Frontiers in genome editing最新文献_第4页

Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation. 利用crispr介导的激活技术表征鸡基因组中的转录增强子。

Frontiers in genome editing Pub Date : 2023-10-25 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1269115

Jeong Hoon Han, Hong Jo Lee, Tae Hyun Kim

{"title":"Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation.","authors":"Jeong Hoon Han, Hong Jo Lee, Tae Hyun Kim","doi":"10.3389/fgeed.2023.1269115","DOIUrl":"10.3389/fgeed.2023.1269115","url":null,"abstract":"DNA regulatory elements intricately control when, where, and how genes are activated. Therefore, understanding the function of these elements could unveil the complexity of the genetic regulation network. Genome-wide significant variants are predominantly found in non-coding regions of DNA, so comprehending the predicted functional regulatory elements is crucial for understanding the biological context of these genomic markers, which can be incorporated into breeding programs. The emergence of CRISPR technology has provided a powerful tool for studying non-coding regulatory elements in genomes. In this study, we leveraged epigenetic data from the Functional Annotation of Animal Genomes project to identify promoter and putative enhancer regions associated with three genes (HBBA, IRF7, and PPARG) in the chicken genome. To identify the enhancer regions, we designed guide RNAs targeting the promoter and candidate enhancer regions and utilized CRISPR activation (CRISPRa) with dCas9-p300 and dCas9-VPR as transcriptional activators in chicken DF-1 cells. By comparing the expression levels of target genes between the promoter activation and the co-activation of the promoter and putative enhancers, we were able to identify functional enhancers that exhibited augmented upregulation. In conclusion, our findings demonstrate the remarkable efficiency of CRISPRa in precisely manipulating the expression of endogenous genes by targeting regulatory elements in the chicken genome, highlighting its potential for functional validation of non-coding regions.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1269115"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720934","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

CRISPR/Cas9 mutagenesis of the Arabidopsis GROWTH-REGULATING FACTOR (GRF) gene family. 拟南芥生长调节因子（GRF）基因家族的CRISPR/Cas9突变。

IF 4.9

Frontiers in genome editing Pub Date : 2023-10-16 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1251557

Juan Angulo, Christopher P Astin, Olivia Bauer, Kelan J Blash, Natalee M Bowen, Nneoma J Chukwudinma, Austin S DiNofrio, Donald O Faletti, Alexa M Ghulam, Chloe M Gusinde-Duffy, Kamaria J Horace, Andrew M Ingram, Kylie E Isaack, Geon Jeong, Randolph J Kiser, Jason S Kobylanski, Madeline R Long, Grace A Manning, Julie M Morales, Kevin H Nguyen, Robin T Pham, Monthip H Phillips, Tanner W Reel, Jenny E Seo, Hiep D Vo, Alexander M Wukoson, Kathryn A Yeary, Grace Y Zheng, Wolfgang Lukowitz

{"title":"CRISPR/Cas9 mutagenesis of the Arabidopsis GROWTH-REGULATING FACTOR (GRF) gene family.","authors":"Juan Angulo, Christopher P Astin, Olivia Bauer, Kelan J Blash, Natalee M Bowen, Nneoma J Chukwudinma, Austin S DiNofrio, Donald O Faletti, Alexa M Ghulam, Chloe M Gusinde-Duffy, Kamaria J Horace, Andrew M Ingram, Kylie E Isaack, Geon Jeong, Randolph J Kiser, Jason S Kobylanski, Madeline R Long, Grace A Manning, Julie M Morales, Kevin H Nguyen, Robin T Pham, Monthip H Phillips, Tanner W Reel, Jenny E Seo, Hiep D Vo, Alexander M Wukoson, Kathryn A Yeary, Grace Y Zheng, Wolfgang Lukowitz","doi":"10.3389/fgeed.2023.1251557","DOIUrl":"10.3389/fgeed.2023.1251557","url":null,"abstract":"Genome editing in plants typically relies on T-DNA plasmids that are mobilized by Agrobacterium-mediated transformation to deliver the CRISPR/Cas machinery. Here, we introduce a series of CRISPR/Cas9 T-DNA vectors for minimal settings, such as teaching labs. Gene-specific targeting sequences can be inserted as annealed short oligonucleotides in a single straightforward cloning step. Fluorescent markers expressed in mature seeds enable reliable selection of transgenic or transgene-free individuals using a combination of inexpensive LED lamps and colored-glass alternative filters. Testing these tools on the Arabidopsis GROWTH-REGULATING FACTOR (GRF) genes, we were able to create a collection of predicted null mutations in all nine family members with little effort. We then explored the effects of simultaneously targeting two, four and eight GRF genes on the rate of induced mutations at each target locus. In our hands, multiplexing was associated with pronounced disparities: while mutation rates at some loci remained consistently high, mutation rates at other loci dropped dramatically with increasing number of single guide RNA species, thereby preventing a systematic mutagenesis of the family.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1251557"},"PeriodicalIF":4.9,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10613670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71429844","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

Hs1Cas12a and Ev1Cas12a confer efficient genome editing in plants. Hs1Cas12a和Ev1Cas12a赋予植物有效的基因组编辑。

Frontiers in genome editing Pub Date : 2023-10-12 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1251903

Gen Li, Yingxiao Zhang, Micah Dailey, Yiping Qi

引用次数: 0

How genome editing changed the world of large animal research. 基因组编辑如何改变了大型动物研究的世界。

Frontiers in genome editing Pub Date : 2023-10-11 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1272687

Konrad Fischer, Angelika Schnieke

{"title":"How genome editing changed the world of large animal research.","authors":"Konrad Fischer, Angelika Schnieke","doi":"10.3389/fgeed.2023.1272687","DOIUrl":"10.3389/fgeed.2023.1272687","url":null,"abstract":"The first genetically modified large animals were developed in 1985 by microinjection to increase the growth of agricultural livestock such as pigs. Since then, it has been a difficult trail due to the lack of genetic tools. Although methods and technologies were developed quickly for the main experimental mammal, the mouse, e.g., efficient pronuclear microinjection, gene targeting in embryonic stem cells, and omics data, most of it was-and in part still is-lacking when it comes to livestock. Over the next few decades, progress in genetic engineering of large animals was driven less by research for agriculture but more for biomedical applications, such as the production of pharmaceutical proteins in the milk of sheep, goats, or cows, xeno-organ transplantation, and modeling human diseases. Available technologies determined if a desired animal model could be realized, and efficiencies were generally low. Presented here is a short review of how genome editing tools, specifically CRISPR/Cas, have impacted the large animal field in recent years. Although there will be a focus on genome engineering of pigs for biomedical applications, the general principles and experimental approaches also apply to other livestock species or applications.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1272687"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10598601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54232727","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

Recalcitrance to transformation, a hindrance for genome editing of legumes. 对转化的抗拒，是豆类基因组编辑的障碍。

IF 4.9

Frontiers in genome editing Pub Date : 2023-09-21 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1247815

V M Nivya, Jasmine M Shah

{"title":"Recalcitrance to transformation, a hindrance for genome editing of legumes.","authors":"V M Nivya, Jasmine M Shah","doi":"10.3389/fgeed.2023.1247815","DOIUrl":"10.3389/fgeed.2023.1247815","url":null,"abstract":"Plant genome editing, a recently discovered method for targeted mutagenesis, has emerged as a promising tool for crop improvement and gene function research. Many genome-edited plants, such as rice, wheat, and tomato, have emerged over the last decade. As the preliminary steps in the procedure for genome editing involve genetic transformation, amenability to genome editing depends on the efficiency of genetic engineering. Hence, there are numerous reports on the aforementioned crops because they are transformed with relative ease. Legume crops are rich in protein and, thus, are a favored source of plant proteins for the human diet in most countries. However, legume cultivation often succumbs to various biotic/abiotic threats, thereby leading to high yield loss. Furthermore, certain legumes like peanuts possess allergens, and these need to be eliminated as these deprive many people from gaining the benefits of such crops. Further genetic variations are limited in certain legumes. Genome editing has the potential to offer solutions to not only combat biotic/abiotic stress but also generate desirable knock-outs and genetic variants. However, excluding soybean, alfalfa, and Lotus japonicus, reports obtained on genome editing of other legume crops are less. This is because, excluding the aforementioned three legume crops, the transformation efficiency of most legumes is found to be very low. Obtaining a higher number of genome-edited events is desirable as it offers the option to genotypically/phenotypically select the best candidate, without the baggage of off-target mutations. Eliminating the barriers to genetic engineering would directly help in increasing genome-editing rates. Thus, this review aims to compare various legumes for their transformation, editing, and regeneration efficiencies and discusses various solutions available for increasing transformation and genome-editing rates in legumes.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1247815"},"PeriodicalIF":4.9,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10551638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175205","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

Genome-wide CRISPR screens and their applications in infectious disease. 全基因组CRISPR筛选及其在传染病中的应用。

Frontiers in genome editing Pub Date : 2023-09-19 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1243731

Kaveri Srivastava, Bhaswati Pandit

{"title":"Genome-wide CRISPR screens and their applications in infectious disease.","authors":"Kaveri Srivastava, Bhaswati Pandit","doi":"10.3389/fgeed.2023.1243731","DOIUrl":"https://doi.org/10.3389/fgeed.2023.1243731","url":null,"abstract":"Inactivation or targeted disruption of a gene provides clues to assess the function of the gene in many cellular processes. Knockdown or knocking out a gene has been widely used for this purpose. However, recently CRISPR mediated genome editing has taken over the knockout/knockdown system with more precision. CRISPR technique has enabled us to perform targeted mutagenesis or genome editing to address questions in fundamental biology to biomedical research. Its application is wide in understanding the role of genes in the disease process, and response to therapy in cancer, metabolic disorders, or infectious disease. In this article, we have focused on infectious disease and how genome-wide CRISPR screens have enabled us to identify host factors involved in the process of infection. Understanding the biology of the host-pathogen interaction is of immense importance in planning host-directed therapy to improve better management of the disease. Genome-wide CRISPR screens provide strong mechanistic ways to identify the host dependency factors involved in various infections. We presented insights into genome-wide CRISPR screens conducted in the context of infectious diseases both viral and bacterial that led to better understanding of host-pathogen interactions and immune networks. We have discussed the advancement of knowledge pertaining to influenza virus, different hepatitis viruses, HIV, most recent SARS CoV2 and few more. Among bacterial diseases, we have focused on infection with life threatening Mycobacteria, Salmonella, S. aureus, etc. It appears that the CRISPR technique can be applied universally to multiple infectious disease models to unravel the role of known or novel host factors.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1243731"},"PeriodicalIF":0.0,"publicationDate":"2023-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10546192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164720","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

Editorial: Genome edited organisms for agriculture-challenges and perspectives for development and regulation. 社论：基因组编辑的生物对农业的挑战和发展和监管的前景。

Frontiers in genome editing Pub Date : 2023-09-18 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1287973

Michael Eckerstorfer, Sarah Zanon Agapito-Tenfen, Gijs A Kleter

引用次数: 0

Current approaches and potential challenges in the delivery of gene editing cargos into hematopoietic stem and progenitor cells. 将基因编辑货物递送到造血干细胞和祖细胞中的当前方法和潜在挑战。

Frontiers in genome editing Pub Date : 2023-09-15 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1148693

Ramya Murugesan, Karthik V Karuppusamy, Srujan Marepally, Saravanabhavan Thangavel

引用次数: 0

Efficient DNA knock-in using AAV-mediated delivery with 2-cell embryo CRISPR-Cas9 electroporation. 利用 AAV 介导的传递与 2 细胞胚胎 CRISPR-Cas9 电穿孔技术实现高效 DNA 基因敲入。

Frontiers in genome editing Pub Date : 2023-08-25 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1256451

Daniel J Davis, James F McNew, Hailey Maresca-Fichter, Kaiwen Chen, Bhanu P Telugu, Elizabeth C Bryda

