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Journal articles on the topic 'Genome editors'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 February 2022

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1

Goodman, L. "New Editors Join Genome Research." Genome Research 12, no. 8 (2002): 1151. http://dx.doi.org/10.1101/gr.572802.

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2

Scheben, Armin, and David Edwards. "Genome editors take on crops." Science 355, no. 6330 (2017): 1122–23. http://dx.doi.org/10.1126/science.aal4680.

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3

Molla, Kutubuddin A., Simon Sretenovic, Kailash C. Bansal, and Yiping Qi. "Precise plant genome editing using base editors and prime editors." Nature Plants 7, no. 9 (2021): 1166–87. http://dx.doi.org/10.1038/s41477-021-00991-1.

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4

Evanoff, Mallory, and Alexis C. Komor. "Base editors: modular tools for the introduction of point mutations in living cells." Emerging Topics in Life Sciences 3, no. 5 (2019): 483–91. http://dx.doi.org/10.1042/etls20190088.

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Base editors are a new family of programmable genome editing tools that fuse ssDNA (single-stranded DNA) modifying enzymes to catalytically inactive CRISPR-associated (Cas) endonucleases to induce highly efficient single base changes. With dozens of base editors now reported, it is apparent that these tools are highly modular; many combinations of ssDNA modifying enzymes and Cas proteins have resulted in a variety of base editors, each with its own unique properties and potential uses. In this perspective, we describe currently available base editors, highlighting their modular nature and desc

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5

Leslie, Mitch. "‘Old’ genome editors might treat mitochondrial diseases." Science 361, no. 6409 (2018): 1302. http://dx.doi.org/10.1126/science.361.6409.1302.

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6

Burt, Austin, and Anne Deredec. "Self-limiting population genetic control with sex-linked genome editors." Proceedings of the Royal Society B: Biological Sciences 285, no. 1883 (2018): 20180776. http://dx.doi.org/10.1098/rspb.2018.0776.

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In male heterogametic species the Y chromosome is transmitted solely from fathers to sons, and is selected for based only on its impacts on male fitness. This fact can be exploited to develop efficient pest control strategies that use Y-linked editors to disrupt the fitness of female descendants. With simple population genetic and dynamic models we show that Y-linked editors can be substantially more efficient than other self-limiting strategies and, while not as efficient as gene drive approaches, are expected to have less impact on non-target populations with which there is some gene flow. E

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7

Anzalone, Andrew V., Luke W. Koblan, and David R. Liu. "Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors." Nature Biotechnology 38, no. 7 (2020): 824–44. http://dx.doi.org/10.1038/s41587-020-0561-9.

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8

Monsur, Mahmuda Binte, Gaoneng Shao, Yusong Lv, et al. "Base Editing: The Ever Expanding Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Tool Kit for Precise Genome Editing in Plants." Genes 11, no. 4 (2020): 466. http://dx.doi.org/10.3390/genes11040466.

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Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9), a newly developed genome-editing tool, has revolutionized animal and plant genetics by facilitating modification of target genes. This simple, convenient base-editing technology was developed to improve the precision of genome editing. Base editors generate precise point mutations by permanent base conversion at a specific point, with very low levels of insertions and deletions. Different plant base editors have been established by fusing various nucleobase deaminases with Cas9, Cas13, or Cas

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9

Tan, Wenfang, Chris Proudfoot, Simon G. Lillico, and C. Bruce A. Whitelaw. "Gene targeting, genome editing: from Dolly to editors." Transgenic Research 25, no. 3 (2016): 273–87. http://dx.doi.org/10.1007/s11248-016-9932-x.

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10

Hölttä, Mikko, Roberto Nitsch, and Neil Henderson. "Bioanalytical challenges and strategies of CRISPR genome editors." Bioanalysis 13, no. 3 (2021): 169–79. http://dx.doi.org/10.4155/bio-2020-0215.

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Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR) has been used to great effect in vitro to allow scientists to more rapidly investigate molecular pathways that may be involved in disease. The logical progression for the CRISPR machinery is to move from bench to bedside into the world of therapeutics and clinical diagnostics. Depending upon the intended therapeutic use of CRISPR, there are as many bioanalytical challenges in order to resolve scientific questions as drug development and regulatory questions. The aim of this article is to highlight bioanalyt

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11

Luesch, Hendrik, and John B. MacMillan. "Targeting and extending the eukaryotic druggable genome with natural products." Natural Product Reports 37, no. 6 (2020): 744–46. http://dx.doi.org/10.1039/d0np90021d.

