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

Wu, Xuebing, Scott, David A, Kriz, Andrea J, Chiu, Anthony C, Hsu, Patrick D, Dadon, Daniel B, Cheng, Albert W, Trevino, Alexandro E +5 more·2014·Nature Biotechnology

Cited by (947)

Items 101–200 of 947

  1. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein
    Lei, Yong, Zhang, Xiaotian, Su, Jianzhong, Jeong, Mira, Gundry, Michael C., Huang, Yung-Hsin, Zhou, Yubin, Li, Wei, Goodell, Margaret A. · 2017 · Nature Communications
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  3. Structural basis for Cas9 off-target activity
    Pacesa, Martin, Lin, Chun-Han, Cléry, Antoine, Saha, Aakash, Arantes, Pablo R., Bargsten, Katja, Irby, Matthew J., Allain, Frédéric H.-T., Palermo, Giulia, Cameron, Peter et al. · 2022 · Cell
  4. CRISPR-Cas: New Tools for Genetic Manipulations from Bacterial Immunity Systems
    Wenyan Jiang, Luciano A. Marraffini · 2015 · Annual Review of Microbiology
  5. Measuring and Reducing Off-Target Activities of Programmable Nucleases Including CRISPR-Cas9
    Taeyoung Koo, Jungjoon Lee, Jin‐Soo Kim · 2015 · Molecules and Cells
  6. Simple and Rapid In Vivo Generation of Chromosomal Rearrangements using CRISPR/Cas9 Technology
    Rafael B. Blasco, Elif Karaca, Chiara Ambrogio, Taek-Chin Cheong, Emre Karayol, Valerio Giacomo Minero, Claudia Voena, Roberto Chiarle · 2014 · Cell Reports
  7. The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit
    Karthik Murugan, Kesavan Babu, Ramya Sundaresan, Rakhi Rajan, Dipali G. Sashital · 2017 · Molecular Cell
  8. Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling
    Samuel A. Myers, Jason B. Wright, Ryan Peckner, Brian Thomas Kalish, Feng Zhang, Steven A. Carr · 2018 · Nature Methods
  9. High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding
    Evan A. Boyle, Johan O. L. Andreasson, Lauren M. Chircus, Samuel H. Sternberg, Michelle J. Wu, Chantal K. Guegler, Jennifer A. Doudna, William James Greenleaf · 2017 · Proceedings of the National Academy of Sciences
  10. Computational approaches for effective CRISPR guide RNA design and evaluation
    Guanqing Liu, Yong Zhang, Tao Zhang · 2019 · Computational and Structural Biotechnology Journal
  11. Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system
    Xiaoxi Liu, Ayaka Homma, Jamasb Joshua Sayadi, Shu Yang, Jun Ohashi, Toru Takumi · 2016 · Scientific Reports
  12. Efficiency and Inheritance of Targeted Mutagenesis in Maize Using CRISPR-Cas9
    Jinjie Zhu, Ning Song, Silong Sun, Weilong Yang, Haiming Zhao, Weibin Song, Jinsheng Lai · 2015 · Journal of genetics and genomics/Journal of Genetics and Genomics
  13. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
    Shiran Abadi, Winston X. Yan, David Amar, Itay Mayrose · 2017 · PLoS Computational Biology
  14. CRISPR-Cas9: a new and promising player in gene therapy
    Xiao-Jie, Lu, Hui-Ying, Xue, Zun-Ping, Ke, Jin-Lian, Chen, Li-Juan, Ji · 2015 · Journal of Medical Genetics
  15. Site-specific integration in CHO cells mediated by CRISPR/Cas9 and homology-directed DNA repair pathway
    Jae Seong Lee, Thomas Beuchert Kallehauge, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard · 2015 · Scientific Reports
  16. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design
    Justin Smith, Sundari Suresh, Ulrich Schlecht, Manhong Wu, Omar Wagih, Gary Peltz, Ronald Wayne Davis, Lars Michael Steinmetz, Leopold Parts, Robert P. St.Onge · 2016 · Genome biology
  17. High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli
    Suhyung Cho, Donghui Choe, Eun‐Ju Lee, Sun Chang Kim, Bernhard Ørn Palsson, Byung‐Kwan Cho · 2018 · ACS Synthetic Biology
  18. Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation
    Daniel Fuentes, Tomek Swigut, Joanna Wysocka · 2018 · eLife
  19. Delivery and Specificity of CRISPR/Cas9 Genome Editing Technologies for Human Gene Therapy
    Jennifer L. Gori, Patrick D. Hsu, Morgan L. Maeder, Shen Shen, G. Grant Welstead, David A. Bumcrot · 2015 · Human Gene Therapy
  20. Expanding the CRISPR imaging toolset withStaphylococcus aureusCas9 for simultaneous imaging of multiple genomic loci
    Baohui Chen, Jeffrey Hu, Ricardo Almeida, Harrison Liu, Sanjeev Balakrishnan, Christian Covill‐Cooke, Wendell A. Lim, Bo Huang · 2016 · Nucleic Acids Research
  21. A genome-scale screen for synthetic drivers of T cell proliferation
    Mateusz Legut, Zoran Z. Gajic, Maria Guarino, Zharko Daniloski, Jahan A. Rahman, Xinhe Xue, Congyi Lu, Lu Lu, Eleni P. Mimitou, Stephanie Hao et al. · 2022 · Nature
