CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Boob, Aashutosh Girish; Zhu, Zhixin; Intasian, Pattarawan; Jain, Manan; Petrov, Vassily Andrew; Lane, Stephan Thomas; Tan, Shih-I; Xun, Guanhua; Zhao, Huimin

doi:10.1093/nar/gkae062

Title: CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Journal Article · 13 February 2024 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkae062 · OSTI ID:2301778

Boob, Aashutosh Girish ^[1]; Zhu, Zhixin ^[2]; Intasian, Pattarawan ^[3]; Jain, Manan ^[1]; Petrov, Vassily Andrew ^[1]; Lane, Stephan Thomas ^[1]; Tan, Shih-I ^[1]; Xun, Guanhua ^[2];

^[1]

Univ. of Illinois at Urbana-Champaign, IL (United States); Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States); Vidyasirimedhi Institute of Science and Technology, Rayong (Thailand)

The CRISPR/Cas system has emerged as a powerful tool for genome editing in metabolic engineering and human gene therapy. However, locating the optimal site on the chromosome to integrate heterologous genes using the CRISPR/Cas system remains an open question. Selecting a suitable site for gene integration involves considering multiple complex criteria, including factors related to CRISPR/Cas-mediated integration, genetic stability, and gene expression. Consequently, identifying such sites on specific or different chromosomal locations typically requires extensive characterization efforts. To address these challenges, we have developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. This tool leverages ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search, and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. As a proof of concept, we utilized CRISPR-COPIES to characterize neutral integration sites in three diverse species: Saccharomyces cerevisiae, Cupriavidus necator, and HEK293T cells. In addition, we developed a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate that CRISPR-COPIES will serve as a valuable tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, enable rapid strain construction to produce valuable biochemicals, and support human gene and cell therapy applications.

View Journal Article

Cite

Export

Save

Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States); Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE

Grant/Contract Number:: SC0018420

OSTI ID:: 2301778

Alternate ID(s):: OSTI ID: 2309739

Journal Information:: Nucleic Acids Research, Vol. 52, Issue 6; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (76)

Synthetic Biology Toolkit for Marker-Less Integration of Multigene Pathways into Pichia pastoris via CRISPR/Cas9 Gao, Jucan; Xu, Junhao; Zuo, Yimeng ACS Synthetic Biology, Vol. 11, Issue 2 https://doi.org/10.1021/acssynbio.1c00307	journal	January 2022
Discovery and validation of human genomic safe harbor sites for gene and cell therapies Aznauryan, Erik; Yermanos, Alexander; Kinzina, Elvira Cell Reports Methods, Vol. 2, Issue 1 https://doi.org/10.1016/j.crmeth.2021.100154	journal	January 2022
CRISPR-SE: a brute force search engine for CRISPR design Li, Bin; Chen, Poshen B.; Diao, Yarui NAR Genomics and Bioinformatics, Vol. 3, Issue 1 https://doi.org/10.1093/nargab/lqab013	journal	January 2021
HEK293 Cell Line as a Platform to Produce Recombinant Proteins and Viral Vectors Tan, Evan; Chin, Cara Sze Hui; Lim, Zhi Feng Sherman Frontiers in Bioengineering and Biotechnology, Vol. 9 https://doi.org/10.3389/fbioe.2021.796991	journal	December 2021
Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq Brady, Joseph R.; Tan, Melody C.; Whittaker, Charles A. ACS Synthetic Biology, Vol. 9, Issue 9 https://doi.org/10.1021/acssynbio.0c00299	journal	August 2020
Construction of ajmalicine and sanguinarine de novo biosynthetic pathways using stable integration sites in yeast Liu, Tengfei; Gou, Yuanwei; Zhang, Bei Biotechnology and Bioengineering, Vol. 119, Issue 5 https://doi.org/10.1002/bit.28040	journal	January 2022
Improved sgRNA design in bacteria via genome-wide activity profiling Guo, Jiahui; Wang, Tianmin; Guan, Changge Nucleic Acids Research, Vol. 46, Issue 14 https://doi.org/10.1093/nar/gky572	journal	June 2018
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system Wong, Nathan; Liu, Weijun; Wang, Xiaowei Genome Biology, Vol. 16, Issue 1 https://doi.org/10.1186/s13059-015-0784-0	journal	November 2015
ANN-Benchmarks: A benchmarking tool for approximate nearest neighbor algorithms Aumüller, Martin; Bernhardsson, Erik; Faithfull, Alexander Information Systems, Vol. 87 https://doi.org/10.1016/j.is.2019.02.006	journal	January 2020
Characterization of chromosomal integration sites for heterologous gene expression in Saccharomyces cerevisiae Bai Flagfeldt, Dongmei; Siewers, Verena; Huang, Le Yeast, Vol. 26, Issue 10 https://doi.org/10.1002/yea.1705	journal	October 2009
Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping Lian, Jiazhang; Schultz, Carl; Cao, Mingfeng Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13621-4	journal	December 2019
A multi-landing pad DNA integration platform for mammalian cell engineering Gaidukov, Leonid; Wroblewska, Liliana; Teague, Brian Nucleic Acids Research, Vol. 46, Issue 8 https://doi.org/10.1093/nar/gky216	journal	April 2018
A novel series of vectors for chromosomal integration in fission yeast Matsuyama, Akihisa; Shirai, Atsuko; Yoshida, Minoru Biochemical and Biophysical Research Communications, Vol. 374, Issue 2 https://doi.org/10.1016/j.bbrc.2008.07.015	journal	September 2008
Location Effects of a Reporter Gene on Expression Levels and on Native Protein Synthesis in Lactococcus lactis and Saccharomyces cerevisiae Thompson, A.; Gasson, M. J. Applied and Environmental Microbiology, Vol. 67, Issue 8 https://doi.org/10.1128/AEM.67.8.3434-3439.2001	journal	August 2001
Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801 Madhu, Swati; Sengupta, Annesha; Sarnaik, Aditya P. ACS Synthetic Biology, Vol. 12, Issue 6 https://doi.org/10.1021/acssynbio.3c00019	journal	May 2023
A Highly Characterized Synthetic Landing Pad System for Precise Multicopy Gene Integration in Yeast Bourgeois, Leanne; Pyne, Michael E.; Martin, Vincent J. J. ACS Synthetic Biology, Vol. 7, Issue 11 https://doi.org/10.1021/acssynbio.8b00339	journal	October 2018
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes Engler, Carola; Gruetzner, Ramona; Kandzia, Romy PLoS ONE, Vol. 4, Issue 5 https://doi.org/10.1371/journal.pone.0005553	journal	May 2009
The sound of silence: Transgene silencing in mammalian cell engineering Cabrera, Alan; Edelstein, Hailey I.; Glykofrydis, Fokion Cell Systems, Vol. 13, Issue 12 https://doi.org/10.1016/j.cels.2022.11.005	journal	December 2022
Genome-wide landscape of position effects on heterogeneous gene expression in Saccharomyces cerevisiae Wu, Xiao-Le; Li, Bing-Zhi; Zhang, Wen-Zheng Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0872-3	journal	July 2017
Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform Mikkelsen, Michael Dalgaard; Buron, Line Due; Salomonsen, Bo Metabolic Engineering, Vol. 14, Issue 2 https://doi.org/10.1016/j.ymben.2012.01.006	journal	March 2012
A largely random AAV integration profile after LPLD gene therapy Kaeppel, Christine; Beattie, Stuart G.; Fronza, Raffaele Nature Medicine, Vol. 19, Issue 7 https://doi.org/10.1038/nm.3230	journal	June 2013
Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy Davé, Utpal P.; Akagi, Keiko; Tripathi, Rati PLoS Genetics, Vol. 5, Issue 5 https://doi.org/10.1371/journal.pgen.1000491	journal	May 2009
Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel Akhtar, Waseem; de Jong, Johann; Pindyurin, Alexey V. Cell, Vol. 154, Issue 4 https://doi.org/10.1016/j.cell.2013.07.018	journal	August 2013
Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence Semenova, E.; Jore, M. M.; Datsenko, K. A. Proceedings of the National Academy of Sciences, Vol. 108, Issue 25, p. 10098-10103 https://doi.org/10.1073/pnas.1104144108	journal	June 2011
GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes Poudel, Ravin; Rodriguez, Lidimarie Trujillo; Reisch, Christopher R. GigaScience, Vol. 11 https://doi.org/10.1093/gigascience/giac007	journal	April 2022
Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO2 valorization Pan, Haojie; Wang, Jia; Wu, Haoliang Biotechnology for Biofuels, Vol. 14, Issue 1 https://doi.org/10.1186/s13068-021-02063-0	journal	November 2021
High-Resolution Mapping of the Escherichia coli Chromosome Reveals Positions of High and Low Transcription Scholz, Scott A.; Diao, Rucheng; Wolfe, Michael B. Cell Systems, Vol. 8, Issue 3 https://doi.org/10.1016/j.cels.2019.02.004	journal	March 2019
A landing pad system for multicopy gene integration in Issatchenkia orientalis Fatma, Zia; Tan, Shih-I; Boob, Aashutosh Girish Metabolic Engineering, Vol. 78 https://doi.org/10.1016/j.ymben.2023.06.010	journal	July 2023
CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning Konstantakos, Vasileios; Nentidis, Anastasios; Krithara, Anastasia Nucleic Acids Research, Vol. 50, Issue 7 https://doi.org/10.1093/nar/gkac192	journal	March 2022
CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences Lin, Y.; Cradick, T. J.; Brown, M. T. Nucleic Acids Research, Vol. 42, Issue 11 https://doi.org/10.1093/nar/gku402	journal	May 2014
Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus Everitt, Richard G.; Didelot, Xavier; Batty, Elizabeth M. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms4956	journal	May 2014
High-level semi-synthetic production of the potent antimalarial artemisinin Paddon, C. J.; Westfall, P. J.; Pitera, D. J. Nature, Vol. 496, Issue 7446 https://doi.org/10.1038/nature12051	journal	April 2013
Applications of CRISPR technologies in research and beyond Barrangou, Rodolphe; Doudna, Jennifer A. Nature Biotechnology, Vol. 34, Issue 9 https://doi.org/10.1038/nbt.3659	journal	September 2016
DNA targeting specificity of RNA-guided Cas9 nucleases Hsu, Patrick D.; Scott, David A.; Weinstein, Joshua A. Nature Biotechnology, Vol. 31, Issue 9, p. 827-832 https://doi.org/10.1038/nbt.2647	journal	July 2013
Gene therapy for follistatin mitigates systemic metabolic inflammation and post-traumatic arthritis in high-fat diet–induced obesity Tang, Ruhang; Harasymowicz, Natalia S.; Wu, Chia-Lung Science Advances, Vol. 6, Issue 19 https://doi.org/10.1126/sciadv.aaz7492	journal	May 2020
Expanding the neutral sites for integrated gene expression in Saccharomyces cerevisiae Kong, Sijia; Yu, Wei; Gao, Ning FEMS Microbiology Letters, Vol. 369, Issue 1 https://doi.org/10.1093/femsle/fnac081	journal	August 2022
High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method Gietz, R. Daniel; Schiestl, Robert H. Nature Protocols, Vol. 2, Issue 1 https://doi.org/10.1038/nprot.2007.13	journal	January 2007
Selection of chromosomal DNA libraries using a multiplex CRISPR system Ryan, Owen W.; Skerker, Jeffrey M.; Maurer, Matthew J. eLife, Vol. 3 https://doi.org/10.7554/eLife.03703	journal	August 2014
PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction Enghiad, Behnam; Xue, Pu; Singh, Nilmani Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-30355-y	journal	May 2022
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing Labun, Kornel; Montague, Tessa G.; Krause, Maximilian Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz365	journal	May 2019
EasyClone: method for iterative chromosomal integration of multiple genes Saccharomyces cerevisiae Jensen, Niels B.; Strucko, Tomas; Kildegaard, Kanchana R. FEMS Yeast Research, Vol. 14, Issue 2 https://doi.org/10.1111/1567-1364.12118	journal	March 2014
Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity Moreb, E. A.; Lynch, M. D. Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-25339-3	journal	August 2021
Gene therapy for spinal muscular atrophy: the Qatari experience Ali, Hossamaldein Gaber; Ibrahim, Khalid; Elsaid, Mahmoud Fawzi Gene Therapy, Vol. 28, Issue 10-11 https://doi.org/10.1038/s41434-021-00273-7	journal	July 2021
Screening neutral sites for metabolic engineering of methylotrophic yeast Ogataea polymorpha Yu, Wei; Gao, Jiaoqi; Zhai, Xiaoxin Synthetic and Systems Biotechnology, Vol. 6, Issue 2 https://doi.org/10.1016/j.synbio.2021.03.001	journal	June 2021
Challenges and opportunities of bioprocessing 5-aminolevulinic acid using genetic and metabolic engineering: a critical review Yi, Ying-Chen; Shih, I-Tai; Yu, Tzu-Hsuan Bioresources and Bioprocessing, Vol. 8, Issue 1 https://doi.org/10.1186/s40643-021-00455-6	journal	October 2021
Chromatin Architecture of the Human Genome Gilbert, Nick; Boyle, Shelagh; Fiegler, Heike Cell, Vol. 118, Issue 5 https://doi.org/10.1016/j.cell.2004.08.011	journal	September 2004
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets Steinegger, Martin; Söding, Johannes Nature Biotechnology, Vol. 35, Issue 11 https://doi.org/10.1038/nbt.3988	journal	October 2017
Cloning and disruption of the Pichia pastoris ARG1, ARG2, ARG3, HIS1, HIS2, HIS5, HIS6 genes and their use as auxotrophic markers Nett, Juergen H.; Hodel, Nikolai; Rausch, Sebastian Yeast, Vol. 22, Issue 4 https://doi.org/10.1002/yea.1202	journal	March 2005
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale Liew, Fungmin Eric; Nogle, Robert; Abdalla, Tanus Nature Biotechnology https://doi.org/10.1038/s41587-021-01195-w	journal	February 2022
CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation Müller Paul, Hans; Istanto, Dave D.; Heldenbrand, Jacob BMC Bioinformatics, Vol. 23, Issue 1 https://doi.org/10.1186/s12859-022-04593-2	journal	February 2022
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA Fonfara, Ines; Richter, Hagen; Bratovič, Majda Nature, Vol. 532, Issue 7600 https://doi.org/10.1038/nature17945	journal	April 2016
Machine learning approach to gene essentiality prediction: a review Aromolaran, Olufemi; Aromolaran, Damilare; Isewon, Itunuoluwa Briefings in Bioinformatics, Vol. 22, Issue 5 https://doi.org/10.1093/bib/bbab128	journal	April 2021
Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2 Panich, Justin; Fong, Bonnie; Singer, Steven W. Trends in Biotechnology, Vol. 39, Issue 4 https://doi.org/10.1016/j.tibtech.2021.01.001	journal	April 2021
The influence of eukaryotic chromatin state on CRISPR–Cas9 editing efficiencies Verkuijl, Sebald AN; Rots, Marianne G. Current Opinion in Biotechnology, Vol. 55 https://doi.org/10.1016/j.copbio.2018.07.005	journal	February 2019
Targeting Specificity of the CRISPR/Cas9 System Tasan, Ipek; Zhao, Huimin ACS Synthetic Biology, Vol. 6, Issue 9 https://doi.org/10.1021/acssynbio.7b00270	journal	September 2017
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots Schröder, Astrid R. W.; Shinn, Paul; Chen, Huaming Cell, Vol. 110, Issue 4 https://doi.org/10.1016/S0092-8674(02)00864-4	journal	August 2002
Database resources of the national center for biotechnology information Sayers, Eric W.; Bolton, Evan E.; Brister, J. Rodney Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1112	journal	December 2021
Effective gene expression prediction from sequence by integrating long-range interactions Avsec, Žiga; Agarwal, Vikram; Visentin, Daniel Nature Methods, Vol. 18, Issue 10 https://doi.org/10.1038/s41592-021-01252-x	journal	October 2021
Plant nuclear factor Y (NF-Y) B subunits confer drought tolerance and lead to improved corn yields on water-limited acres Nelson, D. E.; Repetti, P. P.; Adams, T. R. Proceedings of the National Academy of Sciences, Vol. 104, Issue 42 https://doi.org/10.1073/pnas.0707193104	journal	October 2007
