Tracking-seq reveals the heterogeneity of off-target effects in CRISPRCas9-mediated genome editing – Nature.com
Posted: July 8, 2024 at 2:37 am
Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229236 (2020).
Article CAS PubMed PubMed Central Google Scholar
Raguram, A., Banskota, S. & Liu, D. R. Therapeutic in vivo delivery of gene editing agents. Cell 185, 28062827 (2022).
Article CAS PubMed PubMed Central Google Scholar
Wang, D., Zhang, F. & Gao, G. CRISPR-based therapeutic genome editing: strategies and in vivo delivery by AAV vectors. Cell 181, 136150 (2020).
Article CAS PubMed PubMed Central Google Scholar
Kim, D., Luk, K., Wolfe, S. A. & Kim, J.-S. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases. Annu. Rev. Biochem. 88, 191220 (2019).
Article CAS PubMed Google Scholar
Tao, J., Bauer, D. E. & Chiarle, R. Assessing and advancing the safety of CRISPRCas tools: from DNA to RNA editing. Nat. Commun. 14, 212 (2023).
Article CAS PubMed PubMed Central Google Scholar
Kim, D. et al. Digenome-seq: genome-wide profiling of CRISPRCas9 off-target effects in human cells. Nat. Methods 12, 237243 (2015).
Article CAS PubMed Google Scholar
Cameron, P. et al. Mapping the genomic landscape of CRISPRCas9 cleavage. Nat. Methods 14, 600606 (2017).
Article CAS PubMed Google Scholar
Tsai, S. Q. et al. CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPRCas9 nuclease off-targets. Nat. Methods 14, 607614 (2017).
Article CAS PubMed PubMed Central Google Scholar
Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPRCas nucleases. Nat. Biotechnol. 33, 187197 (2015).
Article CAS PubMed Google Scholar
Wienert, B. et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 364, 286289 (2019).
Article CAS PubMed PubMed Central Google Scholar
Zou, R. S. et al. Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq+. Nat. Methods 20, 706713 (2023).
Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S. & Gregory, P. D. Genome editing with engineered zinc finger nucleases. Nat. Rev. Genet. 11, 636646 (2010).
Article CAS PubMed Google Scholar
Joung, J. K. & Sander, J. D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 14, 4955 (2013).
Article CAS PubMed Google Scholar
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819823 (2013).
Article CAS PubMed PubMed Central Google Scholar
Anzalone, A. V., Koblan, L. W. & Liu, D. R. Genome editing with CRISPRCas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824844 (2020).
Article CAS PubMed Google Scholar
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420424 (2016).
Article CAS PubMed PubMed Central Google Scholar
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149157 (2019).
Article CAS PubMed PubMed Central Google Scholar
Gaudelli, N. M. et al. Programmable base editing of AT to GC in genomic DNA without DNA cleavage. Nature 551, 464471 (2017).
Article CAS PubMed PubMed Central Google Scholar
Liu, T. & Huang, J. Replication protein A and more: single-stranded DNA-binding proteins in eukaryotic cells. Acta Biochim Biophys. Sin. 48, 665670 (2016).
Article CAS PubMed Google Scholar
Wold, M. S. Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism. Annu. Rev. Biochem. 66, 6192 (1997).
Article CAS PubMed Google Scholar
Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 10061019 (2018).
Article CAS PubMed Google Scholar
Kabeche, L., Nguyen, H., Buisson, R. & Zou, L. A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation. Science 359, 108114 (2018).
Gan, X. et al. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res. 51, 55655583 (2023).
Article CAS PubMed PubMed Central Google Scholar
Amemiya, H. M., Kundaje, A. & Boyle, A. P. The ENCODE blacklist: identification of problematic regions of the genome. Sci. Rep. 9, 9354 (2019).
Article PubMed PubMed Central Google Scholar
Ferrari, M., Twayana, S., Marini, F. & Pellicioli, A. In Genome Instability: Methods and Protocols (eds Muzi-Falconi, M. & Brown, G. W.) 119129 (Humana Press, 2017).