  22. CRISPR /Cas9‐mediated knockout of Ms1 enables the rapid generation of male‐sterile hexaploid wheat lines for use in hybrid seed production
    Anzu Okada, Taj Arndell, Nikolai V. Borisjuk, Niharika Sharma, Nathan S. Watson‐Haigh, Elise J. Tucker, Ute Baumann, Peter Langridge, Ryan Whitford · 2019 · Plant Biotechnology Journal
  23. Evaluating and enhancing target specificity of gene-editing nucleases and deaminases
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  24. CRISPR/Cas9 Immune System as a Tool for Genome Engineering
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  25. A Systematic Analysis of Factors Localized to Damaged Chromatin Reveals PARP-Dependent Recruitment of Transcription Factors
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  26. Recent Progress in CRISPR/Cas9 Technology
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  27. The Impact of Chromatin Dynamics on Cas9-Mediated Genome Editing in Human Cells
    René Daer, Josh Cutts, David A. Brafman, Karmella Ann Haynes · 2016 · ACS Synthetic Biology
  28. Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs
    Cory J. Smith, Leire Abalde-Atristain, Chaoxia He, Brett R. Brodsky, Evan M. Braunstein, Pooja Chaudhari, Yoon-Young Jang, Linzhao Cheng, Zhaohui Ye · 2014 · Molecular Therapy
  29. CRISPR-Cas9D10A nickase-based genotypic and phenotypic screening to enhance genome editing
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  30. Saturation variant interpretation using CRISPR prime editing
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  31. Zebrafish Genome Engineering Using the CRISPR–Cas9 System
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  32. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells
    Susan M. Byrne, Luis Ortiz, Prashant Mali, John Aach, George McDonald Church · 2014 · Nucleic Acids Research
  33. Genome-wide tracking of dCas9-methyltransferase footprints
    Christina Galonska, Jocelyn Charlton, Alexandra L. Mattei, Julie Donaghey, Kendell Clement, Hongcang Gu, Arman W. Mohammad, Elena K. Stamenova, Davide Cacchiarelli, Sven Klages et al. · 2018 · Nature Communications
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    Karen E. Johnson, Virginie Bottero, Stephanie Flaherty, Sujoy Dutta, Vivek Vikram Singh, Bala Chandran · 2014 · PLoS Pathogens
  35. Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9
    Daniel E. Bauer, Matthew C. Canver, Stuart H. Orkin · 2014 · Journal of Visualized Experiments
  36. Targeted activation of diverse CRISPR-Cas systems for mammalian genome editing via proximal CRISPR targeting
    Fuqiang Chen, Xiao Lan Ding, Yongmei Feng, Timothy Seebeck, Yanfang Jiang, Gregory D. Davis · 2017 · Nature Communications
  37. CRISPR interference-based specific and efficient gene inactivation in the brain
    Yi Zheng, Wei Shen, Jian Zhang, Bo Yang, Yaonan Liu, Huihui Qi, Xia Yu, Si‐Yao Lu, Yun Chen, Yuzhou Xu et al. · 2018 · Nature Neuroscience
  38. Quantifying on- and off-target genome editing
    Ayal Hendel, Eli J. Fine, Gang Bao, Matthew Hebden Porteus · 2015 · Trends in biotechnology
  39. Conditional Knockouts Generated by Engineered CRISPR-Cas9 Endonuclease Reveal the Roles of Coronin in C. elegans Neural Development
    Zhongfu Shen, Xianliang Zhang, Yongping Chai, Zhiwen Zhu, Peishan Yi, Guoxin Feng, Wei Li, Guangshuo Ou · 2014 · Developmental Cell
  40. Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression
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  41. Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans
    Xiangyang Chen, Fei Xu, Chengming Zhu, Jiaojiao Ji, Xufei Zhou, Xuezhu Feng, Shouhong Guang · 2014 · Scientific Reports
  42. CRISPR-Cas12a has widespread off-target and dsDNA-nicking effects
    Karthik Murugan, Arun Somwarpet Seetharam, Andrew Josef Severin, Dipali G. Sashital · 2020 · Journal of Biological Chemistry
  43. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives
    Magdy M. Mahfouz, Agnieszka Piatek, C. Neal Stewart · 2014 · Plant Biotechnology Journal
  44. Chromatin accessibility: methods, mechanisms, and biological insights
    Andrés Mansisidor, Viviana I. Risca · 2022 · Nucleus
  45. Genome-wide profiling of adenine base editor specificity by EndoV-seq
    Liang, Puping, Xie, Xiaowei, Zhi, Shengyao, Sun, Hongwei, Zhang, Xiya, Chen, Yu, Chen, Yuxi, Xiong, Yuanyan, Ma, Wenbin, Liu, Dan et al. · 2019 · Nature Communications