Genomics and epigenetics guided identification of tissue-specific genomic safe harbors Shrestha, Dewan; Bag, Aishee; Wu, Ruiqiong Genome Biology, Vol. 23, Issue 1 https://doi.org/10.1186/s13059-022-02770-3	journal	September 2022
Metabolic Engineering: Methodologies and Applications Volk, Michael J.; Tran, Vinh G.; Tan, Shih-I Chemical Reviews, Vol. 123, Issue 9 https://doi.org/10.1021/acs.chemrev.2c00403	journal	December 2022
The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system Baek, Sihyun; Utomo, Joseph Christian; Lee, Ji Young Metabolic Engineering, Vol. 64 https://doi.org/10.1016/j.ymben.2021.01.011	journal	March 2021
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases Bae, S.; Park, J.; Kim, J. -S. Bioinformatics, Vol. 30, Issue 10 https://doi.org/10.1093/bioinformatics/btu048	journal	January 2014
Human Genomic Safe Harbors and the Suicide Gene-Based Safeguard System for iPSC-Based Cell Therapy Kimura, Yasuyoshi; Shofuda, Tomoko; Higuchi, Yuichiro Stem Cells Translational Medicine, Vol. 8, Issue 7 https://doi.org/10.1002/sctm.18-0039	journal	March 2019
Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses Shimizu, Rie; Chou, Kenta; Orita, Izumi BMC Microbiology, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2180-13-169	journal	July 2013
High-level secretion of human growth hormone by Escherichia coli Chang, Chung Nan; Key, Michael; Bochner, Barry Gene, Vol. 55, Issue 2-3 https://doi.org/10.1016/0378-1119(87)90279-4	journal	January 1987
Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica Baisya, Dipankar; Ramesh, Adithya; Schwartz, Cory Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-28540-0	journal	February 2022
Towards a fully automated algorithm driven platform for biosystems design HamediRad, Mohammad; Chao, Ran; Weisberg, Scott Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13189-z	journal	November 2019
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 Doench, John G.; Fusi, Nicolo; Sullender, Meagan Nature Biotechnology, Vol. 34, Issue 2 https://doi.org/10.1038/nbt.3437	journal	January 2016
Gene Insertion Into Genomic Safe Harbors for Human Gene Therapy Papapetrou, Eirini P.; Schambach, Axel Molecular Therapy, Vol. 24, Issue 4 https://doi.org/10.1038/mt.2016.38	journal	April 2016
Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells Mansouri, Maysam; Fussenegger, Martin Protein & Cell, Vol. 13, Issue 7 https://doi.org/10.1007/s13238-021-00876-1	journal	September 2021
Internal guide RNA interactions interfere with Cas9-mediated cleavage Thyme, Summer B.; Akhmetova, Laila; Montague, Tessa G. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11750	journal	June 2016
The evolution, evolvability and engineering of gene regulatory DNA Vaishnav, Eeshit Dhaval; de Boer, Carl G.; Molinet, Jennifer Nature, Vol. 603, Issue 7901 https://doi.org/10.1038/s41586-022-04506-6	journal	March 2022
SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells Zhang, Meng; Ehmann, Mary Elisabeth; Matukumalli, Srija Nature Communications, Vol. 14, Issue 1 https://doi.org/10.1038/s41467-023-41468-3	journal	September 2023
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools Luo, Hao; Lin, Yan; Liu, Tao Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa917	journal	October 2020

Similar Records

A landing pad system for multicopy gene integration in Issatchenkia orientalis

Journal Article · 2023 · Metabolic Engineering · OSTI ID:1993846

Fatma, Zia; Tan, Shih-I; Boob, Aashutosh Girish; +1 more

Improving CRISPR/Cas9-mediated genome editing efficiency in Yarrowia lipolytica using direct tRNA-sgRNA fusions

Journal Article · 2020 · Metabolic Engineering · OSTI ID:1851146

Abdel-Mawgoud, A. M.; Stephanopoulos, G.

Using the Endogenous CRISPR-Cas System of Heliobacterium modesticaldum To Delete the Photochemical Reaction Center Core Subunit Gene

Journal Article · 2019 · Applied and Environmental Microbiology · OSTI ID:1631821

Baker, Patricia L.; Orf, Gregory S.; Kevershan, Kimberly; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
synthetic biology and assembly cloning
computational methods
targeted gene modification

Title: CRISPR-COPIES: an in silico platform for discovery of neutral integration sites for CRISPR/Cas-facilitated gene integration

Citation Formats

References (76)

Similar Records

Related Subjects