Impact of chromatin context on Cas9-induced DNA double-strand break repair pathway balance

Cas9 deactivation with photocleavable guide RNAs

(2021) Roger S. Zou et al.   MOLECULAR CELL

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

How to maintain the genome in nuclear space

(2020) Ioanna Mitrentsi et al.   CURRENT OPINION IN CELL BIOLOGY

The MRE11 complex: A versatile toolkit for the repair of broken DNA

(2020) Giordano Reginato et al.   DNA REPAIR

Very fast CRISPR on demand

(2020) Yang Liu et al.   SCIENCE

Cell cycle dynamics of lamina‐associated DNA

(2020) Tom van Schaik et al.   EMBO REPORTS

CRISPRoff enables spatio-temporal control of CRISPR editing

(2020) Jared Carlson-Stevermer et al.   Nature Communications

A Snapshot on the Cis Chromatin Response to DNA Double-Strand Breaks

(2019) Thomas Clouaire et al.   TRENDS IN GENETICS

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9

(2019) Basudeb Maji et al.   CELL

CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing

(2019) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

DNA double-strand break repair-pathway choice in somatic mammalian cells

(2019) Ralph Scully et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

(2019) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency

(2019) Santiago Gisler et al.   Nature Communications

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

(2019) Kale Kundert et al.   Nature Communications

Simultaneous precise editing of multiple genes in human cells

(2019) Stephan Riesenberg et al.   NUCLEIC ACIDS RESEARCH

Advances in genome editing through control of DNA repair pathways

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

UDiTaS™, a genome editing detection method for indels and genome rearrangements

(2018) Georgia Giannoukos et al.   BMC GENOMICS

Kinetics and Fidelity of the Repair of Cas9-Induced Double-Strand DNA Breaks

(2018) Eva K. Brinkman et al.   MOLECULAR CELL

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

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

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies

(2018) Rohan N. Shah et al.   MOLECULAR CELL

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures

(2018) Thomas Clouaire et al.   MOLECULAR CELL

Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia

(2018) Christopher J. Ott et al.   CANCER CELL

Target-Specific Precision of CRISPR-Mediated Genome Editing

(2018) Anob M. Chakrabarti et al.   MOLECULAR CELL

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Heterochromatin delays CRISPR-Cas9 mutagenesis but does not influence the outcome of mutagenic DNA repair

(2018) Eirini M. Kallimasioti-Pazi et al.   PLOS BIOLOGY

Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency

(2017) Kristopher Torp Jensen et al.   FEBS LETTERS

Clustering of Drosophila housekeeping promoters facilitates their expression

(2017) Marc Corrales et al.   GENOME RESEARCH

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

The control of DNA repair by the cell cycle

(2017) Nicole Hustedt et al.   NATURE CELL BIOLOGY

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

Genome-wide mapping of histone H3K9me2 in acute myeloid leukemia reveals large chromosomal domains associated with massive gene silencing and sites of genome instability

(2017) Anna C. Salzberg et al.   PLoS One

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Nuclear compartmentalization of DNA repair

(2016) Alkmini Kalousi et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2016) Maria Jasin et al.   DNA REPAIR

A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin

(2016) Aniek Janssen et al.   GENES & DEVELOPMENT

Temporal and Spatial Uncoupling of DNA Double Strand Break Repair Pathways within Mammalian Heterochromatin

(2016) Katerina Tsouroula et al.   MOLECULAR CELL

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

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

(2016) Christopher D Richardson et al.   NATURE BIOTECHNOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Probing the impact of chromatin conformation on genome editing tools

(2016) Xiaoyu Chen et al.   NUCLEIC ACIDS RESEARCH

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb 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

DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation

(2016) Emil Mladenov et al.   SEMINARS IN CANCER BIOLOGY

The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells

(2016) René M. Daer et al.   ACS Synthetic Biology

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Alternative end-joining repair pathways are the ultimate backup for abrogated classical non-homologous end-joining and homologous recombination repair: Implications for the formation of chromosome translocations

(2015) George Iliakis et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Mammalian polymerase θ promotes alternative NHEJ and suppresses recombination

(2015) Pedro A. Mateos-Gomez et al.   NATURE

Heterochromatic breaks move to the nuclear periphery to continue recombinational repair

(2015) Taehyun Ryu et al.   NATURE CELL BIOLOGY

ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors

(2015) Christian Schmidl et al.   NATURE METHODS

SETDB1, HP1 and SUV39 promote repositioning of 53BP1 to extend resection during homologous recombination in G2 cells

(2015) Meryem Alagoz et al.   NUCLEIC ACIDS RESEARCH

DNA double strand break repair pathway choice: a chromatin based decision?

(2015) T Clouaire et al.   Nucleus

DNA double strand break repair pathway choice: a chromatin based decision?

(2015) T Clouaire et al.   Nucleus

Roles of chromatin remodellers in DNA double strand break repair

(2014) Penny A. Jeggo et al.   EXPERIMENTAL CELL RESEARCH

Nuclear position dictates DNA repair pathway choice

(2014) Charlène Lemaître et al.   GENES & DEVELOPMENT

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases

(2014) Richard L Frock et al.   NATURE BIOTECHNOLOGY

Using TRIP for genome-wide position effect analysis in cultured cells

(2014) Waseem Akhtar et al.   Nature Protocols

Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks

(2014) François Aymard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

SETD2-Dependent Histone H3K36 Trimethylation Is Required for Homologous Recombination Repair and Genome Stability

(2014) Sophia X. Pfister et al.   Cell Reports

Quantifying Genome-Editing Outcomes at Endogenous Loci with SMRT Sequencing

(2014) Ayal Hendel et al.   Cell Reports

SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint

(2014) Sílvia Carvalho et al.   eLife

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

(2014) Steven Lin et al.   eLife

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

LBR and Lamin A/C Sequentially Tether Peripheral Heterochromatin and Inversely Regulate Differentiation

(2013) Irina Solovei et al.   CELL

Differential contribution of HP1 proteins to DNA end resection and homology-directed repair

(2013) Gaston Soria et al.   CELL CYCLE

HP1 promotes tumor suppressor BRCA1 functions during the DNA damage response

(2013) Young-Ho Lee et al.   NUCLEIC ACIDS RESEARCH

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

Playing the End Game: DNA Double-Strand Break Repair Pathway Choice

(2012) J. Ross Chapman et al.   MOLECULAR CELL

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LEDGF (p75) promotes DNA-end resection and homologous recombination

(2012) Mads Daugaard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair

(2011) Irene Chiolo et al.   CELL

A dual role for A-type lamins in DNA double-strand break repair

(2011) Abena B. Redwood et al.   CELL CYCLE

HP1α recruitment to DNA damage by p150CAF-1 promotes homologous recombination repair

(2011) Céline Baldeyron et al.   JOURNAL OF CELL BIOLOGY

Enabling high-throughput ligation-independent cloning and protein expression for the family of ubiquitin specific proteases

(2011) Mark P.A. Luna-Vargas et al.   JOURNAL OF STRUCTURAL BIOLOGY

DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin

(2011) Burkhard Jakob et al.   NUCLEIC ACIDS RESEARCH

PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update

(2011) X. Wang et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Dual Roles for DNA Polymerase Theta in Alternative End-Joining Repair of Double-Strand Breaks in Drosophila

(2010) Sze Ham Chan et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Histone H3 methylation links DNA damage detection to activation of the tumour suppressor Tip60

(2009) Yingli Sun et al.   NATURE CELL BIOLOGY

piggyBac can bypass DNA synthesis during cut and paste transposition

(2008) Rupak Mitra et al.   EMBO JOURNAL

ATM Signaling Facilitates Repair of DNA Double-Strand Breaks Associated with Heterochromatin

(2008) Aaron A. Goodarzi et al.   MOLECULAR CELL

MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings

(2008) Mitch McVey et al.   TRENDS IN GENETICS