Stoler, N. & Nekrutenko, A. Sequencing error profiles of Illumina sequencing instruments. NAR Genom. Bioinform. 3, lqab019 (2021).
Article PubMed PubMed Central Google Scholar
Kim, D., Kim, S., Kim, S., Park, J. & Kim, J.-S. Genome-wide target specificities of CRISPRCas9 nucleases revealed by multiplex Digenome-seq. Genome Res. 26, 406415 (2016).
Article CAS PubMed PubMed Central Google Scholar
Lei, Z. et al. Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors. Nat. Methods 18, 643651 (2021).
Article CAS PubMed Google Scholar
Liang, P. et al. Genome-wide profiling of adenine base editor specificity by EndoV-seq. Nat. Commun. 10, 67 (2019).
Article CAS PubMed PubMed Central Google Scholar
Liang, S.-Q. et al. Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Nat. Methods 20, 898907 (2023).
Article CAS PubMed Google Scholar
Kim, D. Y., Moon, S. B., Ko, J.-H., Kim, Y.-S. & Kim, D. Unbiased investigation of specificities of prime editing systems in human cells. Nucleic Acids Res. 48, 1057610589 (2020).
Article CAS PubMed PubMed Central Google Scholar
Zuo, E. et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Science 364, 289292 (2019).
Article CAS PubMed PubMed Central Google Scholar
Duan, J. et al. Genome-wide identification of CRISPR/Cas9 off-targets in human genome. Cell Res. 24, 10091012 (2014).
Article CAS PubMed PubMed Central Google Scholar
Frangoul, H. et al. CRISPRCas9 gene editing for sickle cell disease and -thalassemia. N. Engl. J. Med. 384, 252260 (2021).
Article CAS PubMed Google Scholar
Nakamura-Ishizu, A., Takizawa, H. & Suda, T. The analysis, roles and regulation of quiescence in hematopoietic stem cells. Development 141, 46564666 (2014).
Article CAS PubMed Google Scholar
Chang, H. H. Y., Pannunzio, N. R., Adachi, N. & Lieber, M. R. Non-homologous DNA end joining and alternative pathways to double-strand break repair. Nat. Rev. Mol. Cell Biol. 18, 495506 (2017).
Article CAS PubMed PubMed Central Google Scholar
Wienert, B., Wyman, S. K., Yeh, C. D., Conklin, B. R. & Corn, J. E. CRISPR off-target detection with DISCOVER-seq. Nat. Protoc. 15, 17751799 (2020).
Article CAS PubMed PubMed Central Google Scholar
Wheeler, D. L. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 33, D39D45 (2005).
Article CAS PubMed Google Scholar
Zhang, H. et al. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat. Commun. 12, 6566 (2021).
Article CAS PubMed PubMed Central Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841842 (2010).
Article CAS PubMed PubMed Central Google Scholar
Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. & Karolchik, D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26, 22042207 (2010).
Article CAS PubMed PubMed Central Google Scholar
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160W165 (2016).
Article CAS PubMed PubMed Central Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357359 (2012).
Article CAS PubMed PubMed Central Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).
Article PubMed PubMed Central Google Scholar
Bleckwehl, T. et al. Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Nat. Commun. 12, 5771 (2021).
Article CAS PubMed PubMed Central Google Scholar
Man, N. et al. p300 suppresses the transition of myelodysplastic syndromes to acute myeloid leukemia. JCI Insight 6, e138478 (2021).
Article PubMed PubMed Central Google Scholar
Ji, L. et al. TOPORS, a tumor suppressor protein, contributes to the maintenance of higher-order chromatin architecture. Biochim. Biophys. Acta Gene Regul. Mech. 1863, 194518 (2020).
Article CAS PubMed Google Scholar
Lex, R. K. et al. GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling. eLife 9, e50670 (2020).
Article CAS PubMed PubMed Central Google Scholar
Boix, C. A., James, B. T., Park, Y. P., Meuleman, W. & Kellis, M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature 590, 300307 (2021).
Article CAS PubMed PubMed Central Google Scholar
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224226 (2019).