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The Natural Product Reports themed collection on targeting and extending the eukaryotic druggable genome with natural products is introduced by the Guest Editors, Hendrik Luesch and John B. MacMillan.

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12

Kim, Do Yon, Su Bin Moon, Jeong-Heon Ko, Yong-Sam Kim, and Daesik Kim. "Unbiased investigation of specificities of prime editing systems in human cells." Nucleic Acids Research 48, no. 18 (2020): 10576–89. http://dx.doi.org/10.1093/nar/gkaa764.

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Abstract Prime editors (PEs) enable targeted precise editing, including the generation of substitutions, insertions and deletions, in eukaryotic genomes. However, their genome-wide specificity has not been explored. Here, we developed Nickase-based Digenome-seq (nDigenome-seq), an in vitro assay that uses whole-genome sequencing to identify single-strand breaks induced by CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) nickase. We used nDigenome-seq to screen for potential genome-wide off-target sites of Cas9 H840A nickase, a PE component,

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13

Kim, Daesik, Kevin Luk, Scot A. Wolfe, and Jin-Soo Kim. "Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases." Annual Review of Biochemistry 88, no. 1 (2019): 191–220. http://dx.doi.org/10.1146/annurev-biochem-013118-111730.

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Programmable nucleases and deaminases, which include zinc-finger nucleases, transcription activator-like effector nucleases, CRISPR RNA-guided nucleases, and RNA-guided base editors, are now widely employed for the targeted modification of genomes in cells and organisms. These gene-editing tools hold tremendous promise for therapeutic applications. Importantly, these nucleases and deaminases may display off-target activity through the recognition of near-cognate DNA sequences to their target sites, resulting in collateral damage to the genome in the form of local mutagenesis or genomic rearran

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14

Saha, Krishanu, Erik J. Sontheimer, P. J. Brooks, et al. "The NIH Somatic Cell Genome Editing program." Nature 592, no. 7853 (2021): 195–204. http://dx.doi.org/10.1038/s41586-021-03191-1.

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AbstractThe move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium’s plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Cen

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15

Eid, Ayman, Sahar Alshareef, and Magdy M. Mahfouz. "CRISPR base editors: genome editing without double-stranded breaks." Biochemical Journal 475, no. 11 (2018): 1955–64. http://dx.doi.org/10.1042/bcj20170793.

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The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off-target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used t

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Kim, Uijin, Nahyun Kim, and Ha Youn Shin. "Modeling Non-Alcoholic Fatty Liver Disease (NAFLD) Using “Good-Fit” Genome-Editing Tools." Cells 9, no. 12 (2020): 2572. http://dx.doi.org/10.3390/cells9122572.

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Non-alcoholic fatty liver disease (NAFLD), which affects both adults and children, is the most common liver disorder worldwide. NAFLD is characterized by excess fat accumulation in the liver in the absence of significant alcohol use. NAFLD is strongly associated with obesity, insulin resistance, metabolic syndrome, as well as specific genetic polymorphisms. Severe NAFLD cases can further progress to cirrhosis, hepatocellular carcinoma (HCC), or cardiovascular complications. Here, we describe the pathophysiological features and critical genetic variants associated with NAFLD. Recent advances in

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17

Ahn, Chang Ho, Mummadireddy Ramya, Hye Ryun An, et al. "Progress and Challenges in the Improvement of Ornamental Plants by Genome Editing." Plants 9, no. 6 (2020): 687. http://dx.doi.org/10.3390/plants9060687.

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Biotechnological approaches have been used to modify the floral color, size, and fragrance of ornamental plants, as well as to increase disease resistance and vase life. Together with the advancement of whole genome sequencing technologies, new plant breeding techniques have rapidly emerged in recent years. Compared to the early versions of gene editing tools, such as meganucleases (MNs), zinc fingers (ZFNs), and transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) is capable of altering a genome more efficiently and with h

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18

Christensen, Chloe L., Rhea E. Ashmead, and Francis Y. M. Choy. "Cell and Gene Therapies for Mucopolysaccharidoses: Base Editing and Therapeutic Delivery to the CNS." Diseases 7, no. 3 (2019): 47. http://dx.doi.org/10.3390/diseases7030047.

