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Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish

https://doi.org/10.1371/journal.pone.0182528

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/0168-9525(94)90091-4openalex-snapshot

Zebrafish: genetic tools for studying vertebrate development

inferredcites →https://doi.org/10.1016/s0959-437x(00)00074-5openalex-snapshot

Zebrafish: a model system for the study of human disease

inferredcites →https://doi.org/10.1021/acs.biochem.5b01108openalex-snapshot

Nucleosomes Inhibit Cas9 Endonuclease Activity in Vitro

inferredcites →https://doi.org/10.1021/acssynbio.5b00299openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nature04979openalex-snapshot

A genomic code for nucleosome positioning

inferredcites →https://doi.org/10.1038/nature07667openalex-snapshot

The DNA-encoded nucleosome organization of a eukaryotic genome

inferredcites →https://doi.org/10.1038/nbt.2501openalex-snapshot

Efficient genome editing in zebrafish using a CRISPR-Cas system

inferredcites →https://doi.org/10.1038/nbt.2889openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nbt.2916openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nbt.3026openalex-snapshot

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nmeth.3360openalex-snapshot

Rapid reverse genetic screening using CRISPR in zebrafish

inferredcites →https://doi.org/10.1038/nmeth.3473openalex-snapshot

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

inferredcites →https://doi.org/10.1038/nmeth.3543openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nsmb.1636openalex-snapshot

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo

inferredcites →https://doi.org/10.1073/pnas.1308335110openalex-snapshot

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

inferredcites →https://doi.org/10.1093/bioinformatics/btn119openalex-snapshot

GeneTrack—a genomic data processing and visualization framework

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/nar/gkp1043openalex-snapshot

Are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

inferredcites →https://doi.org/10.1101/gr.098509.109openalex-snapshot

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging

inferredcites →https://doi.org/10.1101/gr.157750.113openalex-snapshot

Canonical nucleosome organization at promoters forms during genome activation

inferredcites →https://doi.org/10.1101/gr.163394.113openalex-snapshot

Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases

inferredcites →https://doi.org/10.1101/gr.191452.115openalex-snapshot

Sequence determinants of improved CRISPR sgRNA design

inferredcites →https://doi.org/10.1126/science.1246981openalex-snapshot

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

inferredcites →https://doi.org/10.1126/science.aaf7907openalex-snapshot

Whole-organism lineage tracing by combinatorial and cumulative genome editing

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

inferredcites →https://doi.org/10.1242/dev.115584openalex-snapshot

Precise and efficient genome editing in zebrafish using the CRISPR/Cas9 system

inferredcites →https://doi.org/10.1371/journal.pone.0157365openalex-snapshot

Neurodegeneration and Epilepsy in a Zebrafish Model of CLN3 Disease (Batten Disease)

inferredcites →https://doi.org/10.18632/oncotarget.9613openalex-snapshot

Reprofiling using a zebrafish melanoma model reveals drugs cooperating with targeted therapeutics

inferredcites →https://doi.org/10.7554/elife.12677openalex-snapshot

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4194127openalex-extracted

Meioc-Piwil1 Complexes Regulate Ribosome Biogenesis for the Differentiation of Germline Stem Cells

inferred← citeshttps://doi.org/10.1007/978-981-95-6722-5_5openalex-snapshot

Bioinformatics Tools in Cereal Genome Editing

inferred← citeshttps://doi.org/10.1007/s00018-019-03064-xopenalex-snapshot

LION: a simple and rapid method to achieve CRISPR gene editing

inferred← citeshttps://doi.org/10.1007/s00253-019-10298-zopenalex-snapshot

CRISPR-Cas9 assisted functional gene editing in the mushroom Ganoderma lucidum

inferred← citeshttps://doi.org/10.1016/j.copbio.2018.07.005openalex-snapshot

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

inferred← citeshttps://doi.org/10.1016/j.molcel.2017.09.017openalex-snapshot

High-Throughput Approaches to Pinpoint Function within the Noncoding Genome

inferred← citeshttps://doi.org/10.1016/j.ymthe.2019.10.008openalex-snapshot

Computational Analysis Concerning the Impact of DNA Accessibility on CRISPR-Cas9 Cleavage Efficiency

inferred← citeshttps://doi.org/10.1021/acssynbio.4c00053openalex-snapshot

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

inferred← citeshttps://doi.org/10.1021/jacs.8b05469openalex-snapshot

Sharpening the Scissors: Mechanistic Details of CRISPR/Cas9 Improve Functional Understanding and Inspire Future Research

