Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications

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

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

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

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

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CRISPR-Cas systems for editing, regulating and targeting genomes

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Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

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

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Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

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

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Rationally engineered Cas9 nucleases with improved specificity

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

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antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

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DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

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CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

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Engineered CRISPR-Cas9 nucleases with altered PAM specificities

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Highly efficient Cas9-mediated transcriptional programming

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A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

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RNA-guided gene activation by CRISPR-Cas9-based transcription factors

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CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo

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CRISPR RNA–guided activation of endogenous human genes

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High-throughput functional genomics using CRISPR-Cas9

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

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

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

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Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds

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Principles of genetic circuit design

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E-CRISP: fast CRISPR target site identification

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CRISPR-Cas immunity in prokaryotes

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Optical control of mammalian endogenous transcription and epigenetic states

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Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

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Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

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Engineered gene circuits

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Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

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Hereditary hemorrhagic telangiectasia: genetics and molecular diagnostics in a new era

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A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria

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Functional annotation of native enhancers with a Cas9–histone demethylase fusion

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CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

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Conformational control of DNA target cleavage by CRISPR–Cas9

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Self‐processing of ribozyme‐flanked RNAs into guide RNAs in vitro and in vivo for CRISPR‐mediated genome editing

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Comparison of Cas9 activators in multiple species

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CRISPR-Cas9 Based Engineering of Actinomycetal Genomes

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

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Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae

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COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

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Multicolor CRISPR labeling of chromosomal loci in human cells

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RNA‐guided transcriptional regulation in planta via synthetic dC as9‐based transcription factors

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Dynamics of CRISPR-Cas9 genome interrogation in living cells

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Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

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Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility.

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Cas9 gRNA engineering for genome editing, activation and repression

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Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

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

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Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi)

Cleto, S., Jensen, J. V. K., Wendisch, V. F., & Lu, T. K. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.5b00216 · Cited by 266 · see citing works

Multi‐input CRISPR/Cas genetic circuits that interface host regulatory networks

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Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis

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Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells

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Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

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A CRISPR/Cas9-Based System for Reprogramming Cell Lineage Specification

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CRISPR transcriptional repression devices and layered circuits in mammalian cells

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Conditionally Stabilized dCas9 Activator for Controlling Gene Expression in Human Cell Reprogramming and Differentiation

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CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediated Multiplex Transcriptional Repression in E. coli

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

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A new age in functional genomics using CRISPR/Cas9 in arrayed library screening

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

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Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes inEscherichia coli

Cress, B. F., Jones, J. A., Kim, D. C., Leitz, Q. D., Englaender, J. A., Collins, S. M., Linhardt, R. J., & Koffas, M. A. G. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw231 · Cited by 86 · see citing works

Orthogonal Modular Gene Repression in Escherichia coli Using Engineered CRISPR/Cas9

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Cell–Cell Communication in Yeast Using Auxin Biosynthesis and Auxin Responsive CRISPR Transcription Factors

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Bacterial signaling systems as platforms for rational design of new generations of biosensors

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Gene transcription repression in Clostridium beijerinckii using CRISPR‐dCas9

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Zinc Fingers, TAL Effectors, or Cas9-Based DNA Binding Proteins: What’s Best for Targeting Desired Genome Loci?

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Enhancing Stress-Resistance for Efficient Microbial Biotransformations by Synthetic Biology

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Characterization of Cas9–Guide RNA OrthologsPreprint

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Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi)

Wendisch, V. F., Cleto, S., Jensen, J. V. K., & Lu, T. K. (2016) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 7 · see citing works

Heavy Metal Pollutions: State of the Art and Innovation in Phytoremediation

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A potent Cas9-derived gene activator for plant and mammalian cells

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

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Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts

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CRISPR / dC as9 platforms in plants: strategies and applications beyond genome editing

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Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis

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Non-B-Form DNA Is Enriched at Centromeres

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Immunity to CRISPR Cas9 and Cas12a therapeutics

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CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences

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Gel-forming mucin interactome drives mucus viscoelasticity

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Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering

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CRISPR/Cas-Based In Vitro Diagnostic Platforms for Cancer Biomarker Detection

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Rational engineering of synthetic microbial systems: from single cells to consortia

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Engineering orthogonal dual transcription factors for multi-input synthetic promoters

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Recent Progress and Future Prospect of CRISPR/Cas-Derived Transcription Activation (CRISPRa) System in Plants

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Progress in gene editing tools, implications and success in plants: a review

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Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism

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Cutting Edge Genetics: CRISPR/Cas9 Editing of Plant Genomes

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Microbial CRISPRi and CRISPRa Systems for Metabolic Engineering

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Synthetic Biology: Engineering Living Systems from Biophysical Principles

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CRISPR/Cas13-Based Platforms for a Potential Next-Generation Diagnosis of Colorectal Cancer through Exosomes Micro-RNA Detection: A Review

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Engineered CRISPR Systems for Next Generation Gene Therapies

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Massively parallel CRISPRi assays reveal concealed thermodynamic determinants of dCas12a binding

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Building a genome engineering toolbox in nonmodel prokaryotic microbes

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Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae

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A single plasmid based CRISPR interference in Synechocystis 6803 – A proof of concept

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Recent progress in prompt molecular detection of liquid biopsy using Cas enzymes: innovative approaches for cancer diagnosis and analysis

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Genome Engineering Tools in Plant Synthetic Biology

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Epigenomic engineering for Down syndrome

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Terminal Uridylyl Transferase Mediated Site-Directed Access to Clickable Chromatin Employing CRISPR-dCas9

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Application of Synthetic Biology Approaches to High-Yield Production of Mycosporine-like Amino Acids

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Genome sequencing of biocontrol strain Bacillus amyloliquefaciens Bam1 and further analysis of its heavy metal resistance mechanism

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Technological advancements in the CRISPR toolbox for improving plant salt tolerance

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Knockout mutation in TaD27 enhances number of productive tillers in hexaploid wheat

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Dead Cas(t) light on new life: CRISPRa-mediated reprogramming of somatic cells into neurons

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Mucosal RNA and protein expression as the next frontier in IBS: abnormal function despite morphologically intact small intestinal mucosa

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Plant Epigenomics

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Generation of PAX7 Reporter Cells to Investigate Skeletal Myogenesis from Human Pluripotent Stem Cells

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Modern Tools for Detection and Diagnosis of Plant Pathogens

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Transcriptomic Signatures in Lung Allografts and Their Therapeutic Implications

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Network-Based Computational Modeling to Unravel Gene Essentiality

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Engineering Plants for Metal Tolerance and Accumulation

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Analysis of Transcriptional Regulation in Bone Cells

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Different Approach on our Cells and the Use of CRISPR/Cas 9 Technology: Super Gene'ethic

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Establishment of a CRISPR-Based Lentiviral Activation Library for Transcription Factor Screening in Porcine Cells

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Analysis of Transcriptional Regulation in Bone Cells

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Establishment of a CRISPR/dCas9 Activation Library for Screening Transcription Factors Co-Regulating OCT4 with GATA4 in Pig Cells

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A novel carcinogenic mouse model by site‐directed insertion of tandem human HRAS large DNA fragment into 15E1 site

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Effective Strategies for Translating CRISPR-dCas Systems to Diverse Microbes

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Vers le développement d'une nouvelle approche pour étudier les mécanismes moléculaires impliqués dans la formation des aérenchymes racinaires chez le riz

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Synthetic Biology: An Overview

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