPR-Cpf1-Assisted Multiplex Genome Editing and Transcriptional Repression in Streptomyces

(2018) Lei Li et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Extension of the crRNA enhances Cpf1 gene editing in vitro and in vivo

(2018) Hyo Min Park et al.   Nature Communications

Tamoxifen- and Mifepristone-Inducible Versions of CRISPR Effectors, Cas9 and Cpf1

(2018) Alazne Dominguez-Monedero et al.   ACS Synthetic Biology

An integrated CRISPR Bombyx mori genome editing system with improved efficiency and expanded target sites

(2017) Sanyuan Ma et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

CRISPR-offinder: a CRISPR guide RNA design and off-target searching tool for user-defined protospacer adjacent motif

(2017) Changzhi Zhao et al.   International Journal of Biological Sciences

Targeted mutagenesis in rice using CRISPR-Cpf1 system

(2017) Xixun Hu et al.   Journal of Genetics and Genomics

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a

(2017) Daan C. Swarts et al.   MOLECULAR CELL

Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1

(2017) Takashi Yamano et al.   MOLECULAR CELL

Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes

(2017) Gaelen T. Hess et al.   MOLECULAR CELL

CRISPR/Cas9-mediated gene editing in human zygotes using Cas9 protein

(2017) Lichun Tang et al.   MOLECULAR GENETICS AND GENOMICS

Multiplex Gene Editing in Rice Using the CRISPR-Cpf1 System

(2017) Mugui Wang et al.   Molecular Plant

Erratum: Multiplex gene editing by CRISPR–Cpf1 using a single crRNA array

(2017) Bernd Zetsche et al.   NATURE BIOTECHNOLOGY

Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Engineered Cpf1 variants with altered PAM specificities

(2017) Linyi Gao et al.   NATURE BIOTECHNOLOGY

Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors

(2017) Y Esther Tak et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Diversity and evolution of class 2 CRISPR–Cas systems

(2017) Sergey Shmakov et al.   NATURE REVIEWS MICROBIOLOGY

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae

(2017) Michal A. Świat et al.   NUCLEIC ACIDS RESEARCH

A ‘new lease of life’: FnCpf1 possesses DNA cleavage activity for genome editing in human cells

(2017) Mengjun Tu et al.   NUCLEIC ACIDS RESEARCH

Generation of targeted mutant rice using a CRISPR-Cpf1 system

(2017) Rongfang Xu et al.   PLANT BIOTECHNOLOGY JOURNAL

Efficient targeted DNA editing and replacement inChlamydomonas reinhardtiiusing Cpf1 ribonucleoproteins and single-stranded DNA

(2017) Aron Ferenczi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas: Adapting to change

(2017) Simon A. Jackson et al.   SCIENCE

CRISPR/Cpf1 enables fast and simple genome editing of Saccharomyces cerevisiae

(2017) René Verwaal et al.   YEAST

Engineering cell signaling using tunable CRISPR–Cpf1-based transcription factors

(2017) Yuchen Liu et al.   Nature Communications

Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery

(2017) Holly A. Rees et al.   Nature Communications

CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum

(2017) Yu Jiang et al.   Nature Communications

CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing

(2017) Miguel A. Moreno-Mateos et al.   Nature Communications

CRISPR/Cpf1-mediated DNA-free plant genome editing

(2017) Hyeran Kim et al.   Nature Communications

Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence

(2017) Ting Zheng et al.   Scientific Reports

Efficient Transcriptional Gene Repression by Type V-A CRISPR-Cpf1 from Eubacterium eligens

(2017) Seong Keun Kim et al.   ACS Synthetic Biology

Catalytic Activities of Ribozymes and DNAzymes in Water and Mixed Aqueous Media

(2017) Shu-ichi Nakano et al.   Catalysts

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

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

CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice

(2017) Yu Zhang et al.   Science Advances

Multiplex gene regulation by CRISPR-ddCpf1

(2017) Xiaochun Zhang et al.   Cell Discovery

Engineering CRISPR–Cpf1 crRNAs and mRNAs to maximize genome editing efficiency

(2017) Bin Li et al.   Nature Biomedical Engineering

Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases

(2017) Matthew B. Begemann et al.   Scientific Reports

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA

(2016) Takashi Yamano et al.   CELL

Studying the features of 57 confirmed CRISPR loci in 29 strains ofEscherichia coli

