Gene and genome editing最新文献

On the edge of deletion: Using natural and engineered microhomology to edit the human genome 在删除的边缘：利用自然和工程微观组学编辑人类基因组

Gene and genome editing Pub Date : 2024-04-04 DOI: 10.1016/j.ggedit.2024.100033

Gabriel Martínez-Gálvez, Suji Lee, Ryo Niwa, Knut Woltjen

{"title":"On the edge of deletion: Using natural and engineered microhomology to edit the human genome","authors":"Gabriel Martínez-Gálvez, Suji Lee, Ryo Niwa, Knut Woltjen","doi":"10.1016/j.ggedit.2024.100033","DOIUrl":"https://doi.org/10.1016/j.ggedit.2024.100033","url":null,"abstract":"<div><p>As long read sequencing becomes more commonplace in genome analysis, the number of deletion variants associated with human traits and disease are anticipated to continue growing at a rate that may well outpace the increase in novel single nucleotide variant (SNV) discoveries. Such a paradigm shift will be met with an increased demand for gene editing technologies that enable functional analyses in a human model system such as induced pluripotent stem (iPS) cells. The outcome of gene editing is ultimately determined by cellular repair pathways and can be predicted by the surrounding DNA sequence. As multiple studies have revealed microhomology at the edges of natural deletion variants, eliciting microhomology mediated end joining (MMEJ) presents a reliable approach to create specific deletions. In this review, we discuss the shifting trends in human genome variant discovery, briefly review DNA repair processes and the associated prediction algorithms, demonstrate the utility of MMEJ in generating both loss- and gain-of-function alleles, and finally speculate on the impact these advances will have on the future of human functional genomics.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"7 ","pages":"Article 100033"},"PeriodicalIF":0.0,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666388024000030/pdfft?md5=1024b75be75729f9ffa2a12b96be88b6&pid=1-s2.0-S2666388024000030-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140548404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploration of isothermal nucleic acid amplification techniques in the biomedical field 探索生物医学领域的等温核酸扩增技术

Gene and genome editing Pub Date : 2024-01-21 DOI: 10.1016/j.ggedit.2024.100032

Sukanya Kundu , Rajat Varshney , Sourabh Sulabh

{"title":"Exploration of isothermal nucleic acid amplification techniques in the biomedical field","authors":"Sukanya Kundu , Rajat Varshney , Sourabh Sulabh","doi":"10.1016/j.ggedit.2024.100032","DOIUrl":"10.1016/j.ggedit.2024.100032","url":null,"abstract":"<div><p>Nucleic acid amplification techniques (NATs) are frequently used in the molecular biology arena. Polymerase chain reaction (PCR) and its variants are one of the most popular NATs. The requirement of a sophisticated thermocycler and skilled technician for PCR limits its use in resource-limited laboratories and fields. Alternatively, the isothermal amplification technique can also deliver proficiency, simplicity, sensitivity, and fidelity without the need for the thermocycler. Several isothermal methods have been devised and newer concepts are also emerging. Some of them are loop-mediated isothermal amplification, whole genome amplification, rolling circle amplification, nucleic acid sequence-based amplification, and polymerase spiral reaction. These cost-effective, practicable, and easy-to-perform diagnostic assays are in current trends to identify pathogens, tumors, embryo sex, and genetically modified organisms. Isothermal amplification can also be used in microfluidic devices and point-of-need diagnostics. This review focuses on the development of common isothermal processes, their characteristics, and their acceptance over the PCR.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"7 ","pages":"Article 100032"},"PeriodicalIF":0.0,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666388024000029/pdfft?md5=0b7a8be74e2f4e2b7c336ad2ca5874f7&pid=1-s2.0-S2666388024000029-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139540501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Antimicrobial resistance (AMR) management using CRISPR-Cas based genome editing 利用基于 CRISPR-Cas 的基因组编辑技术管理抗微生物抗药性 (AMR)

Gene and genome editing Pub Date : 2024-01-09 DOI: 10.1016/j.ggedit.2024.100031

Debmitra Sen , Poulami Mukhopadhyay

{"title":"Antimicrobial resistance (AMR) management using CRISPR-Cas based genome editing","authors":"Debmitra Sen , Poulami Mukhopadhyay","doi":"10.1016/j.ggedit.2024.100031","DOIUrl":"10.1016/j.ggedit.2024.100031","url":null,"abstract":"<div><p>Antimicrobial resistance is a serious threat to the human population and might be responsible for the emergence as well as re-emergence of various infectious diseases. The staggard development of new antibiotics and the resistance acquired by the pathogens against the existing antibiotics is indeed a menace and has aggravated due to the ongoing pandemic. CRISPR-Cas systems, an inherent immune mechanism present in prokaryotes is one of the most popular tools that was first harnessed in 2014 for selective removal of genes responsible for antimicrobial resistance. Gradually gaining considerable momentum in the field of genetics, medicine, and biotechnology, CRISPR-Cas technologies have been rapidly utilized in gene editing in human cells, designing animal models for disease progression studies to develop insect-resistant crop varieties and repurpose inherent bacterial CRISPR-Cas systems for target specific elimination of pathogens. The main aim of this review is to discuss how the CRISPR-Cas systems have been utilized to produce new-generation antimicrobials, associated delivery vehicles and challenges, and the prospects of these powerful antimicrobials.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"7 ","pages":"Article 100031"},"PeriodicalIF":0.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2666388024000017/pdfft?md5=26ad9864911fa551d5f5b8d836d00efa&pid=1-s2.0-S2666388024000017-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139455782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Looking back 回顾

Gene and genome editing Pub Date : 2023-11-07 DOI: 10.1016/j.ggedit.2023.100029

Eric B. Kmiec

引用次数: 0

Lead off commentary 导语

Gene and genome editing Pub Date : 2023-11-07 DOI: 10.1016/j.ggedit.2023.100030

Eric B. Kmiec

引用次数: 0

Computational design of guide RNAs and vector to knockout LasR gene of Pseudomonas aeruginosa 铜绿假单胞菌LasR基因敲除引导rna和载体的计算设计

Gene and genome editing Pub Date : 2023-10-06 DOI: 10.1016/j.ggedit.2023.100028

Lekshmi Radha KesavanNair

{"title":"Computational design of guide RNAs and vector to knockout LasR gene of Pseudomonas aeruginosa","authors":"Lekshmi Radha KesavanNair","doi":"10.1016/j.ggedit.2023.100028","DOIUrl":"https://doi.org/10.1016/j.ggedit.2023.100028","url":null,"abstract":"<div><p>CRISPR-cas9 genome editing has received much attention in recent years due to its wide applications to treat various genetic disorders, cancer, and infectious diseases caused by harmful pathogens. <em>Pseudomonas aeruginosa</em> is one of the most prominent opportunistic pathogens that cause major concern in health care due to its antibiotic resistance. Quorum sensing inhibition is an effective means of treating this multidrug-resistant bacterial infection. In the present work, an <em>in silico</em> gene editing strategy was performed to knock out the LasR gene, responsible for regulating the expression of virulence-associated genes and biofilm formation in <em>P. aeruginosa</em>. To design appropriate guide RNA (gRNA) hits, the study explores four computational tools: ChopChop, Cas-Designer, Crispor, and Benchling which determine 18 gRNA hits out of 102 gRNAs, 39 hits out of 115, 6 hits out of 115, and 15 hits out of 115, respectively. About 19 hits that satisfy all the parameters mentioned in more than one tool were selected for further analysis. Thereafter, analysis of the 19 hits recommends gRNAs 1, 8, 14, 16, 17, and 19 as the top hits and subsequently, secondary structure analysis of the top hits using the RNAfold server ascertained gRNAs 1 and 16 as the best lead gRNAs. In addition, target-specific oligos and single guide RNAs (sgRNAs) for the selected leads were designed using the NEBiocalculator, followed by the <em>in silico</em> construction of the guide RNA expression vector using SnapGene software. However, the guide RNAs designed by computational methods need to be tested <em>in vitro</em> to determine their efficiency in knocking out the LasR gene.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"6 ","pages":"Article 100028"},"PeriodicalIF":0.0,"publicationDate":"2023-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49737173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome editing for biodiesel production in oleaginous microalga, Nannochloropsis species 基因组编辑用于产油微藻，纳米绿藻物种的生物柴油生产

Gene and genome editing Pub Date : 2023-08-02 DOI: 10.1016/j.ggedit.2023.100027

Tomokazu Kurita , Masako Iwai , Hiroyuki Ohta , Tetsushi Sakuma , Takashi Yamamoto

{"title":"Genome editing for biodiesel production in oleaginous microalga, Nannochloropsis species","authors":"Tomokazu Kurita , Masako Iwai , Hiroyuki Ohta , Tetsushi Sakuma , Takashi Yamamoto","doi":"10.1016/j.ggedit.2023.100027","DOIUrl":"https://doi.org/10.1016/j.ggedit.2023.100027","url":null,"abstract":"<div><p>Algae are oxygen-producing photosynthetic aquatic organisms. Algal biodiesels have attracted attention because these fuels are produced via photosynthesis, which assimilates CO<sub>2</sub>. Algal biodiesels are sustainable, not competitive with food production, and have higher productivity compared with terrestrial plants. However, the production costs of algal biodiesels are much higher than those of fossil fuels. Therefore, improvement of algal lipid productivity is essential for the practical use of algal biodiesels. To achieve this, the application of genome-editing systems for the molecular breeding of algae is expected to generate “high-performance algae.” Here, we review the genome-editing technologies developed for the oleaginous microalgae, <em>Nannochloropsis</em> species, which are the most promising algae for producing algal-biodiesel feedstock. In this review, we discuss the development of genome-editing systems for gene disruption, transgene-free genome-editing systems, transcriptional regulation systems using nuclease-deficient Cas proteins, and the applications of genome editing in <em>Nannochloropsis</em> species.</p></div>","PeriodicalId":73137,"journal":{"name":"Gene and genome editing","volume":"6 ","pages":"Article 100027"},"PeriodicalIF":0.0,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49737174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CRISPR/Cas9-mediated knock-in in ebony gene using a PCR product donor template in Drosophila 利用PCR产物供体模板在果蝇中介导CRISPR/ cas9介导的黑檀基因敲入

Gene and genome editing Pub Date : 2023-06-01 DOI: 10.1016/j.ggedit.2023.100025

Kathy Clara Bui, Daichi Kamiyama

引用次数: 0

The methylation inhibitor 3DZNep promotes HDR pathway choice during CRISPR-Cas9 genome editing 甲基化抑制剂3DZNep在CRISPR-Cas9基因组编辑过程中促进HDR途径的选择

Gene and genome editing Pub Date : 2023-06-01 DOI: 10.1016/j.ggedit.2022.100023

Nadja Bischoff , Sandra Wimberger , Ralf Kühn , Anne Laugesen , Volkan Turan , Brian Daniel Larsen , Claus Storgaard Sørensen , Kristian Helin , Eric Paul Bennett , Marcello Maresca , Cord Brakebusch

引用次数: 0

Facilitating genome function understanding using genome editing dependent bioimaging techniques 使用依赖基因组编辑的生物成像技术促进对基因组功能的理解

Gene and genome editing Pub Date : 2023-06-01 DOI: 10.1016/j.ggedit.2022.100022

Hiroshi Ochiai

引用次数: 0