Article CAS PubMed PubMed Central Google Scholar
Zhu, M. et al. Tracking-seq reveals the heterogeneity of off-target effects in CRISPR/Cas9-mediated genome editing. NCBI https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236360 (2024).
Xu, R. Offtracker. GitHub https://github.com/Lan-lab/offtracker (2024).
- 'CRISPR pill' instructs harmful bacteria to self-destruct - National Hog Farmer [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- Highly sensitive CRISPR diagnostic tool created - BioNews [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- More Tooth, More Tail in CRISPR Operations | GEN - Genetic Engineering & Biotechnology News (press release) [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- Quick, Sensitive Diagnostic Tests with CRISPR - Technology Networks [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- MPEG LA Invites CRISPR-Cas9 Patents to be Pooled in a One-Stop License - Yahoo Finance [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- What Is CRISPR? - livescience.com [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- CRISPR and Stem Cells Identify Novel Chlamydia Drug Targets - Genetic Engineering & Biotechnology News [Last Updated On: April 26th, 2017] [Originally Added On: April 26th, 2017]
- CRISPR webinar: HGF discusses IP landscape - Life Sciences Intellectual Property Review (subscription) [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- CRISPR.com was for sale, and you won't guess who bought it - STAT [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- CRISPR Pill May Be Key in Fight Against Antibiotic Resistance - Singularity Hub [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- Intellia (NTLA), CRISPR Therapeutics (CRSP) Receive U.S. Patent for CRISPR/Cas9 Ribonucleoprotein Complexes - StreetInsider.com [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- transOMIC technologies Launches transEDIT-dual CRISPR ... - PR Newswire (press release) [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- Global CRISPR Market Forecast 2017-2025 - Research and Markets ... - Business Wire (press release) [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- Quick, Sensitive Diagnostic Tests with CRISPR | Technology Networks - Technology Networks [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- CRISPR/Cas9 and Targeted Genome Editing: A New Era in ... [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- CRISPR - Wikipedia [Last Updated On: April 27th, 2017] [Originally Added On: April 27th, 2017]
- CRISPR Used To Modify Multiple Genes In Rice - Asian Scientist Magazine [Last Updated On: April 28th, 2017] [Originally Added On: April 28th, 2017]
- Current CRISPR Patent Dispute, Explained - CALIFORNIA [Last Updated On: April 28th, 2017] [Originally Added On: April 28th, 2017]
- CEOs of top gene-editing firms got huge compensation hikes last year - Boston Business Journal [Last Updated On: April 28th, 2017] [Originally Added On: April 28th, 2017]
- CRISPR-SMART Cells Regenerate Cartilage, Secrete Anti-Arthritis Drug - Genetic Engineering & Biotechnology News [Last Updated On: April 29th, 2017] [Originally Added On: April 29th, 2017]
- Another CRISPR Trial Begins - GenomeWeb [Last Updated On: April 29th, 2017] [Originally Added On: April 29th, 2017]
- China Is Racing Ahead of the US in the Quest to Cure Cancer With CRISPR - Gizmodo [Last Updated On: April 29th, 2017] [Originally Added On: April 29th, 2017]
- CRISPR Gene Editing - CRISPR/Cas9 - Horizon Discovery [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- CRISPR | Broad Institute [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- Questions and Answers about CRISPR | Broad Institute [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- CRISPR Genome Engineering Resources | learn, share, and discuss [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- CRISPR Technology Scientists on Their Gene Editing Tool - TIME [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- Cas9 - Wikipedia [Last Updated On: May 1st, 2017] [Originally Added On: May 1st, 2017]
- Using CRISPR against cancer shows success in mice - Futurity - Futurity: Research News [Last Updated On: May 2nd, 2017] [Originally Added On: May 2nd, 2017]
- Using CRISPR to Find Treatments for Aggressive Pediatric Brain Cancer - Bioscience Technology [Last Updated On: May 2nd, 2017] [Originally Added On: May 2nd, 2017]
- CRISPR Eliminates HIV in Live Animals - Genetic Engineering & Biotechnology News [Last Updated On: May 2nd, 2017] [Originally Added On: May 2nd, 2017]
- The CRISPR patent dispute - Europe and the US - BioNews [Last Updated On: May 2nd, 2017] [Originally Added On: May 2nd, 2017]
- How Scientists Think CRISPR Will Change Medicine - TIME [Last Updated On: May 3rd, 2017] [Originally Added On: May 3rd, 2017]
- What you need to know about the legal battle over CRISPR patents - Genetic Literacy Project [Last Updated On: May 4th, 2017] [Originally Added On: May 4th, 2017]
- Scientists have eliminated HIV in mice using CRISPR - TechCrunch [Last Updated On: May 4th, 2017] [Originally Added On: May 4th, 2017]
- CRISPR Therapeutics Appoints Samarth Kulkarni, Ph.D. as President, Expanding Role Beyond Chief Business Officer ... - GlobeNewswire (press release) [Last Updated On: May 4th, 2017] [Originally Added On: May 4th, 2017]
- ECDC says risk from contaminated CRISPR kits low - CIDRAP [Last Updated On: May 4th, 2017] [Originally Added On: May 4th, 2017]
- CRISPR Could Transform the Way We Diagnose Disease - Gizmodo [Last Updated On: May 4th, 2017] [Originally Added On: May 4th, 2017]
- A cancer gene also grows stem cells, CRISPR in monkey embryo ... - Speaking of Research [Last Updated On: May 5th, 2017] [Originally Added On: May 5th, 2017]
- New CRISPR Technique Can Potentially Stop Cancer In Its Tracks - Wall Street Pit [Last Updated On: May 6th, 2017] [Originally Added On: May 6th, 2017]
- CRISPR gene-editing tool targets cancer's "command center" - Gizmag - New Atlas [Last Updated On: May 7th, 2017] [Originally Added On: May 7th, 2017]
- Update: CRISPR - Radiolab [Last Updated On: May 7th, 2017] [Originally Added On: May 7th, 2017]
- Cambridge gene editing firm CRISPR to use delivery tech honed ... - Boston Business Journal [Last Updated On: May 9th, 2017] [Originally Added On: May 9th, 2017]
- Oxford Genetics licenses CRISPR tech to power synbio push - FierceBiotech [Last Updated On: May 10th, 2017] [Originally Added On: May 10th, 2017]
- What You Need to Know About the New CRISPR Cancer Treatment - BOSS Magazine [Last Updated On: May 11th, 2017] [Originally Added On: May 11th, 2017]
- CRISPR: The Future of Medicine and Human Evolution - in-Training [Last Updated On: May 12th, 2017] [Originally Added On: May 12th, 2017]
- Intellia Therapeutics Announces Progress with CRISPR/Cas9 at the American Society of Gene & Cell Therapy Annual ... - GlobeNewswire (press... [Last Updated On: May 13th, 2017] [Originally Added On: May 13th, 2017]
- Pac-Man like CRISPR enzymes discovered - Lab News [Last Updated On: May 13th, 2017] [Originally Added On: May 13th, 2017]
- Coming age of CRISPR gene editing: What in heck is the 'Pink Chicken Project'? - Genetic Literacy Project [Last Updated On: May 15th, 2017] [Originally Added On: May 15th, 2017]
- Intellia moves closer to clinic with CRISPR tech - FierceBiotech [Last Updated On: May 15th, 2017] [Originally Added On: May 15th, 2017]
- Will CRISPR Technology Create a New "Human" Species? - Big Think [Last Updated On: May 15th, 2017] [Originally Added On: May 15th, 2017]
