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

Nanobody-mediated control of gene expression and epigenetic memory

(2021) Mike V. Van et al.   Nature Communications

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects

(2020) Daniel Hofacker et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs

(2020) Marco Jost et al.   NATURE BIOTECHNOLOGY

Design and analysis of CRISPR–Cas experiments

(2020) Ruth E. Hanna et al.   NATURE BIOTECHNOLOGY

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

(2019) Henriette O’Geen et al.   Epigenetics & Chromatin

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Epigenome editing strategies for the functional annotation of CTCF insulators

(2019) Daniel R. Tarjan et al.   Nature Communications

Advances in genome editing through control of DNA repair pathways

(2019) Charles D. Yeh et al.   NATURE CELL BIOLOGY

Editing the Epigenome: Reshaping the Genomic Landscape

(2018) Liad Holtzman et al.   Annual Review of Genomics and Human Genetics

OUP accepted manuscript

(2018)   BIOINFORMATICS

Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element

(2018) Seung Woo Cho et al.   CELL

A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology

(2018) Xiaoshu Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural basis for DNMT3A-mediated de novo DNA methylation

(2018) Zhi-Min Zhang et al.   NATURE

p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells

(2018) Robert J. Ihry et al.   NATURE MEDICINE

Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells

(2018) Tafadzwa Mlambo et al.   NUCLEIC ACIDS RESEARCH

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation

(2018) Ruby Yu et al.   NATURE

Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability

(2018) Nahid Iglesias et al.   NATURE

Highly efficient genome editing via CRISPR–Cas9 in human pluripotent stem cells is achieved by transient BCL-XL overexpression

(2018) Xiao-Lan Li et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas guides the future of genetic engineering

(2018) Gavin J. Knott et al.   SCIENCE

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

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

(2017) Y Esther Tak et al.   NATURE METHODS

Am I ready for CRISPR? A user's guide to genetic screens

(2017) John G. Doench   NATURE REVIEWS GENETICS

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

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

(2016) Angelo Amabile et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Angelman syndrome — insights into a rare neurogenetic disorder

(2016) Karin Buiting et al.   Nature Reviews Neurology

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Nucleosome breathing and remodeling constrain CRISPR-Cas9 function

(2016) R Stefan Isaac et al.   eLife

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution

(2015) Yonatan Stelzer et al.   CELL

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

(2015) Silvana Konermann et al.   NATURE

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Tau and neurodegenerative disease: the story so far

(2015) Khalid Iqbal et al.   Nature Reviews Neurology

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Restricted epigenetic inheritance of H3K9 methylation

(2015) P. N. C. B. Audergon et al.   SCIENCE

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

(2014) Luke A. Gilbert et al.   CELL

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Epigenetic inheritance uncoupled from sequence-specific recruitment

(2014) K. Ragunathan et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Luke A. Gilbert et al.   CELL

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

(2010) Matthew G. Guenther et al.   Cell Stem Cell

A recombinant polypeptide extends the in vivo half-life of peptides and proteins in a tunable manner

(2009) Volker Schellenberger et al.   NATURE BIOTECHNOLOGY