  46. Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9
    Alberto Stolfi, Shashank Gandhi, Farhana Salek, Lionel Christiaen · 2014 · Development
  47. CCR5 Disruption in Induced Pluripotent Stem Cells Using CRISPR/Cas9 Provides Selective Resistance of Immune Cells to CCR5-tropic HIV-1 Virus
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  48. CRISPR technologies for bacterial systems: Current achievements and future directions
    Kyeong Rok Choi, Sang Yup Lee · 2016 · Biotechnology Advances
  49. Efficient Generation of Myostatin Gene Mutated Rabbit by CRISPR/Cas9
    Qingyan Lv, Lin Yuan, Jichao Deng, Mao Chen, Yong Wang, Jian Zeng, Zhanjun Li, Liangxue Lai · 2016 · Scientific Reports
  50. Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage
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  51. CRISPR-Cas9 for in vivo Gene Therapy: Promise and Hurdles
    Wei-Jing Dai, Liyao Zhu, Zhongyi Yan, Yong Xu, Qilong Wang, Xiaojie Lu · 2016 · Molecular Therapy — Nucleic Acids
  52. Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing
    Nicolas Wyvekens, Ved V. Topkar, Cyd Khayter, J. Keith Joung, Shengdar Q. Tsai · 2015 · Human Gene Therapy
  53. Probing the impact of chromatin conformation on genome editing tools
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  54. The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies
    Sebald A. N. Verkuijl, Marianne G. Rots · 2018 · Current Opinion in Biotechnology
  55. The chemistry of Cas9 and its CRISPR colleagues
    Janice S. Chen, Jennifer A. Doudna · 2017 · Nature Reviews Chemistry
  56. DNA stretching induces Cas9 off-target activity
    Matthew D. Newton, Ben Taylor, Rosalie P.C. Driessen, Leonie Roos, Nevena Cvetešić, Shenaz Allyjaun, Boris Lenhard, Maria Emanuela Cuomo, David Rueda · 2019 · Nature Structural & Molecular Biology
  57. In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila
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  58. Reprogramming metabolic pathways in vivo with CRISPR/Cas9 genome editing to treat hereditary tyrosinaemia
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  59. Induced Pluripotent Stem Cells: Reprogramming Platforms and Applications in Cell Replacement Therapy
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  60. One-step generation of triple knockout CHO cell lines using CRISPR/Cas9 and fluorescent enrichment
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  61. Genetic advances in systemic lupus erythematosus: an update
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  62. Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
    Lovorka Stojic, Aaron T. L. Lun, Jasmin Mangei, Patrice Mascalchi, Valentina Quarantotti, Alexis R. Barr, Chris Bakal, John C. Marioni, Fanni V. Gergely, Duncan T. Odom · 2018 · Nucleic Acids Research
  63. CRISPR/Cas-based genome engineering in natural product discovery
    Yaojun Tong, Tilmann Weber, Sang Yup Lee · 2018 · Natural Product Reports
  64. “Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs
    Venetia Pliatsika, Isidore Rigoutsos · 2015 · Biology Direct
  65. Computational Tools and Resources for CRISPR/Cas Genome Editing
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  66. In Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design
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  67. Modulating chromatin accessibility by transactivation and targeting proximal dsgRNAs enhances Cas9 editing efficiency in vivo
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  68. Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
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  69. CRISPR/Cas9‐mediated genome editing: From basic research to translational medicine
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  70. The Current State and Future of CRISPR-Cas9 gRNA Design Tools
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  71. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage
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  72. Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing
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  73. CRISPR/Cas9-mediated noncoding RNA editing in human cancers
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  74. Genome editing by natural and engineered CRISPR-associated nucleases
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  76. In Vitro Enzymology of Cas9
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