inferred← citeshttps://doi.org/10.1038/s41467-022-31034-8openalex-snapshot

SpG and SpRY variants expand the CRISPR toolbox for genome editing in zebrafish

inferred← citeshttps://doi.org/10.1038/s41598-018-33817-wopenalex-snapshot

Ionizing radiation induces transgenerational effects of DNA methylation in zebrafish

inferred← citeshttps://doi.org/10.1038/s41598-024-57699-3openalex-snapshot

Establishment of a zebrafish inbred strain, M-AB, capable of regular breeding and genetic manipulation

inferred← citeshttps://doi.org/10.1038/s42003-022-03308-wopenalex-snapshot

Wuschel2 enables highly efficient CRISPR/Cas-targeted genome editing during rapid de novo shoot regeneration in sorghum

inferred← citeshttps://doi.org/10.1063/1.5127302openalex-snapshot

Site-directed targeting of transcriptional activation-associated proteins to repressed chromatin restores CRISPR activity

inferred← citeshttps://doi.org/10.1089/crispr.2021.0039openalex-snapshot

Strategies for Enhancing the Homology-Directed Repair Efficiency of CRISPR-Cas Systems

inferred← citeshttps://doi.org/10.1089/crispr.2023.0033openalex-snapshot

Trichostatin A for Efficient CRISPR-Cas9 Gene Editing of Human Pluripotent Stem Cells

inferred← citeshttps://doi.org/10.1093/bioinformatics/btag483openalex-snapshot

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency

inferred← citeshttps://doi.org/10.1093/nar/gkab467openalex-snapshot

A cleavage-based surrogate reporter for the evaluation of CRISPR–Cas9 cleavage efficiency

inferred← citeshttps://doi.org/10.1093/nar/gkad736openalex-snapshot

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

inferred← citeshttps://doi.org/10.1101/228601openalex-snapshot

Histone modifications and active gene expression are associated with enhanced CRISPR activity in de-silenced chromatin

inferred← citeshttps://doi.org/10.1101/469544openalex-snapshot

Towards best-practice approaches for CRISPR/Cas9 gene engineering

inferred← citeshttps://doi.org/10.1101/gad.353802.126openalex-snapshot

MEIOSIN retains a STRA8-independent activity that contributes to meiotic gene activation across vertebrates

inferred← citeshttps://doi.org/10.1182/blood.2022018924openalex-snapshot

Novel extragenic genomic safe harbors for precise therapeutic T cell engineering

inferred← citeshttps://doi.org/10.1186/s12864-022-09012-7openalex-snapshot

Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity

inferred← citeshttps://doi.org/10.1186/s13072-020-0329-yopenalex-snapshot

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish

inferred← citeshttps://doi.org/10.1371/journal.pgen.1008640openalex-snapshot

Sycp2 is essential for synaptonemal complex assembly, early meiotic recombination and homologous pairing in zebrafish spermatocytes

inferred← citeshttps://doi.org/10.1371/journal.pone.0196238openalex-snapshot

Chromatin accessibility is associated with CRISPR-Cas9 efficiency in the zebrafish (Danio rerio)

inferred← citeshttps://doi.org/10.2108/zs230052openalex-snapshot

CRISPR-Cas9-Mediated Gene Knockout in a Non-Model Sea Urchin, Heliocidaris crassispina

inferred← citeshttps://doi.org/10.2144/btn-2018-0187openalex-snapshot

Guidelines for Optimized Gene Knockout Using CRISPR/Cas9

inferred← citeshttps://doi.org/10.3389/fcell.2020.00319openalex-snapshot

Genome Editing Fidelity in the Context of DNA Sequence and Chromatin Structure

inferred← citeshttps://doi.org/10.3389/fcell.2021.664377openalex-snapshot

Sycp1 Is Not Required for Subtelomeric DNA Double-Strand Breaks but Is Required for Homologous Alignment in Zebrafish Spermatocytes

inferred← citeshttps://doi.org/10.3390/biom12081123openalex-snapshot

A Machine Learning Approach to Identify the Importance of Novel Features for CRISPR/Cas9 Activity Prediction

inferred← citeshttps://doi.org/10.3892/ol.2018.9157openalex-snapshot

A tetracycline‑inducible CRISPR/Cas9 system, targeting two long non‑coding RNAs, suppresses the malignant behavior of bladder cancer cells

inferred← citeshttps://doi.org/10.6084/m9.figshare.26550874openalex-snapshot

Additional file 1 of Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity

inferred← citeshttps://doi.org/10.64898/2026.03.04.709545openalex-snapshot

MEIOSIN retains an intrinsic STRA8-independent activity that drives meiotic entry across vertebrate evolution

inferred← citeshttps://doi.org/10.7150/ijbs.37152openalex-snapshot

Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity

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