Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing

Gene regulation in time and space during X-chromosome inactivation

(2022) Agnese Loda et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A split prime editor with untethered reverse transcriptase and circular RNA template

(2022) Bin Liu et al.   NATURE BIOTECHNOLOGY

Multiplexed genome regulation in vivo with hyper-efficient Cas12a

(2022) Lucie Y. Guo et al.   NATURE CELL BIOLOGY

Scalable biological signal recording in mammalian cells using Cas12a base editors

(2022) Hannah R. Kempton et al.   Nature Chemical Biology

CRISPR-Mediated Synergistic Epigenetic and Transcriptional Control

(2022) Antonia A. Dominguez et al.   CRISPR Journal

Integrated lncRNA function upon genomic and epigenomic regulation

(2022) Allison B. Herman et al.   MOLECULAR CELL

Nested epistasis enhancer networks for robust genome regulation

(2022) Xueqiu Lin et al.   SCIENCE

Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome

(2022) Matthew G. Durrant et al.   NATURE BIOTECHNOLOGY

KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA–DNA triplexes and HP1 binding

(2022) Xiaoli Zhang et al.   NATURE CELL BIOLOGY

Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity

(2022) Monica E. Neugebauer et al.   NATURE BIOTECHNOLOGY

Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases

(2022) Matthew T. N. Yarnall et al.   NATURE BIOTECHNOLOGY

CRISPR technologies for precise epigenome editing

(2021) Muneaki Nakamura et al.   NATURE CELL BIOLOGY

Engineering 3D genome organization

(2021) Haifeng Wang et al.   NATURE REVIEWS GENETICS

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

(2021) Olivia M. de Goede et al.   CELL

B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells

(2021) Bingfei Yu et al.   CELL

Interrogation of the dynamic properties of higher-order heterochromatin using CRISPR-dCas9

(2021) Yuchen Gao et al.   MOLECULAR CELL

Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing

(2021) Xiaoshu Xu et al.   MOLECULAR CELL

NORAD-induced Pumilio phase separation is required for genome stability

(2021) Mahmoud M. Elguindy et al.   NATURE

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

(2021) Luke W. Koblan et al.   NATURE BIOTECHNOLOGY

Transgenic mice for in vivo epigenome editing with CRISPR-based systems

(2021) Matthew P. Gemberling et al.   NATURE METHODS

Essential Roles for RNA in Shaping Nuclear Organization

(2021) Sofia A. Quinodoz et al.   Cold Spring Harbor Perspectives in Biology

Enhanced Cas12a multi-gene regulation using a CRISPR array separator

(2021) Jens P Magnusson et al.   eLife

Enhanced prime editing systems by manipulating cellular determinants of editing outcomes

(2021) Peter J. Chen et al.   CELL

Engineered pegRNAs improve prime editing efficiency

(2021) James W. Nelson et al.   NATURE BIOTECHNOLOGY

Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing

(2021) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Multiple Input Sensing and Signal Integration Using a Split Cas12a System

(2020) Hannah R. Kempton et al.   MOLECULAR CELL

Directed evolution of adenine base editors with increased activity and therapeutic application

(2020) Nicole M. Gaudelli et al.   NATURE BIOTECHNOLOGY

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

(2020) Michelle F. Richter et al.   NATURE BIOTECHNOLOGY

Dual base editor catalyzes both cytosine and adenine base conversions in human cells

(2020) Xiaohui Zhang et al.   NATURE BIOTECHNOLOGY

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

(2020) Julian Grünewald et al.   NATURE BIOTECHNOLOGY

Regulation of human telomerase in homeostasis and disease

(2020) Caitlin M. Roake et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Long Noncoding RNAs: Molecular Modalities to Organismal Functions

(2020) John L. Rinn et al.   Annual Review of Biochemistry

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

(2020) Mandana Arbab et al.   CELL

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells

(2020) Ibrahim C. Kurt et al.   NATURE BIOTECHNOLOGY

Glycosylase base editors enable C-to-A and C-to-G base changes

(2020) Dongdong Zhao et al.   NATURE BIOTECHNOLOGY

Bacterial Retrons Function In Anti-Phage Defense

(2020) Adi Millman et al.   CELL

Structure of the miniature type V-F CRISPR-Cas effector enzyme

(2020) Satoru N. Takeda et al.   MOLECULAR CELL

Structural modularity of the XIST ribonucleoprotein complex

(2020) Zhipeng Lu et al.   Nature Communications

Increasing the specificity of CRISPR systems with engineered RNA secondary structures

(2019) D. Dewran Kocak et al.   NATURE BIOTECHNOLOGY

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Probing and engineering liquid-phase organelles

(2019) Dan Bracha et al.   NATURE BIOTECHNOLOGY

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs

(2018) Maria Samata et al.   Annual Review of Biochemistry

Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria

(2018) Chen Dong et al.   Nature Communications

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

(2018) Yanxia Liu et al.   Cell Stem Cell

Programmed DNA destruction by miniature CRISPR-Cas14 enzymes

(2018) Lucas B. Harrington et al.   SCIENCE

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

(2017) Nicole M. Gaudelli et al.   NATURE

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

(2017) Y Bill Kim et al.   NATURE BIOTECHNOLOGY

Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

(2017) Kelsi A. Lindblad et al.   RNA

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

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

(2016) Ines Fonfara et al.   NATURE

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

(2016) Alexis C. Komor et al.   NATURE

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

Chromosome fusions triggered by noncoding RNA

(2016) John R. Bracht et al.   RNA Biology

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

An RNA-aptamer-based two-color CRISPR labeling system

(2016) Siyuan Wang et al.   Scientific Reports

EBV Noncoding RNA Binds Nascent RNA to Drive Host PAX5 to Viral DNA

(2015) Nara Lee et al.   CELL

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

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

(2015) Bernd Zetsche et al.   CELL

LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure

(2015) Anna Postepska-Igielska et al.   MOLECULAR CELL

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

(2015) Silvana Konermann et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

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

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

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

(2015) David M Shechner 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

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Noncoding RNA transcription targets AID to divergently transcribed loci in B cells

(2014) Evangelos Pefanis et al.   NATURE

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification

(2014) Jeffrey J Quinn et al.   NATURE BIOTECHNOLOGY

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

(2013) Lei S. Qi et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

Dogma Derailed: The Many Influences of RNA on the Genome

(2013) Leah R. Sabin et al.   MOLECULAR CELL

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Airn Transcriptional Overlap, But Not Its lncRNA Products, Induces Imprinted Igf2r Silencing

(2012) P. A. Latos et al.   SCIENCE

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

(2012) M. Jinek et al.   SCIENCE

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

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

(2011) Elitza Deltcheva et al.   NATURE

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

A dermal HOX transcriptional program regulates site-specific epidermal fate

(2008) J. L. Rinn et al.   GENES & DEVELOPMENT