(2016) Seyyed Soheil Rahmatabadi et al.   JOURNAL OF BASIC MICROBIOLOGY

Correction for Barka et al., Taxonomy, Physiology, and Natural Products of Actinobacteria

(2016) Essaid Ait Barka et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9

(2016) Seiichi Hirano et al.   MOLECULAR CELL

The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA

(2016) Ines Fonfara et al.   NATURE

The crystal structure of Cpf1 in complex with CRISPR RNA

(2016) De Dong et al.   NATURE

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

(2016) Alexis C. Komor et al.   NATURE

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells

(2016) Benjamin P Kleinstiver et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells

(2016) Daesik Kim et al.   NATURE BIOTECHNOLOGY

A photoactivatable Cre–loxP recombination system for optogenetic genome engineering

(2016) Fuun Kawano et al.   Nature Chemical Biology

Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs

(2016) Fillip Port et al.   NATURE METHODS

Directing cellular information flow via CRISPR signal conductors

(2016) Yuchen Liu et al.   NATURE METHODS

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

In vivo high-throughput profiling of CRISPR–Cpf1 activity

(2016) Hui K Kim et al.   NATURE METHODS

Kinetics of the CRISPR-Cas9 effector complex assembly and the role of 3′-terminal segment of guide RNA

(2016) Vladimir Mekler et al.   NUCLEIC ACIDS RESEARCH

Efficient delivery of genome-editing proteins using bioreducible lipid nanoparticles

(2016) Ming Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Prarthana Mohanraju et al.   SCIENCE

Bacterial Genome Editing with CRISPR-Cas9: Deletion, Integration, Single Nucleotide Modification, and Desirable “Clean” Mutant Selection in Clostridium beijerinckii as an Example

(2016) Yi Wang et al.   ACS Synthetic Biology

CRISPR-based genome editing and expression control systems inClostridium acetobutylicumandClostridium beijerinckii

(2016) Qi Li et al.   Biotechnology Journal

Efficient targeted mutagenesis of rice and tobacco genomes using Cpf1 from Francisella novicida

(2016) Akira Endo et al.   Scientific Reports

“Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

(2015) Venetia Pliatsika et al.   Biology Direct

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Small Molecules Enhance CRISPR Genome Editing in Pluripotent Stem Cells

(2015) Chen Yu et al.   Cell Stem Cell

The New State of the Art: Cas9 for Gene Activation and Repression

(2015) Marie F. La Russa et al.   MOLECULAR AND CELLULAR BIOLOGY

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

A mechanism for the suppression of homologous recombination in G1 cells

(2015) Alexandre Orthwein 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

Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells

(2015) Ayal Hendel et al.   NATURE BIOTECHNOLOGY

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition

(2015) Benjamin P Kleinstiver 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

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

(2015) Levi G. Lowder et al.   PLANT PHYSIOLOGY

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy

(2015) C. Long et al.   SCIENCE

Polyelectrolyte complexes of hTERT siRNA and polyethyleneimine: Effect of degree of PEG grafting on biological and cellular activity

(2015) Fatemeh Safari et al.   Artificial Cells Nanomedicine and Biotechnology

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

(2014) Lior Nissim et al.   MOLECULAR CELL

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

(2014) Lukasz Swiech et al.   NATURE BIOTECHNOLOGY

High-Efficiency Multiplex Genome Editing of Streptomyces Species Using an Engineered CRISPR/Cas System

(2014) Ryan E. Cobb et al.   ACS Synthetic Biology

Modernizing the Nonhomologous End-Joining Repertoire: Alternative and Classical NHEJ Share the Stage

(2013) Ludovic Deriano et al.   Annual Review of Genetics

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

(2013) N. A. Kearns et al.   DEVELOPMENT

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Repair of Double-Strand Breaks by End Joining

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

Zscan4 restores the developmental potency of embryonic stem cells

(2013) Tomokazu Amano et al.   Nature Communications

Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP)

(2013) Toshitsugu Fujita et al.   Scientific Reports

Temporal Control of Retroviral Transgene Expression in Newborn Cells in the Adult Brain

(2013) Simon M.G. Braun et al.   Stem Cell Reports

Conditional gene manipulation: Cre-ating a new biological era

(2012) Jian Zhang et al.   Journal of Zhejiang University-SCIENCE B

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

(2012) M. Jinek et al.   SCIENCE

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52–ssDNA complexes

(2010) Jill M. Grimme et al.   NUCLEIC ACIDS RESEARCH