{"title":"Efficient DNA knock-in using AAV-mediated delivery with 2-cell embryo CRISPR-Cas9 electroporation.","authors":"Daniel J Davis, James F McNew, Hailey Maresca-Fichter, Kaiwen Chen, Bhanu P Telugu, Elizabeth C Bryda","doi":"10.3389/fgeed.2023.1256451","DOIUrl":"10.3389/fgeed.2023.1256451","url":null,"abstract":"Recent advances in CRISPR-Cas genome editing technology have been instrumental in improving the efficiency to produce genetically modified animal models. In this study we have combined four very promising approaches to come up with a highly effective pipeline to produce knock-in mouse and rat models. The four combined methods include: AAV-mediated DNA delivery, single-stranded DNA donor templates, 2-cell embryo modification, and CRISPR-Cas ribonucleoprotein (RNP) electroporation. Using this new combined approach, we were able to produce successfully targeted knock-in rat models containing either Cre or Flp recombinase sequences with knock-in efficiencies over 90%. Furthermore, we were able to produce a knock-in mouse model containing a Cre recombinase targeted insertion with over 50% knock-in efficiency directly comparing efficiencies to other commonly used approaches. Our modified AAV-mediated DNA delivery with 2-cell embryo CRISPR-Cas9 RNP electroporation technique has proven to be highly effective for generating both knock-in mouse and knock-in rat models.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1256451"},"PeriodicalIF":0.0,"publicationDate":"2023-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10485772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220069","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

Potentials of genotypes, morpho-physio-biochemical traits, and growing media on shelf life and future prospects of gene editing in tomatoes. 基因型、形态生理生化性状和生长介质对番茄货架期的影响及基因编辑的未来前景。

IF 4.9

Frontiers in genome editing Pub Date : 2023-08-23 eCollection Date: 2023-01-01 DOI: 10.3389/fgeed.2023.1203485

Renu Yadav, Sarika Jaiswal, Tripti Singhal, Rohit Kumar Mahto, S B Verma, Ramesh Kumar Yadav, Rajendra Kumar

{"title":"Potentials of genotypes, morpho-physio-biochemical traits, and growing media on shelf life and future prospects of gene editing in tomatoes.","authors":"Renu Yadav, Sarika Jaiswal, Tripti Singhal, Rohit Kumar Mahto, S B Verma, Ramesh Kumar Yadav, Rajendra Kumar","doi":"10.3389/fgeed.2023.1203485","DOIUrl":"10.3389/fgeed.2023.1203485","url":null,"abstract":"Background: To study the genetic basis of the impact of genotypes and morpho-physio-biochemical traits under different organic and inorganic fertilizer doses on the shelf life attribute of tomatoes, field experiments were conducted in randomized block designs during the rabi seasons of 2018-2019 and 2019-2020. The experiment comprised three diverse nutrient environments [T1-organic; T2-inorganic; T3-control (without any fertilizers)] and five tomato genotypes with variable growth habits, specifically Angoorlata (Indeterminate), Avinash-3 (semi-determinate), Swaraksha (semi-determinate), Pusa Sheetal (semi-determinate), and Pusa Rohini (determinate). Results: The different tomato genotypes behaved apparently differently from each other in terms of shelf life. All the genotypes had maximum shelf life when grown in organic environments. However, the Pusa Sheetal had a maximum shelf life of 8.35 days when grown in an organic environment and showed an increase of 12% over the control. The genotype Pusa Sheetal, organic environment and biochemical trait Anthocyanin provides a promise as potential contributor to improve the keeping quality of tomatoes. Conclusion: The genotype Pusa Sheetal a novel source for shelf life, organic environment, and anthocyanin have shown promises for extended shelf life in tomatoes. Thus, the identified trait and genotype can be utilized in tomato improvement programs. Furthermore, this identified trait can also be targeted for its quantitative enhancement in order to increase tomato shelf life through a genome editing approach. A generalized genome editing mechanism is consequently suggested.","PeriodicalId":73086,"journal":{"name":"Frontiers in genome editing","volume":"5 ","pages":"1203485"},"PeriodicalIF":4.9,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10481343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10184973","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