- Caribou Bioscience's CEO on CRISPR's legal and ethical challenges - TechCrunch [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Cut Out the Hype: Gene Editing With CRISPR and the Truth about Superhuman 'Designer Babies' - WhatIsEpigenetics.com (blog) [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- CRISPR-Cas.org [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Synthego's genetic toolkit aims to make CRISPR more accessible - TechCrunch [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- What is CRISPR? A Beginner's Guide | Digital Trends [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Geneticists Enlist Engineered Virus and CRISPR to Battle Citrus Disease - Scientific American [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Editas delays IND for Allergan-partnered CRISPR program - FierceBiotech [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Easy DNA Editing Will Remake the World. Buckle Up - WIRED [Last Updated On: May 16th, 2017] [Originally Added On: May 16th, 2017]
- Can CRISPR feed the world? - Phys.org - Phys.Org [Last Updated On: May 19th, 2017] [Originally Added On: May 19th, 2017]
- Gene-editing tool 'CRISPR' gaining massive attention - KMOV.com [Last Updated On: May 19th, 2017] [Originally Added On: May 19th, 2017]
- Fixing the tomato: CRISPR edits correct plant-breeding snafu - Nature.com [Last Updated On: May 19th, 2017] [Originally Added On: May 19th, 2017]
- Beyond just promise, CRISPR is delivering in the lab today - The Conversation US [Last Updated On: May 20th, 2017] [Originally Added On: May 20th, 2017]
- What is CRISPR-Cas9, and will it change the world? | Alphr - Alphr [Last Updated On: May 20th, 2017] [Originally Added On: May 20th, 2017]
- Fixing the Tomato: CRISPR Edits Correct Plant-Breeding Snafu ... - Scientific American [Last Updated On: May 20th, 2017] [Originally Added On: May 20th, 2017]
- This UK Biotech uses CRISPR-Cas9 To Fight Bacterial Resistance - Labiotech.eu (blog) [Last Updated On: May 21st, 2017] [Originally Added On: May 21st, 2017]
- Can CRISPR feed the world? | Horizon: the EU Research ... - Horizon magazine [Last Updated On: May 21st, 2017] [Originally Added On: May 21st, 2017]
- Will this gene-editing tool cure the diseases of the future? - Sacramento Bee [Last Updated On: May 23rd, 2017] [Originally Added On: May 23rd, 2017]
- How the CRISPR-Cas9 System is Redefining Drug Discovery - Labiotech.eu (blog) [Last Updated On: May 23rd, 2017] [Originally Added On: May 23rd, 2017]
- Scientists are using gene editing to create the perfect tomato for your salad - Quartz [Last Updated On: May 24th, 2017] [Originally Added On: May 24th, 2017]
- Fine-tuning CRISPR to Create Popular Mouse Models - Technology Networks [Last Updated On: May 25th, 2017] [Originally Added On: May 25th, 2017]
- Scientists Are Using CRISPR To "Program" Living Cells - Futurism - Futurism [Last Updated On: May 25th, 2017] [Originally Added On: May 25th, 2017]
- CRISPR gene editing puts the brakes on cancer cells - Cosmos [Last Updated On: May 26th, 2017] [Originally Added On: May 26th, 2017]
- Watch This Scientist Brilliantly Explain CRISPR to Everyone from a Child to a Ph.D. - Patheos (blog) [Last Updated On: May 27th, 2017] [Originally Added On: May 27th, 2017]
- Using CRISPR gene editing to slow cancer growth | FierceBiotech - FierceBiotech [Last Updated On: May 27th, 2017] [Originally Added On: May 27th, 2017]
- How A Gene Editing Tool Went From Labs To A Middle-School Classroom - NPR [Last Updated On: May 27th, 2017] [Originally Added On: May 27th, 2017]
- In Just a Few Short Years, CRISPR Has Sparked a Research Revolution - Futurism [Last Updated On: May 29th, 2017] [Originally Added On: May 29th, 2017]
- CRISPR Is Taking Over Science, Breaks Out Of Labs And Invades Schools - EconoTimes [Last Updated On: May 30th, 2017] [Originally Added On: May 30th, 2017]
- Gene-editing technique scientists hope will cure cancer and all ... - The Independent [Last Updated On: May 30th, 2017] [Originally Added On: May 30th, 2017]
- CRISPR Gene-Editing Can Cause Hundreds of Unexpected ... - ScienceAlert [Last Updated On: May 30th, 2017] [Originally Added On: May 30th, 2017]