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Although individually uncommon, rare diseases collectively account for a considerable proportion of disease impact worldwide. A group of rare genetic diseases called the mucopolysaccharidoses (MPSs) are characterized by accumulation of partially degraded glycosaminoglycans cellularly. MPS results in varied systemic symptoms and in some forms of the disease, neurodegeneration. Lack of treatment options for MPS with neurological involvement necessitates new avenues of therapeutic investigation. Cell and gene therapies provide putative alternatives and when coupled with genome editing technologie

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19

Averina, Olga A., Oleg A. Permyakov, Olga O. Grigorieva, et al. "Comparative Analysis of Genome Editors Efficiency on a Model of Mice Zygotes Microinjection." International Journal of Molecular Sciences 22, no. 19 (2021): 10221. http://dx.doi.org/10.3390/ijms221910221.

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Genome editing is an indispensable tool for functional genomics. The caveat of the genome-editing pipeline is a prevalence of error-prone non-homologous end joining over homologous recombination, while only the latter is suitable to introduce particularly desired genetic variants. To overcome this problem, a toolbox of genome engineering was appended by a variety of improved instruments. In this work, we compared the efficiency of a number of recently suggested improved systems for genome editing applied to the same genome regions on a murine zygote model via microinjection. As a result, we ob

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20

Rabinowitz, Roy, Shiran Abadi, Shiri Almog, and Daniel Offen. "Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing." Nucleic Acids Research 48, W1 (2020): W340—W347. http://dx.doi.org/10.1093/nar/gkaa215.

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Abstract Base editing is a genome-editing approach that employs the CRISPR/Cas system to precisely install point mutations within the genome. A deaminase enzyme is fused to a deactivated Cas and enables transition conversions. The diversified repertoire of base editors provides a wide range of base editing possibilities. However, existing base editors cannot induce transversion substitutions and activate only within a specified region relative to the binding site, thus, they cannot precisely correct every point mutation. Here, we present BE-FF (Base Editors Functional Finder), a novel computat

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21

Hernandez-Gordillo, Victor, Thomas Caleb Casolaro, Mo R. Ebrahimkhani, and Samira Kiani. "Multicellular systems to translate somatic cell genome editors to human." Current Opinion in Biomedical Engineering 16 (December 2020): 72–81. http://dx.doi.org/10.1016/j.cobme.2020.100249.

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22

Gürel, Filiz, Yingxiao Zhang, Simon Sretenovic, and Yiping Qi. "CRISPR-Cas nucleases and base editors for plant genome editing." aBIOTECH 1, no. 1 (2019): 74–87. http://dx.doi.org/10.1007/s42994-019-00010-0.

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23

Trancoso, Inês, Ryo Morimoto, and Thomas Boehm. "Co-evolution of mutagenic genome editors and vertebrate adaptive immunity." Current Opinion in Immunology 65 (August 2020): 32–41. http://dx.doi.org/10.1016/j.coi.2020.03.001.

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24

Green, Eric D., and Christopher R. Donohue. "Special Issue Editors’ Introduction: “Genomics and the Human Genome Project”." Journal of the History of Biology 51, no. 4 (2018): 625–29. http://dx.doi.org/10.1007/s10739-018-9548-5.

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25

Urnov, Fyodor D. "The Cas9 Hammer—and Sickle: A Challenge for Genome Editors." CRISPR Journal 4, no. 1 (2021): 6–13. http://dx.doi.org/10.1089/crispr.2021.29120.fur.

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26

Kantor, Ariel, Michelle McClements, and Robert MacLaren. "CRISPR-Cas9 DNA Base-Editing and Prime-Editing." International Journal of Molecular Sciences 21, no. 17 (2020): 6240. http://dx.doi.org/10.3390/ijms21176240.

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Many genetic diseases and undesirable traits are due to base-pair alterations in genomic DNA. Base-editing, the newest evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas-based technologies, can directly install point-mutations in cellular DNA without inducing a double-strand DNA break (DSB). Two classes of DNA base-editors have been described thus far, cytosine base-editors (CBEs) and adenine base-editors (ABEs). Recently, prime-editing (PE) has further expanded the CRISPR-base-edit toolkit to all twelve possible transition and transversion mutations, as well a

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27

Liu, Jun-Jie, Natalia Orlova, Benjamin L. Oakes, et al. "CasX enzymes comprise a distinct family of RNA-guided genome editors." Nature 566, no. 7743 (2019): 218–23. http://dx.doi.org/10.1038/s41586-019-0908-x.

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28

Kim, Daesik, Da-eun Kim, Gyeorae Lee, Sung-Ik Cho, and Jin-Soo Kim. "Genome-wide target specificity of CRISPR RNA-guided adenine base editors." Nature Biotechnology 37, no. 4 (2019): 430–35. http://dx.doi.org/10.1038/s41587-019-0050-1.

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29

Lapinaite, Audrone, Gavin J. Knott, Cody M. Palumbo, et al. "DNA capture by a CRISPR-Cas9–guided adenine base editor." Science 369, no. 6503 (2020): 566–71. http://dx.doi.org/10.1126/science.abb1390.

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CRISPR-Cas–guided base editors convert A•T to G•C, or C•G to T•A, in cellular DNA for precision genome editing. To understand the molecular basis for DNA adenosine deamination by adenine base editors (ABEs), we determined a 3.2-angstrom resolution cryo–electron microscopy structure of ABE8e in a substrate-bound state in which the deaminase domain engages DNA exposed within the CRISPR-Cas9 R-loop complex. Kinetic and structural data suggest that ABE8e catalyzes DNA deamination up to ~1100-fold faster than earlier ABEs because of mutations that stabilize DNA substrates in a constrained, transfer

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30

Huang, Tony P., Gregory A. Newby, and David R. Liu. "Precision genome editing using cytosine and adenine base editors in mammalian cells." Nature Protocols 16, no. 2 (2021): 1089–128. http://dx.doi.org/10.1038/s41596-020-00450-9.

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31

Arroyo-Olarte, Ruben D., Ricardo Bravo Rodríguez, and Edgar Morales-Ríos. "Genome Editing in Bacteria: CRISPR-Cas and Beyond." Microorganisms 9, no. 4 (2021): 844. http://dx.doi.org/10.3390/microorganisms9040844.

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Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids. The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing. In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent

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32

Li, Chang, Aphrodite Georgakopoulou, Arpit Mishra та ін. "In vivo HSPC gene therapy with base editors allows for efficient reactivation of fetal γ-globin in β-YAC mice". Blood Advances 5, № 4 (2021): 1122–35. http://dx.doi.org/10.1182/bloodadvances.2020003702.

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Abstract Base editors are capable of installing precise genomic alterations without creating double-strand DNA breaks. In this study, we targeted critical motifs regulating γ-globin reactivation with base editors delivered via HDAd5/35++ vectors. Through optimized design, we successfully produced a panel of cytidine and adenine base editor (ABE) vectors targeting the erythroid BCL11A enhancer or recreating naturally occurring hereditary persistence of fetal hemoglobin (HPFH) mutations in the HBG1/2 promoter. All 5 tested vectors efficiently installed target base conversion and led to γ-globin

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33

Zhang, Yan, Yijun Ruan, and Guoliang Li. "The 5th International 3D Genomics Workshop 2018: conference report." Epigenomics 11, no. 12 (2019): 1353–57. http://dx.doi.org/10.2217/epi-2019-0185.

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The International 3D Genomics Workshop is an annual international scientific conference focused on the research of the 3D structure of the genome in the nucleus. The 5th International 3D Genomics Workshop 2018 was held at the International Academic Center of Huazhong Agricultural University on the 13th–14th of October 2018. It attracted >150 international and local participants, including leading researchers in the field of the 3D genomics and editors from top journals. The main topic of the conference was the research achievements newly published or unpublished on the 3D genome area. The i

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34

Tabassum, Javaria, Shakeel Ahmad, Babar Hussain, Amos Musyoki Mawia, Aqib Zeb, and Luo Ju. "Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives." Agronomy 11, no. 7 (2021): 1359. http://dx.doi.org/10.3390/agronomy11071359.

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Food crop production and quality are two major attributes that ensure food security. Rice is one of the major sources of food that feeds half of the world’s population. Therefore, to feed about 10 billion people by 2050, there is a need to develop high-yielding grain quality of rice varieties, with greater pace. Although conventional and mutation breeding techniques have played a significant role in the development of desired varieties in the past, due to certain limitations, these techniques cannot fulfill the high demands for food in the present era. However, rice production and grain qualit

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35

Liu, Jun-Jie, Natalia Orlova, Benjamin L. Oakes, et al. "Author Correction: CasX enzymes comprise a distinct family of RNA-guided genome editors." Nature 568, no. 7752 (2019): E8—E10. http://dx.doi.org/10.1038/s41586-019-1084-8.

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36

Gu, Sifeng, Zsolt Bodai, Quinn T. Cowan, and Alexis C. Komor. "Base editors: Expanding the types of DNA damage products harnessed for genome editing." Gene and Genome Editing 1 (June 2021): 100005. http://dx.doi.org/10.1016/j.ggedit.2021.100005.

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37

Trikoz, Elena N., Diana M. Mustafina-Bredikhina, and Elena E. Gulyaeva. "Legal regulation of gene editing procedure: USA and EU experience." RUDN Journal of Law 25, no. 1 (2021): 67–86. http://dx.doi.org/10.22363/2313-2337-2021-25-1-67-86.

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The problem of legal regulation of gene editing in recent years has obviously become global in nature due to the lack of unified systematic legislation in the world. The authors set a goal to study the main existing regulatory legal acts and determine whether there is currently an array of legislation that protects and at the same time establishes responsibility for the editors of the genome and persons who have given consent to it, before future generations, who will receive the edited gene, but who did not actually ask for it. The authors analyzed the most known general public cases related

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38

Dua, Seema, Kamlesh Kumari Bajwa, Atul Prashar, et al. "Empowering of reproductive health of farm animals through genome editing technology." Journal of Reproductive Healthcare and Medicine 2 (January 25, 2021): 4. http://dx.doi.org/10.25259/jrhm_17_2020.

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To cater the exponential growth of human population, need to improve food production and quality through modern biotechnology with limited recourses in a way that has minimal impact on the environment. The selective breeding and genomic selection have attended the momentum gain in livestock productivity. Recent advancement in genome-editing technologies offers exciting prospects for the production of healthy and prolific livestock. Genome editing involves altering genetic material by manipulation, addition, or removal of certain deoxyribonucleic acid (DNA) sequences at a specific locus in a wa

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39

Lee, Sangsin, Ning Ding, Yidi Sun, et al. "Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects." Science Advances 6, no. 29 (2020): eaba1773. http://dx.doi.org/10.1126/sciadv.aba1773.

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Cytosine base editors (CBEs) enable efficient cytidine-to-thymidine (C-to-T) substitutions at targeted loci without double-stranded breaks. However, current CBEs edit all Cs within their activity windows, generating undesired bystander mutations. In the most challenging circumstance, when a bystander C is adjacent to the targeted C, existing base editors fail to discriminate them and edit both Cs. To improve the precision of CBE, we identified and engineered the human APOBEC3G (A3G) deaminase; when fused to the Cas9 nickase, the resulting A3G-BEs exhibit selective editing of the second C in th

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Jin, Shuai, Qiang Gao, and Caixia Gao. "An unbiased method for evaluating the genome-wide specificity of base editors in rice." Nature Protocols 16, no. 1 (2020): 431–57. http://dx.doi.org/10.1038/s41596-020-00423-y.

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41

Xie, Ruosen, Yuyuan Wang, and Shaoqin Gong. "External stimuli-responsive nanoparticles for spatially and temporally controlled delivery of CRISPR–Cas genome editors." Biomaterials Science 9, no. 18 (2021): 6012–22. http://dx.doi.org/10.1039/d1bm00558h.

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In this review, we summarize the state-of-the-art non-viral vectors that exploit external stimuli (i.e., light, magnetic field, and ultrasound) for spatially and temporally controlled genome editing and their in vitro and in vivo applications.

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Sabyasachi Das and Masayuki Hirano. "Editorial [Hot Topic: Comparative Genomics and Genome Evolution (Guest Editors: Sabyasachi Das and Masayuki Hirano)]." Current Genomics 13, no. 2 (2012): 85. http://dx.doi.org/10.2174/138920212799860715.

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43

Upadhyaya, Meena. "ICRF handbook of genome analysis: Nigel K. Spurr, Bryan D. Young, Stephen P. Bryant (Editors)." Human Genetics 103, no. 3 (1998): 372–73. http://dx.doi.org/10.1007/s004390050834.

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44

He, Zuyong, Xuan Shi, Meirui Liu, et al. "Comparison of surrogate reporter systems for enrichment of cells with mutations induced by genome editors." Journal of Biotechnology 221 (March 2016): 49–54. http://dx.doi.org/10.1016/j.jbiotec.2016.01.009.

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45

Gendron, William A. C., Jeffrey D. Rubin, Michael J. Hansen, et al. "Unlocking loxP to Track Genome Editing In Vivo." Genes 12, no. 8 (2021): 1204. http://dx.doi.org/10.3390/genes12081204.

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The development of CRISPR-associated proteins, such as Cas9, has led to increased accessibility and ease of use in genome editing. However, additional tools are needed to quantify and identify successful genome editing events in living animals. We developed a method to rapidly quantify and monitor gene editing activity non-invasively in living animals that also facilitates confocal microscopy and nucleotide level analyses. Here we report a new CRISPR “fingerprinting” approach to activating luciferase and fluorescent proteins in mice as a function of gene editing. This system is based on experi

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46

Naeem, Muhammad, Saman Majeed, Mubasher Zahir Hoque, and Irshad Ahmad. "Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing." Cells 9, no. 7 (2020): 1608. http://dx.doi.org/10.3390/cells9071608.

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Gene editing that makes target gene modification in the genome by deletion or addition has revolutionized the era of biomedicine. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 emerged as a substantial tool due to its simplicity in use, less cost and extraordinary efficiency than the conventional gene-editing tools, including zinc finger nucleases (ZFNs) and Transcription activator-like effector nucleases (TALENs). However, potential off-target activities are crucial shortcomings in the CRISPR system. Numerous types of approaches have been developed to reduce off-targe

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McCann, Jennifer L., Daniel J. Salamango, Emily K. Law, William L. Brown, and Reuben S. Harris. "MagnEdit—interacting factors that recruit DNA-editing enzymes to single base targets." Life Science Alliance 3, no. 4 (2020): e201900606. http://dx.doi.org/10.26508/lsa.201900606.

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Although CRISPR/Cas9 technology has created a renaissance in genome engineering, particularly for gene knockout generation, methods to introduce precise single base changes are also highly desirable. The covalent fusion of a DNA-editing enzyme such as APOBEC to a Cas9 nickase complex has heightened hopes for such precision genome engineering. However, current cytosine base editors are prone to undesirable off-target mutations, including, most frequently, target-adjacent mutations. Here, we report a method to “attract” the DNA deaminase, APOBEC3B, to a target cytosine base for specific editing

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48

Guo, Dayong, Xiaojing Li, Pan Zhu, et al. "Online High-throughput Mutagenesis Designer Using Scoring Matrix of Sequence-specific Endonucleases." Journal of Integrative Bioinformatics 12, no. 1 (2015): 35–48. http://dx.doi.org/10.1515/jib-2015-283.

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Summary CRISPR Cas9 and other sequence-specific endonucleases are fundamental genome editors supporting gene knockout and gene therapy. A speedy and accurate computational allele designer is required for a high through-put gene mutagenesis pipeline using these new techniques. An automatic system, Cas9 online designer (COD), was created to screen Cas9 targets and off-targets, as well as to provide gene knockout and genotyping strategies. A gene knockout rat model was successfully created and genotyped under the direction of this online system confirming its ability to predict real targets and o

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Song, Beomjong, Chan Young Kang, Jun Hee Han, Masanobu Kano, Arthur Konnerth, and Sangsu Bae. "In vivo genome editing in single mammalian brain neurons through CRISPR-Cas9 and cytosine base editors." Computational and Structural Biotechnology Journal 19 (2021): 2477–85. http://dx.doi.org/10.1016/j.csbj.2021.04.051.

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Standage-Beier, Kylie, Stefan J. Tekel, Nicholas Brookhouser, et al. "A transient reporter for editing enrichment (TREE) in human cells." Nucleic Acids Research 47, no. 19 (2019): e120-e120. http://dx.doi.org/10.1093/nar/gkz713.

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Abstract Current approaches to identify cell populations that have been modified with deaminase base editing technologies are inefficient and rely on downstream sequencing techniques. In this study, we utilized a blue fluorescent protein (BFP) that converts to green fluorescent protein (GFP) upon a C-to-T substitution as an assay to report directly on base editing activity within a cell. Using this assay, we optimize various base editing transfection parameters and delivery strategies. Moreover, we utilize this assay in conjunction with flow cytometry to develop a transient reporter for editin

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