Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites

Cas9 deactivation with photocleavable guide RNAs

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

Loop extrusion as a mechanism for formation of DNA damage repair foci

(2021) Coline Arnould et al.   NATURE

Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication

(2021) Vinay Tripuraneni et al.   GENOME RESEARCH

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

(2021) Ruben Schep et al.   MOLECULAR CELL

Enhanced prime editing systems by manipulating cellular determinants of editing outcomes

(2021) Peter J. Chen et al.   CELL

Mapping the genetic landscape of DNA double-strand break repair

(2021) Jeffrey A. Hussmann et al.   CELL

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

(2020) Ivan E. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells

(2020) Alan S. Wang et al.   MOLECULAR CELL

CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity

(2020) Cicera R. Lazzarotto et al.   NATURE BIOTECHNOLOGY

Very fast CRISPR on demand

(2020) Yang Liu et al.   SCIENCE

DNA double-strand breaks induce H2Ax phosphorylation domains in a contact-dependent manner

(2020) Patrick L. Collins et al.   Nature Communications

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

(2019) Thomas Clouaire et al.   TRENDS IN GENETICS

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

Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors

(2019) Fabio Pessina et al.   NATURE CELL BIOLOGY

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

(2019) Andrew V. Anzalone et al.   NATURE

Advances in genome editing through control of DNA repair pathways

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

Protein Dynamics in Complex DNA Lesions

(2018) Radoslav Aleksandrov et al.   MOLECULAR CELL

Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks

(2018) Ryan Clarke et al.   MOLECULAR CELL

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

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

(2018) Thomas Clouaire et al.   MOLECULAR CELL

A limited number of double-strand DNA breaks is sufficient to delay cell cycle progression

(2018) Jeroen van den Berg et al.   NUCLEIC ACIDS RESEARCH

Nucleosomes inhibit target cleavage by CRISPR-Cas9 in vivo

(2018) Robert M. Yarrington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas guides the future of genetic engineering

(2018) Gavin J. Knott et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies

(2018) Sebald AN Verkuijl et al.   CURRENT OPINION IN BIOTECHNOLOGY

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics

(2017) John C Rose et al.   NATURE METHODS

Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy

(2017) Mikihiro Shibata et al.   Nature Communications

BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks

(2017) Winston X. Yan et al.   Nature Communications

DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks

(2016) Megan van Overbeek et al.   MOLECULAR CELL

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9

(2016) Digvijay Singh et al.   Nature Communications

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Conformational control of DNA target cleavage by CRISPR–Cas9

(2015) Samuel H. Sternberg et al.   NATURE

Dynamics of CRISPR-Cas9 genome interrogation in living cells

(2015) Spencer C. Knight et al.   SCIENCE

Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code

(2014) David J. Clark   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

(2014) Xuebing Wu et al.   NATURE BIOTECHNOLOGY

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

(2014) Cem Kuscu et al.   NATURE BIOTECHNOLOGY

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

(2014) Shengdar Q Tsai et al.   NATURE BIOTECHNOLOGY

Chromatin Remodeling at DNA Double-Strand Breaks

(2013) Brendan D. Price et al.   CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-dependent dynamic supercoiling is a short-range genomic force

(2013) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Alu elements: know the SINEs

(2011) Prescott Deininger   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY