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Gupta P, Dholaniya PS, Princy K, Madhavan AS, Sreelakshmi Y, Sharma R. Augmenting tomato functional genomics with a genome-wide induced genetic variation resource. FRONTIERS IN PLANT SCIENCE 2024; 14:1290937. [PMID: 38328621 PMCID: PMC10848261 DOI: 10.3389/fpls.2023.1290937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/22/2023] [Indexed: 02/09/2024]
Abstract
Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Biological Sciences, SRM University-AP, Amaravati, Andhra Pradesh, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Kunnappady Princy
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Athira Sethu Madhavan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Coppola A, Lombari P, Mazzella E, Capolongo G, Simeoni M, Perna AF, Ingrosso D, Borriello M. Zebrafish as a Model of Cardiac Pathology and Toxicity: Spotlight on Uremic Toxins. Int J Mol Sci 2023; 24:ijms24065656. [PMID: 36982730 PMCID: PMC10052014 DOI: 10.3390/ijms24065656] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Chronic kidney disease (CKD) is an increasing health care problem. About 10% of the general population is affected by CKD, representing the sixth cause of death in the world. Cardiovascular events are the main mortality cause in CKD, with a cardiovascular risk 10 times higher in these patients than the rate observed in healthy subjects. The gradual decline of the kidney leads to the accumulation of uremic solutes with a negative effect on every organ, especially on the cardiovascular system. Mammalian models, sharing structural and functional similarities with humans, have been widely used to study cardiovascular disease mechanisms and test new therapies, but many of them are rather expensive and difficult to manipulate. Over the last few decades, zebrafish has become a powerful non-mammalian model to study alterations associated with human disease. The high conservation of gene function, low cost, small size, rapid growth, and easiness of genetic manipulation are just some of the features of this experimental model. More specifically, embryonic cardiac development and physiological responses to exposure to numerous toxin substances are similar to those observed in mammals, making zebrafish an ideal model to study cardiac development, toxicity, and cardiovascular disease.
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Affiliation(s)
- Annapaola Coppola
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Patrizia Lombari
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Elvira Mazzella
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Giovanna Capolongo
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Mariadelina Simeoni
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Alessandra F. Perna
- Department of Translational Medical Science, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Diego Ingrosso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Margherita Borriello
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Correspondence:
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Jhingan S, Kumar A, Harloff HJ, Dreyer F, Abbadi A, Beckmann K, Obermeier C, Jung C. Direct access to millions of mutations by whole genome sequencing of an oilseed rape mutant population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:866-880. [PMID: 36575585 DOI: 10.1111/tpj.16079] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Induced mutations are an essential source of genetic variation in plant breeding. Ethyl methanesulfonate (EMS) mutagenesis has been frequently applied, and mutants have been detected by phenotypic or genotypic screening of large populations. In the present study, a rapeseed M2 population was derived from M1 parent cultivar 'Express' treated with EMS. Whole genomes were sequenced from fourfold (4×) pools of 1988 M2 plants representing 497 M2 families. Detected mutations were not evenly distributed and displayed distinct patterns across the 19 chromosomes with lower mutation rates towards the ends. Mutation frequencies ranged from 32/Mb to 48/Mb. On average, 284 442 single nucleotide polymorphisms (SNPs) per M2 DNA pool were found resulting from EMS mutagenesis. 55% of the SNPs were C → T and G → A transitions, characteristic for EMS induced ('canonical') mutations, whereas the remaining SNPs were 'non-canonical' transitions (15%) or transversions (30%). Additionally, we detected 88 725 high confidence insertions and deletions per pool. On average, each M2 plant carried 39 120 canonical mutations, corresponding to a frequency of one mutation per 23.6 kb. Approximately 82% of such mutations were located either 5 kb upstream or downstream (56%) of gene coding regions or within intergenic regions (26%). The remaining 18% were located within regions coding for genes. All mutations detected by whole genome sequencing could be verified by comparison with known mutations. Furthermore, all sequences are accessible via the online tool 'EMSBrassica' (http://www.emsbrassica.plantbreeding.uni-kiel.de), which enables direct identification of mutations in any target sequence. The sequence resource described here will further add value for functional gene studies in rapeseed breeding.
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Affiliation(s)
- Srijan Jhingan
- Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany
| | - Avneesh Kumar
- Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany
| | - Hans-Joachim Harloff
- Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany
| | - Felix Dreyer
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Katrin Beckmann
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363, Holtsee, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-Kiel University, Olshausenstrasse 40, 24098, Kiel, Germany
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Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies. Int J Mol Sci 2023; 24:ijms24020923. [PMID: 36674433 PMCID: PMC9865676 DOI: 10.3390/ijms24020923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Low-level tumor somatic DNA mutations in tissue and liquid biopsies obtained from cancer patients can have profound implications for development of metastasis, prognosis, choice of treatment, follow-up, or early cancer detection. Unless detected, such low-frequency DNA alterations can misinform patient management decisions or become missed opportunities for personalized medicine. Next-generation sequencing technologies and digital-PCR can resolve low-level mutations but require access to specialized instrumentation, time, and resources. Enzymatic-based approaches to detection of low-level mutations provide a simple, straightforward, and affordable alternative to enrich and detect such alterations and is broadly available to low-resource laboratory settings. This review summarizes the traditional uses of enzymatic mutation detection and describes the latest exciting developments, potential, and applications with specific reference to the field of liquid biopsy in cancer.
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Wang Y, Salt DE, Koornneef M, Aarts MGM. Construction and analysis of a Noccaea caerulescens TILLING population. BMC PLANT BIOLOGY 2022; 22:360. [PMID: 35869423 PMCID: PMC9308233 DOI: 10.1186/s12870-022-03739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 06/27/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Metals such as Zn or Cd are toxic to plant and humans when they are exposed in high quantities through contaminated soil or food. Noccaea caerulescens, an extraordinary Zn/Cd/Ni hyperaccumulating species, is used as a model plant for metal hyperaccumulation and phytoremediation studies. Current reverse genetic techniques to generate mutants based on transgenesis is cumbersome due to the low transformation efficiency of this species. We aimed to establish a mutant library for functional genomics by a non-transgenic approach, to identify mutants with an altered mineral profiling, and to screen for mutations in bZIP19, a regulator of Zn homeostasis in N. caerulescens. RESULTS To generate the N. caerulescens mutant library, 3000 and 5000 seeds from two sister plants of a single-seed recurrent inbred descendant of the southern French accession Saint-Félix-de-Pallières (SF) were mutagenized respectively by 0.3 or 0.4% ethyl methane sulfonate (EMS). Two subpopulations of 5000 and 7000 M2 plants were obtained after 0.3 or 0.4% EMS treatment. The 0.4% EMS treatment population had a higher mutant frequency and was used for TILLING. A High Resolution Melting curve analysis (HRM) mutation screening platform was optimized and successfully applied to detect mutations for NcbZIP19, encoding a transcription factor controlling Zn homeostasis. Of four identified point mutations in NcbZIP19, two caused non-synonymous substitutions, however, these two mutations did not alter the ionome profile compared to the wild type. Forward screening of the 0.4% EMS treatment population by mineral concentration analysis (ionomics) in leaf material of each M2 plant revealed putative mutants affected in the concentration of one or more of the 20 trace elements tested. Several of the low-Zn mutants identified in the ionomic screen did not give progeny, illustrating the importance of Zn for the species. The mutant frequency of the population was evaluated based on an average of 2.3 knockout mutants per tested monogenic locus. CONCLUSIONS The 0.4% EMS treatment population is effectively mutagenized suitable for forward mutant screens and TILLING. Difficulties in seed production in low Zn mutants, obtained by both forward and reverse genetic approach, hampered further analysis of the nature of the low Zn phenotypes.
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Affiliation(s)
- Yanli Wang
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- College of Horticulture Science & Technology, Hebei Normal University of Science & Technology, No 360, West of HeBei street, Qinhuang Dao, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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BRCA1 and BRCA2 screening of nine Chilean founder mutations through allelic-discrimination and real-time PCR in breast/ovarian cancer patients. Mol Biol Rep 2022; 49:7531-7539. [PMID: 35596815 PMCID: PMC9123627 DOI: 10.1007/s11033-022-07561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/04/2022] [Indexed: 11/02/2022]
Abstract
BACKGROUND In a previous work, we identified nine founder mutations present in close to 80% of BRCA1 and BRCA2 mutation carriers, and distributed across the country. The presence of founder mutations constitutes a valuable opportunity to develop new strategies for genetic screening. Genetic tests are primarily performed by NGS sequencing, which requires sophisticated and expensive equipment, and it takes 2-3 weeks for the results to be informed to the patient. In addition, genetic tests are not covered by insurance companies in Latin American countries. In this work, we present the standardization and technical validation of a real-time PCR based methodology for allelic discrimination in order to identify the nine Chilean founder mutations in BRCA1 and BRCA2 genes. METHODS AND RESULTS We designed nine pairs of probes and nine pairs of primers to amplify synchronically nine regions of the BRCA1/BRCA2 genes by real-time PCR, in order to identify the nine founder mutations through allelic discrimination analyses. Technical validation was performed using 90 positive and 90 negative samples for each mutation. The methodology was tested in a second group of 60 patients. Our method correctly classified carriers and non-carriers of one of the nine Chilean founder mutations with a 100% specificity and 100% sensitivity, compared with Sanger sequencing performance. CONCLUSIONS We develop an inexpensive, simple, and fast mutation detection method that could be implemented locally in Hospitals from the Private to Public health system. This methodology may be useful for the screening of BRCA1 and BRCA2 mutations in other populations.
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Sharma V, Mishra A, Sharma H, Kumar P, Roy JK. Unraveling novel and rare mutations for alpha-amylase and key transcription factors in EMS-induced wheat mutants for amylose by TILLING. Mol Biol Rep 2022; 49:5427-5436. [PMID: 35092561 DOI: 10.1007/s11033-022-07155-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/17/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND TILLING (Targeting Induced Local Lesions in Genomes) is a reverse-genetic strategy that is used to locate an allelic series of induced point mutations in genes of interest. High-throughput TILLING allows the rapid and cost-effective detection of induced point mutations in populations of chemically mutagenized individuals. Grain amylose content is the major constraints for its nutritional quality and have drawn research interest. Identification of allelic variations in genes involved in starch biosynthesis in wheat endosperm is pre-requisite to amenable for nutritional quality improvement. METHODS AND RESULTS In this study, 44 EMS-induced (M4 generation) mutant lines having variation for amylose content were used for TILLING sequencing. Overall 2098.08 kb of the sequence was analyzed, and the average mutation density was 1/65.56 kb. In analysis, at the high depth score a total of 32 variations were identified including three natural variations, 76% transitions, 10% transversions, and 14% InDels respectively. The substitutions led to intronic variants, UTRs and up-downstream gene variants in Alpha-amylase, TabZIP77.1, TabZIP1 and Myb respectively. In the Myb transcription factor two missense mutations recorded namely Myb_7B c.680G > A and c.1358 T > C led to p.Gly227Asp and p.Met453Thr and c.1390G > A one substitution in Myb_7D led to p.Val464Ile. CONCLUSION The identified missense substitutions were predicted to affect the protein function; hence they may have a probable role in context to the amylose content in mutants. The mutations ascertained in the current study will help in gene discovery in wheat and identified mutants can be used as genetic resources to improve nutritional quality of wheat.
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Affiliation(s)
- Vinita Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.,Indian Institute of Science Education & Research, Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Ankita Mishra
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.
| | - Pankaj Kumar
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India
| | - Joy K Roy
- National Agri-Food Biotechnology Institute (NABI), Sector-81, SAS Nagar, 140 306, Mohali, Punjab, India.
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Banakar R, Rai KM, Zhang F. CRISPR DNA- and RNP-Mediated Genome Editing via Nicotiana benthamiana Protoplast Transformation and Regeneration. Methods Mol Biol 2022; 2464:65-82. [PMID: 35258825 DOI: 10.1007/978-1-0716-2164-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated system) has become the multipurpose tool to manipulate plant genome via their programmable sequence recognition, binding, and cleavage activities. Efficient plant genome modification often requires robust plant transformation. For most plant species, the CRISPR/Cas reagents are delivered into plants as plasmids by Agrobacterium-mediated T-DNA transfer or biolistic approaches. However, these methods are generally inefficient, heavily genotype dependent, and low throughput. Among the alternative plant transformation approaches, the protoplast-based transformation holds the potential to directly deliver DNA, RNA, or protein molecules into plant cells in an efficient and high-throughput manner. Here, we presented a robust and simplified protocol for protoplast-based DNA/ribonucleoprotein (RNP )-mediated genome editing in the model species Nicotiana benthamiana. Using this protocol, we have achieved the gene editing efficiency at 30-60% in protoplasts and 50-80% in regenerated calli and plants. The edited protoplasts can be readily regenerated without selection agents owing to highly efficient DNA or preassembled RNP transformation frequency. Lastly, this protocol utilized an improved culture media regime to overcome the complex media composition used in the previous studies. It offers quick turnaround time and higher throughput to facilitate the development of new genetic engineering technologies and holds the promise to combine with other genetic and genomic tools for fundamental and translational plant research.
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Affiliation(s)
- Raviraj Banakar
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
| | - Krishan M Rai
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA
| | - Feng Zhang
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, Saint Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, Saint Paul, MN, USA.
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Xiong Y, Tang H. A Sensitive PCR-Based Method for Somatic Mutations Enrichment and Screening. Cancer Manag Res 2021; 13:8099-8107. [PMID: 34737638 PMCID: PMC8558320 DOI: 10.2147/cmar.s335679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022] Open
Abstract
Background EGFR and KRAS are the most frequently mutated genes in lung cancers, occurring in about 60% of all cases. Mutation genes assay has emerged as a promising blood-based biomarker for monitoring cancer dynamics noninvasively. However, detection can be challenging in patients where plasma often contains low levels of tumor-derived DNA fragments. Methods We have developed a nuclease-based enrichment assay for detecting mutant alleles. The procedure is based on Surveyor endonuclease cleaves mismatched DNA molecules, and these DNA fragments were enriched for mutation screening. We screened lung cancer specimens for mutations in exons 18 and 21 of EGFR, and the majority of activating mutations in lung cancer occur in codons 12 (G12X) and 13 (G13X) of exon 2 of the KRAS gene. The method screened all mutant genes with the same pair primers and three relevant TaqMan probes. Results The method can effectively remove wild-type sequences and enrich mutation DNA, and the sensitivity detectable mutant allele frequencies (MAF) achieved 0.001%. The method increases the sensitivity and efficiency of mutation DNA for cancers screening. This highlights the importance of complex DNA variation like mutations in exon 21 of EGFR and exon 2 of the KRAS gene detected by the same probe. Conclusion We developed a simple and sensitive methodology for mutation gene screening. The method is a cost-effective and sensitive method for mutation DNA enrichment and detection.
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Affiliation(s)
- Yaming Xiong
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Hailing Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
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Karaman K, Kizil S, Başak M, Uzun B, Yol E. Development of EMS-induced Mutagenized Groundnut Population and Discovery of Point Mutations in the ahFAD2 and Ara h 1 Genes by TILLING. J Oleo Sci 2021; 70:1631-1640. [PMID: 34732635 DOI: 10.5650/jos.ess21075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Reducing allergenicity and increasing oleic content are important goals in groundnut breeding studies. Ara h 1 is a major allergen gene and Delta(12)-fatty-acid desaturase (FAD2) is responsible for converting oleic into linoleic acid. These genes have homoeologues with one copy in each subgenome, identified as Ara h 1.01, Ara h 1.02, ahFAD2A and ahFAD2B in tetraploid groundnut. To alter functional properties of these genes we have generated an Ethyl Methane Sulfonate (EMS) induced mutant population to be used in Targeting Induced Local Lesions in Genomes (TILLING) approach. Seeds were exposed to two EMS concentrations and the germination rates were calculated as 90.1% (1353 plants) for 0.4% and 60.4% (906 plants) for 1.2% EMS concentrations in the M1 generation. Among the 1541 M2 mutants, 768 were analyzed by TILLING using four homoeologous genes. Two heterozygous mutations were identified in the ahFAD2B and ahFAD2A gene regions from 1.2% and 0.4% EMS-treated populations, respectively. The mutation in ahFAD2B resulted in an amino acid change, which was serine to threonine predicted to be tolerated according to SIFT analysis. The other mutation causing amino acid change, glycine to aspartic acid was predicted to affect protein function in ahFAD2A. No mutations were detected in Ara h 1.01 and Ara h 1.02 for both EMS-treatments after sequencing. We estimated the overall mutation rate to be 1 mutation every 2139 kb. The mutation frequencies were also 1/317 kb for ahFAD2A in 0.4% EMS and 1/466 kb for ahFAD2B in 1.2% EMS treatments. The results demonstrated that TILLING is a powerful tool to interfere with gene function in crops and the mutagenized population developed in this study can be used as an efficient reverse genetics tool for groundnut improvement and functional genomics.
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Affiliation(s)
- Kürşat Karaman
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Sibel Kizil
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Merve Başak
- Department of Medicinal and Aromatic Plants, Akev University
| | - Bülent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University
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Zhang B, Li S, Guan Y, Yuan Y. Accurate Detection of Target MicroRNA in Mixed Species of High Sequence Homology Using Target-Protection Rolling Circle Amplification. ACS OMEGA 2021; 6:1516-1522. [PMID: 33490811 PMCID: PMC7818630 DOI: 10.1021/acsomega.0c05279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/04/2023]
Abstract
The close relationships of miRNAs with human diseases highlight the urgent needs for miRNA detection. However, the accurate detection of a target miRNA in mixed miRNAs of high sequence homology presents a great challenge. Herein, a novel method called target-protection rolling circle amplification (TP-RCA) is proposed for this purpose. The protective probe is designed so that it can form a fully complementary duplex with the target miRNA and can also mismatch duplexes with other nontarget miRNAs. These duplexes are treated with a single strand-specific nuclease. Consequently, only the target miRNA in a perfect-match duplex can resist the cleavage of nuclease, whereas the nontarget miRNAs in mismatched duplexes will be digested completely. The protected target miRNA can be detected using RCA reactions. MicroRNA let-7 family members (let-7a-let-7f) and nuclease CEL I were used as proof-of-concept models to evaluate the feasibility of the TP-RCA method under different experimental conditions. The experimental results show that the TP-RCA method can unambiguously detect the target let-7 species in mixtures of let-7 family members even though they may differ by only a single nucleotide. This TP-RCA method significantly improves the detection specificity of miRNAs.
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Affiliation(s)
- Bin Zhang
- Department
of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, Shenyang, Liaoning 110122, China
- Department
of Oral-Maxillofacial Surgery and Plastic Surgery, Stomatology Hospital of China Medical University, Shenyang, Liaoning 110002, China
| | - Shuo Li
- Department
of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, Shenyang, Liaoning 110122, China
| | - Yifu Guan
- Department
of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, Shenyang, Liaoning 110122, China
| | - Ying Yuan
- Department
of Biochemistry and Molecular Biology, School of Life Sciences, China Medical University, Shenyang, Liaoning 110122, China
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Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
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Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Wang Y, Zhang Y, Chen X, Guan X, Wang L. Analysis with biological nanopore: On-pore, off-pore strategies and application in biological fluids. Talanta 2020; 223:121684. [PMID: 33303138 DOI: 10.1016/j.talanta.2020.121684] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
Inspired from ion channels in biology, nanopores have been developed as promising analytical tools. In principle, nanopores provide crucial information from the observation and analysis of ionic current modulations caused by the interaction between target analytes and fluidic pores. In this respect, the biological, chemical and physical parameters of the nanopore regime need to be well-understood and regulated for intermolecular interaction. Because of well-defined molecular structures, biological nanopores consequently are of a focal point, allowing precise interaction analysis at single-molecule level. In this overview, two analytical strategies are summarized and discussed accordingly, upon the challenges arising in case-dependent analysis using biological nanopores. One kind of strategies relies on modification, functionalization and engineering on nanopore confined interface to improve molecular recognition sites (on-pore strategies); The other kind of highlighted strategies concerns to measurement of various chemistry/biochemistry based interactions triggered by employed molecular agents or probes (off-pore strategies). In particularly, a few recent paradigms using these strategies for practical application of accurate analysis of biomarkers in biological fluids are illustrated. To end, the challenging and future outlook of using analytical tools by means of biological nanopores are depicted.
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Affiliation(s)
- Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
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14
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Yao XF, Wu S, Guo L, Liu CM. Efficient CELI endonuclease production in Nicotiana benthamiana through transient expression and applications in detections of mutation and gene editing events. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110469. [PMID: 32539999 DOI: 10.1016/j.plantsci.2020.110469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 06/11/2023]
Abstract
Rapid and low-cost methods of detecting mutations and polymorphisms are crucial for genotyping applications including mutagenesis and gene editing. S1 family endonucleases such as T7E1, EndoV and CELI can potentially be used in enzymatic mismatch detection. Among them, CELI has been shown to be effective in detecting mutations in Targeting Induced Local Lesions IN Genomes (TILLING). However, current method of CELI purification from celery is laborious, and challenging for many non-biochemical laboratories, and the presence of post-translational modifications hinders efficient production of the enzyme in E. coli. Here, we report an efficient system for bulk production of enzymatically active CELI endonuclease through transient expression in a model plant Nicotiana benthamiana. We also optimized the reaction buffer, by additions of Mn2+ and DTT, with enhanced mismatch cleavage activity. Using the new CELI production and reaction system, we were able to routinely detect mismatches in 1/32 mixed mutant and wildtype DNA samples. We believe the newly established system has many applications in characterization of mutations occurred in natural variations, mutagenized populations and gene editing.
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Affiliation(s)
- Xue-Feng Yao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengyang Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lei Guo
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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15
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Development and Characterization of an Ethyl Methane Sulfonate (EMS) Induced Mutant Population in Capsicum annuum L. PLANTS 2020; 9:plants9030396. [PMID: 32210121 PMCID: PMC7154856 DOI: 10.3390/plants9030396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Plant breeding explores genetic diversity in useful traits to develop new, high-yielding, and improved cultivars. Ethyl methane sulfonate (EMS) is a chemical widely used to induce mutations at loci that regulate economically essential traits. Additionally, it can knock out genes, facilitating efforts to elucidate gene functions through the analysis of mutant phenotypes. Here, we developed a mutant population using the small and pungent ornamental Capsicum annuum pepper “Micro-Pep”. This accession is particularly suitable for mutation studies and molecular research due to its compact growth habit and small size. We treated 9500 seeds with 1.3% EMS and harvested 3996 M2 lines. We then selected 1300 (32.5%) independent M2 families and evaluated their phenotypes over four years. The mutants displayed phenotypic variations in plant growth, habit, leaf color and shape, and flower and fruit morphology. An experiment to optimize Targeting Induced Local Lesions IN Genomes (TILLING) in pepper detected nine EMS-induced mutations in the eIF4E gene. The M2 families developed here exhibited broad phenotypic variation and should be valuable genetic resources for functional gene analysis in pepper molecular breeding programs using reverse genetics tools, including TILLING.
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16
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Kumar A, Birnbaum MD, Moorthy BT, Singh J, Palovcak A, Patel DM, Zhang F. Insertion/deletion-activated frame-shift fluorescence protein is a sensitive reporter for genomic DNA editing. BMC Genomics 2019; 20:609. [PMID: 31340764 PMCID: PMC6657097 DOI: 10.1186/s12864-019-5963-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/09/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Reporter methods to quantitatively measure the efficiency and specificity of genome editing tools are important for the development of novel editing techniques and successful applications of available ones. However, the existing methods have major limitations in sensitivity, accuracy, and/or readiness for in vivo applications. Here, we aim to develop a straight-forward method by using nucleotide insertion/deletion resulted from genome editing. In this system, a target sequence with frame-shifting length is inserted after the start codon of a cerulean fluorescence protein (CFP) to inactivate its fluorescence. As such, only a new insertion/deletion event in the target sequence will reactivate the fluorescence. This reporter is therefore termed as "Insertion/deletion-activated frame-shift fluorescence protein". To increase its traceability, an internal ribosome entry site and a red fluorescence protein mCherryFP are placed downstream of the reporter. The percentage of CFP-positive cells can be quantified by fluorescence measuring devices such as flow cytometer as the readout for genome editing frequency. RESULTS To test the background noise level, sensitivity, and quantitative capacity of this new reporter, we applied this approach to examine the efficiency of genome editing of CRISPR/Cas9 on two different targeting sequences and in three different cell lines, in the presence or absence of guide-RNAs with or without efficiency-compromising mutations. We found that the insertion/deletion-activated frame-shift fluorescence protein has very low background signal, can detect low-efficiency genome editing events driven by mutated guideRNAs, and can quantitatively distinguish genome editing by normal or mutated guideRNA. To further test whether the positive editing event detected by this reporter indeed correspond to genuine insertion/deletion on the genome, we enriched the CFP-positive cells to examine their fluorescence under confocal microscope and to analyze the DNA sequence of the reporter in the genome by Sanger sequencing. We found that the positive events captured by this reporter indeed correlates with genuine DNA insertion/deletion in the expected genome location. CONCLUSION The insertion/deletion-activated frame-shift fluorescence protein reporter has very low background, high sensitivity, and is quantitative in nature. It will be able to facilitate the development of new genome editing tools as well as the application of existing tools.
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Affiliation(s)
- Akhilesh Kumar
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
- Present address: Department of Botany, Banaras Hindu University, Varanasi, 221005 India
| | - Michael D. Birnbaum
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Balaji T. Moorthy
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Jayanti Singh
- Department of Otolaryngology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Devang M. Patel
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 USA
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17
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Abstract
TILLING (Targeting Induced Local Lesions IN Genomes), a popular reverse genetics approach in barley research, combines plant mutagenesis with efficient mutation detection for studying biological function of a specific gene. The high mutation frequency within a TILLING population principally enables the identification of induced variations in (almost) all genes of a given species (more precisely a given genotype of a species) of interest, which can be tested for their functional impact on morphological and/or physiological characteristics of the plant. Several TILLING populations induced by chemical mutagenesis were established for barley (Talame et al., Plant Biotechnol J 6:477-485, 2008; Gottwald et al., BMC Res Notes 2:258, 2009; Caldwell et al. Plant J 40:143-150, 2004) and showed the possibility for adapting protocols to develop further populations. This chapter describes a chemical mutagenesis protocol for barley seeds and two independent procedures for efficient single nucleotide polymorphism (SNP) detection in a large number of mutagenized plants either by slab-gel- or capillary gel-based electrophoreses on the LI-COR 4300 DNA Analyzer and the AdvanCE FS96 instruments, respectively.
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Affiliation(s)
- Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Miriam Szurman-Zubrzycka
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Katarzyna Gajek
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Iwona Szarejko
- Faculty of Biology and Environmental Protection, Department of Genetics, University of Silesia, Katowice, Poland
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
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18
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Filer JE, Channon RB, Henry CS, Geiss BJ. A Nuclease Protection ELISA Assay for Colorimetric and Electrochemical Detection of Nucleic Acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2019; 11:1027-1034. [PMID: 31656535 PMCID: PMC6814143 DOI: 10.1039/c8ay02729c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Early and accurate diagnosis is crucial to monitor infection outcomes and provide timely interventions. However, gold standard polymerase chain reaction assays (PCR) are labor-intensive and require expensive reagents and instrumentation. Nuclease protection has been used for decades to detect and quantify nucleic acid but has not yet been investigated as a diagnostic tool for infectious disease. In this work, we describe a nuclease protection enzyme-linked immunosorbent assay (NP-ELISA) for accurate and sensitive detection of nucleic acid. Briefly, binding of a nucleic acid target to an oligo probe protects it from digestion of un-hybridized nucleic acid by S1 nuclease. Following the workflow of an ELISA, a horseradish peroxidase (HRP)-conjugated antibody binds the probe and oxidizes its substrate to generate signal. The assay was validated with three HRP substrates for absorbance, chemiluminescence, and electrochemical readouts, demonstrating great versatility. Electrochemical detection with 3,3',5,5'-Tetramethylbenzidine (TMB) gave the highest assay sensitivity with a limit of detection of 3.72×103 molecules mL-1. Furthermore, non-complementary targets did not generate a response, indicating a high degree of specificity. This proof of principle serves as a stepping stone towards developing miniaturized, multiplexed nuclease protection assays for point-of-care diagnosis.
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Affiliation(s)
- Jessica E. Filer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert B. Channon
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles S. Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
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19
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Richter J, Watson JM, Stasnik P, Borowska M, Neuhold J, Berger M, Stolt-Bergner P, Schoft V, Hauser MT. Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions. Sci Rep 2018; 8:12182. [PMID: 30111865 PMCID: PMC6093868 DOI: 10.1038/s41598-018-30711-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/06/2018] [Indexed: 01/08/2023] Open
Abstract
Resolving functions of closely linked genes is challenging or nearly impossible with classical genetic tools. Four members of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) family are clustered on Arabidopsis chromosome five. To resolve the potentially redundant functions of this subclass of CrRLK1Ls named MEDOS1 to 4 (MDS1 to 4), we generated a single CRISPR/Cas9 transformation vector using a Golden Gate based cloning system to target all four genes simultaneously. We introduce single mutations within and deletions between MDS genes as well as knock-outs of the whole 11 kb gene cluster. The large MDS cluster deletion was inherited in up to 25% of plants lacking the CRISPR/Cas9 construct in the T2 generation. In contrast to described phenotypes of already characterized CrRLK1L mutants, quadruple mds knock-outs were fully fertile, developed normal root hairs and trichomes and responded to pharmacological inhibition of cellulose biosynthesis similar to wildtype. Recently, we demonstrated the role of four CrRLK1L in growth adaptation to metal ion stress. Here we show the involvement of MDS genes in response to Ni2+ during hypocotyl elongation and to Cd2+ and Zn2+ during root growth. Our finding supports the model of an organ specific network of positively and negatively acting CrRLK1Ls.
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Affiliation(s)
- Julia Richter
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - James Matthew Watson
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohrgasse 3, 1030, Vienna, Austria
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030, Vienna, Austria
| | - Peter Stasnik
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Monika Borowska
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohrgasse 3, 1030, Vienna, Austria
| | - Jana Neuhold
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohrgasse 3, 1030, Vienna, Austria
| | - Matthias Berger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Peggy Stolt-Bergner
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohrgasse 3, 1030, Vienna, Austria
| | - Vera Schoft
- Vienna Biocenter Core Facilities GmbH (VBCF), Dr. Bohrgasse 3, 1030, Vienna, Austria.
| | - Marie-Theres Hauser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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Koval T, Dohnálek J. Characteristics and application of S1–P1 nucleases in biotechnology and medicine. Biotechnol Adv 2018; 36:603-612. [DOI: 10.1016/j.biotechadv.2017.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
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21
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Aggeli D, Karas VO, Sinnott-Armstrong NA, Varghese V, Shafer RW, Greenleaf WJ, Sherlock G. Diff-seq: A high throughput sequencing-based mismatch detection assay for DNA variant enrichment and discovery. Nucleic Acids Res 2018; 46:e42. [PMID: 29361139 PMCID: PMC5909455 DOI: 10.1093/nar/gky022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 01/15/2023] Open
Abstract
Much of the within species genetic variation is in the form of single nucleotide polymorphisms (SNPs), typically detected by whole genome sequencing (WGS) or microarray-based technologies. However, WGS produces mostly uninformative reads that perfectly match the reference, while microarrays require genome-specific reagents. We have developed Diff-seq, a sequencing-based mismatch detection assay for SNP discovery without the requirement for specialized nucleic-acid reagents. Diff-seq leverages the Surveyor endonuclease to cleave mismatched DNA molecules that are generated after cross-annealing of a complex pool of DNA fragments. Sequencing libraries enriched for Surveyor-cleaved molecules result in increased coverage at the variant sites. Diff-seq detected all mismatches present in an initial test substrate, with specific enrichment dependent on the identity and context of the variation. Application to viral sequences resulted in increased observation of variant alleles in a biologically relevant context. Diff-Seq has the potential to increase the sensitivity and efficiency of high-throughput sequencing in the detection of variation.
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Affiliation(s)
- Dimitra Aggeli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vlad O Karas
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Vici Varghese
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert W Shafer
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Chen X, Roozbahani GM, Ye Z, Zhang Y, Ma R, Xiang J, Guan X. Label-Free Detection of DNA Mutations by Nanopore Analysis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:11519-11528. [PMID: 29537824 PMCID: PMC6760912 DOI: 10.1021/acsami.7b19774] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cancers are caused by mutations to genes that regulate cell normal functions. The capability to rapid and reliable detection of specific target gene variations can facilitate early disease detection and diagnosis and also enables personalized treatment of cancer. Most of the currently available methods for DNA mutation detection are time-consuming and/or require the use of labels or sophisticated instruments. In this work, we reported a label-free enzymatic reaction-based nanopore sensing strategy to detect DNA mutations, including base substitution, deletion, and insertion. The method was rapid and highly sensitive with a detection limit of 4.8 nM in a 10 min electrical recording. Furthermore, the nanopore assay could differentiate among perfect match, one mismatch, and two mismatches. In addition, simulated serum samples were successfully analyzed. Our developed nanopore-based DNA mutation detection strategy should find useful application in genetic diagnosis.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Zijing Ye
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Rui Ma
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Jialing Xiang
- Department of Biology, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA
- Corresponding author: Tel: 312-567-8922. Fax: 312-567-3494.
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23
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Sánchez M, Le Signor C, Aubert G, Darchy B, Gallardo K, Thompson RD. Targeting Induced Local Lesions IN Genomes (TILLING) in Medicago truncatula. Methods Mol Biol 2018; 1822:71-82. [PMID: 30043297 DOI: 10.1007/978-1-4939-8633-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
TILLING is a reverse genetics strategy that combines the high density of point mutations provided by traditional chemical mutagenesis with rapid screening of DNA pools from a mutagenized population for induced mutations (McCallum et al., Nat Biotechnol 18:455-457, 2000). This high-throughput technique allows the identification of point mutations in any gene of interest.
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Affiliation(s)
- Myriam Sánchez
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France
| | - Christine Le Signor
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France
| | - Gregoire Aubert
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France
| | - Brigitte Darchy
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France
| | - Karine Gallardo
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France
| | - Richard D Thompson
- INRA, University of Bourgogne Franche-Comté, Agroécologie, AgroSup Dijon, F-21000 Dijon, France.
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Gupta P, Reddaiah B, Salava H, Upadhyaya P, Tyagi K, Sarma S, Datta S, Malhotra B, Thomas S, Sunkum A, Devulapalli S, Till BJ, Sreelakshmi Y, Sharma R. Next-generation sequencing (NGS)-based identification of induced mutations in a doubly mutagenized tomato (Solanum lycopersicum) population. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:495-508. [PMID: 28779536 DOI: 10.1111/tpj.13654] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 05/21/2023]
Abstract
The identification of mutations in targeted genes has been significantly simplified by the advent of TILLING (Targeting Induced Local Lesions In Genomes), speeding up the functional genomic analysis of animals and plants. Next-generation sequencing (NGS) is gradually replacing classical TILLING for mutation detection, as it allows the analysis of a large number of amplicons in short durations. The NGS approach was used to identify mutations in a population of Solanum lycopersicum (tomato) that was doubly mutagenized by ethylmethane sulphonate (EMS). Twenty-five genes belonging to carotenoids and folate metabolism were PCR-amplified and screened to identify potentially beneficial alleles. To augment efficiency, the 600-bp amplicons were directly sequenced in a non-overlapping manner in Illumina MiSeq, obviating the need for a fragmentation step before library preparation. A comparison of the different pooling depths revealed that heterozygous mutations could be identified up to 128-fold pooling. An evaluation of six different software programs (camba, crisp, gatk unified genotyper, lofreq, snver and vipr) revealed that no software program was robust enough to predict mutations with high fidelity. Among these, crisp and camba predicted mutations with lower false discovery rates. The false positives were largely eliminated by considering only mutations commonly predicted by two different software programs. The screening of 23.47 Mb of tomato genome yielded 75 predicted mutations, 64 of which were confirmed by Sanger sequencing with an average mutation density of 1/367 Kb. Our results indicate that NGS combined with multiple variant detection tools can reduce false positives and significantly speed up the mutation discovery rate.
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Affiliation(s)
- Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bodanapu Reddaiah
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hymavathi Salava
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Pallawi Upadhyaya
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sneha Datta
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Bharti Malhotra
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusha Sunkum
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sameera Devulapalli
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Bradley John Till
- Plant Breeding and Genetics Laboratory, IAEA Seibersdorf Laboratories, Reaktorstrasse 1, Seibersdorf, Austria
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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25
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Abstract
Species of Chlamydia are the etiologic agent of endemic blinding trachoma, the leading cause of bacterial sexually transmitted diseases, significant respiratory pathogens, and a zoonotic threat. Their dependence on an intracellular growth niche and their peculiar developmental cycle are major challenges to elucidating their biology and virulence traits. The last decade has seen tremendous advances in our ability to perform a molecular genetic analysis of Chlamydia species. Major achievements include the generation of large collections of mutant strains, now available for forward- and reverse-genetic applications, and the introduction of a system for plasmid-based transformation enabling complementation of mutations; expression of foreign, modified, or reporter genes; and even targeted gene disruptions. This review summarizes the current status of the molecular genetic toolbox for Chlamydia species and highlights new insights into their biology and new challenges in the nascent field of Chlamydia genetics.
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Affiliation(s)
- Barbara S Sixt
- Department for Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710; .,Centre de Recherche des Cordeliers, INSERM U1138, Paris 75006, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris 75006, France.,Université Pierre et Marie Curie, Paris 75005, France
| | - Raphael H Valdivia
- Department for Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710;
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26
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Abstract
The zebrafish (Danio rerio) possesses a vertebrate-type retina that is extraordinarily conserved in evolution. This well-organized and anatomically easily accessible part of the central nervous system has been widely investigated in zebrafish, promoting general understanding of retinal development, morphology, function and associated diseases. Over the recent years, genome and protein engineering as well as imaging techniques have experienced revolutionary advances and innovations, creating new possibilities and methods to study zebrafish development and function. In this review, we focus on some of these emerging technologies and how they may impact retinal research in the future. We place an emphasis on genetic techniques, such as transgenic approaches and the revolutionizing new possibilities in genome editing.
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Affiliation(s)
- Stephanie Niklaus
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland.,b Life Science Zurich Graduate Program - Neuroscience , Zurich , Switzerland
| | - Stephan C F Neuhauss
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland
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27
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Ransdell JL, Dranoff E, Lau B, Lo WL, Donermeyer DL, Allen PM, Nerbonne JM. Loss of Navβ4-Mediated Regulation of Sodium Currents in Adult Purkinje Neurons Disrupts Firing and Impairs Motor Coordination and Balance. Cell Rep 2017; 19:532-544. [PMID: 28423317 PMCID: PMC5473293 DOI: 10.1016/j.celrep.2017.03.068] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/16/2017] [Accepted: 03/22/2017] [Indexed: 11/28/2022] Open
Abstract
The resurgent component of voltage-gated Na+ (Nav) currents, INaR, has been suggested to provide the depolarizing drive for high-frequency firing and to be generated by voltage-dependent Nav channel block (at depolarized potentials) and unblock (at hyperpolarized potentials) by the accessory Navβ4 subunit. To test these hypotheses, we examined the effects of the targeted deletion of Scn4b (Navβ4) on INaR and on repetitive firing in cerebellar Purkinje neurons. We show here that Scn4b-/- animals have deficits in motor coordination and balance and that firing rates in Scn4b-/- Purkinje neurons are markedly attenuated. Acute, in vivo short hairpin RNA (shRNA)-mediated "knockdown" of Navβ4 in adult Purkinje neurons also reduced spontaneous and evoked firing rates. Dynamic clamp-mediated addition of INaR partially rescued firing in Scn4b-/- Purkinje neurons. Voltage-clamp experiments revealed that INaR was reduced (by ∼50%), but not eliminated, in Scn4b-/- Purkinje neurons, revealing that additional mechanisms contribute to generation of INaR.
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Affiliation(s)
- Joseph L Ransdell
- Departments of Developmental Biology and Internal Medicine , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Edward Dranoff
- Departments of Developmental Biology and Internal Medicine , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brandon Lau
- Departments of Developmental Biology and Internal Medicine , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wan-Lin Lo
- Department of Pathology and Immunology , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David L Donermeyer
- Department of Pathology and Immunology , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Paul M Allen
- Department of Pathology and Immunology , Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeanne M Nerbonne
- Departments of Developmental Biology and Internal Medicine , Washington University School of Medicine, St. Louis, MO 63110, USA.
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28
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Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis. Nat Protoc 2017; 12:581-603. [PMID: 28207001 DOI: 10.1038/nprot.2016.165] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator. Second, FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates the testing of new nuclease reagents and the generation of edited cell pools or clonal cell lines, reducing the number of clones that need to be generated and increasing the ease with which they are screened. The pipeline shortens the time line, but it most prominently reduces the workload of cell-line editing, which may be completed within 4 weeks.
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29
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Gong H, Liu M, Klomp J, Merrill BJ, Rehman J, Malik AB. Method for Dual Viral Vector Mediated CRISPR-Cas9 Gene Disruption in Primary Human Endothelial Cells. Sci Rep 2017; 7:42127. [PMID: 28198371 PMCID: PMC5309830 DOI: 10.1038/srep42127] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
Human endothelial cells (ECs) are widely used to study mechanisms of angiogenesis, inflammation, and endothelial permeability. Targeted gene disruption induced by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-Associated Protein 9 (Cas9) nuclease gene editing is potentially an important tool for definitively establishing the functional roles of individual genes in ECs. We showed that co-delivery of adenovirus encoding EGFP-tagged Cas9 and lentivirus encoding a single guide RNA (sgRNA) in primary human lung microvascular ECs (HLMVECs) disrupted the expression of the Tie2 gene and protein. Tie2 disruption increased basal endothelial permeability and prevented permeability recovery following injury induced by the inflammatory stimulus thrombin. Thus, gene deletion via viral co-delivery of CRISPR-Cas9 in primary human ECs provides a novel platform to investigate signaling mechanisms of normal and perturbed EC function without the need for clonal expansion.
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Affiliation(s)
- Haixia Gong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Menglin Liu
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jeff Klomp
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Bradley J. Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Genome Editing Core, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Jalees Rehman
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Asrar B. Malik
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
- The Center for Lung and Vascular Biology, University of Illinois College of Medicine, Chicago, IL 60612, USA
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30
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Bui TGT, Hoa NTL, Yen JY, Schafleitner R. PCR-based assays for validation of single nucleotide polymorphism markers in rice and mungbean. Hereditas 2017; 154:3. [PMID: 28149257 PMCID: PMC5270362 DOI: 10.1186/s41065-016-0024-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/20/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Single nucleotide polymorphism (SNP) markers are the method of choice for genetic analyses including diversity and quantitative trait loci (QTL) studies. Marker validation is essential for QTL studies, but the cost and workload are considerable when large numbers of markers need to be verified. Marker systems with low development costs would be most suitable for this task. RESULTS We have tested allele specific polymerase chain reaction (PCR), tetra markers and a genotyping tool based on the single strand specific nuclease CEL-I to verify randomly selected SNP markers identified previously either with a SNP array or by genotyping by sequencing in rice and mungbean, respectively. The genotyping capacity of allele-specific PCR and tetra markers was affected by the sequence context surrounding the SNP; SNPs located in repeated sequences and in GC-rich stretches could not be correctly identified. In contrast, CEL-I digestion of mixed fragments produced from test and reference DNA reliably pinpointed the correct genotypes, yet scoring of the genotypes became complicated when multiple SNPs were present in the PCR fragments. A cost analysis showed that as long the sample number remains small, CEL-I genotyping is more cost-effective than tetra markers. CONCLUSIONS CEL-I genotyping performed better in terms of genotyping accuracy and costs than tetra markers. The method is highly useful for validating SNPs in small to medium size germplasm panels.
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Affiliation(s)
- Thu Giang Thi Bui
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi, Vietnam
| | - Nguyen Thi Lan Hoa
- Plant Resources Center, Vietnam Academy of Agricultural Sciences, An Khanh, Hoai Duc, Ha Noi, Vietnam
| | - Jo-yi Yen
- World Vegetable Center, 60 Yi Min Liao, Shanhua, Tainan, 74151 Taiwan
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31
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Machitani M, Sakurai F, Wakabayashi K, Nakatani K, Takayama K, Tachibana M, Mizuguchi H. Inhibition of CRISPR/Cas9-Mediated Genome Engineering by a Type I Interferon-Induced Reduction in Guide RNA Expression. Biol Pharm Bull 2017; 40:272-277. [PMID: 28250269 DOI: 10.1248/bpb.b16-00700] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated genome engineering technology is a powerful tool for generation of cells and animals with engineered mutations in their genomes. In order to introduce the CRISPR/Cas9 system into target cells, nonviral and viral vectors are often used; however, such vectors trigger innate immune responses associated with production of type I interferons (IFNs). We have recently demonstrated that type I IFNs inhibit short-hairpin RNA-mediated gene silencing, which led us to hypothesize that type I IFNs may also inhibit CRISPR/Cas9-mediated genome mutagenesis. Here we investigated this hypothesis. A single-strand annealing assay using a reporter plasmid demonstrated that CRISPR/Cas9-mediated cleavage efficiencies of the target double-stranded DNA were significantly reduced by IFNα. A mismatch recognition nuclease-dependent genotyping assay also demonstrated that IFNα reduced insertion or deletion (indel) mutation levels by approximately half. Treatment with IFNα did not alter Cas9 protein expression levels, whereas the copy numbers of guide RNA (gRNA) were significantly reduced by IFNα stimulation. These results indicate that type I IFNs significantly reduce gRNA expression levels following introduction of the CRISPR/Cas9 system in the cells, leading to a reduction in the efficiencies of CRISPR/Cas9-mediated genome mutagenesis. Our findings provide important clues for the achievement of efficient genome engineering using the CRISPR/Cas9 system.
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Affiliation(s)
- Mitsuhiro Machitani
- Laboratory of Biochemistry and Molecular Biology, Graduate School of Pharmaceutical Sciences, Osaka University
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32
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Fondong VN, Nagalakshmi U, Dinesh-Kumar SP. Novel Functional Genomics Approaches: A Promising Future in the Combat Against Plant Viruses. PHYTOPATHOLOGY 2016; 106:1231-1239. [PMID: 27392181 DOI: 10.1094/phyto-03-16-0145-fi] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advances in functional genomics and genome editing approaches have provided new opportunities and potential to accelerate plant virus control efforts through modification of host and viral genomes in a precise and predictable manner. Here, we discuss application of RNA-based technologies, including artificial micro RNA, transacting small interfering RNA, and Cas9 (clustered regularly interspaced short palindromic repeat-associated protein 9), which are currently being successfully deployed in generating virus-resistant plants. We further discuss the reverse genetics approach, targeting induced local lesions in genomes (TILLING) and its variant, known as EcoTILLING, that are used in the identification of plant virus recessive resistance gene alleles. In addition to describing specific applications of these technologies in plant virus control, this review discusses their advantages and limitations.
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Affiliation(s)
- Vincent N Fondong
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Ugrappa Nagalakshmi
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
| | - Savithramma P Dinesh-Kumar
- First author: Department of Biological Sciences, Delaware State University, Dover; second author: Department of Plant Biology, College of Biological Sciences, University of California, Davis; and third author: Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis
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33
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Zheng X, Yang S, Zhang D, Zhong Z, Tang X, Deng K, Zhou J, Qi Y, Zhang Y. Effective screen of CRISPR/Cas9-induced mutants in rice by single-strand conformation polymorphism. PLANT CELL REPORTS 2016; 35:1545-54. [PMID: 27007717 DOI: 10.1007/s00299-016-1967-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/01/2016] [Indexed: 05/22/2023]
Abstract
A method based on DNA single-strand conformation polymorphism is demonstrated for effective genotyping of CRISPR/Cas9-induced mutants in rice. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) has been widely adopted for genome editing in many organisms. A large proportion of mutations generated by CRISPR/Cas9 are very small insertions and deletions (indels), presumably because Cas9 generates blunt-ended double-strand breaks which are subsequently repaired without extensive end-processing. CRISPR/Cas9 is highly effective for targeted mutagenesis in the important crop, rice. For example, homozygous mutant seedlings are commonly recovered from CRISPR/Cas9-treated calli. However, many current mutation detection methods are not very suitable for screening homozygous mutants that typically carry small indels. In this study, we tested a mutation detection method based on single-strand conformational polymorphism (SSCP). We found it can effectively detect small indels in pilot experiments. By applying the SSCP method for CRISRP-Cas9-mediated targeted mutagenesis in rice, we successfully identified multiple mutants of OsROC5 and OsDEP1. In conclusion, the SSCP analysis will be a useful genotyping method for rapid identification of CRISPR/Cas9-induced mutants, including the most desirable homozygous mutants. The method also has high potential for similar applications in other plant species.
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Affiliation(s)
- Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Shixin Yang
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Dengwei Zhang
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Kejun Deng
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China
| | - Yiping Qi
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, People's Republic of China.
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34
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Comeron JM, Reed J, Christie M, Jacobs JS, Dierdorff J, Eberl DF, Manak JR. A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations. MICROARRAYS (BASEL, SWITZERLAND) 2016; 5:E7. [PMID: 27600073 PMCID: PMC5003483 DOI: 10.3390/microarrays5020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/21/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.
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Affiliation(s)
- Josep M Comeron
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
| | - Jordan Reed
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Matthew Christie
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Julia S Jacobs
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Jason Dierdorff
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
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35
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Miyaoka Y, Berman JR, Cooper SB, Mayerl SJ, Chan AH, Zhang B, Karlin-Neumann GA, Conklin BR. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Sci Rep 2016; 6:23549. [PMID: 27030102 PMCID: PMC4814844 DOI: 10.1038/srep23549] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/25/2016] [Indexed: 01/02/2023] Open
Abstract
Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR–based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator–like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology.
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Affiliation(s)
- Yuichiro Miyaoka
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, 94158, USA
| | - Jennifer R Berman
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, 94588, USA
| | - Samantha B Cooper
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, 94588, USA
| | - Steven J Mayerl
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, 94158, USA
| | - Amanda H Chan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, 94158, USA
| | - Bin Zhang
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, California, 94588, USA
| | | | - Bruce R Conklin
- Gladstone Institute of Cardiovascular Disease, San Francisco, California, 94158, USA.,Departments of Medicine and Cellular and Molecular Pharmacology, University of California, San Francisco, California, 94143, USA
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36
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Nishizawa-Yokoi A, Cermak T, Hoshino T, Sugimoto K, Saika H, Mori A, Osakabe K, Hamada M, Katayose Y, Starker C, Voytas DF, Toki S. A Defect in DNA Ligase4 Enhances the Frequency of TALEN-Mediated Targeted Mutagenesis in Rice. PLANT PHYSIOLOGY 2016; 170:653-66. [PMID: 26668331 PMCID: PMC4734567 DOI: 10.1104/pp.15.01542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/10/2015] [Indexed: 05/02/2023]
Abstract
We have established methods for site-directed mutagenesis via transcription activator-like effector nucleases (TALENs) in the endogenous rice (Oryza sativa) waxy gene and demonstrated stable inheritance of TALEN-induced somatic mutations to the progeny. To analyze the role of classical nonhomologous end joining (cNHEJ) and alternative nonhomologous end joining (altNHEJ) pathways in TALEN-induced mutagenesis in plant cells, we investigated whether a lack of DNA Ligase4 (Lig4) affects the kinetics of TALEN-induced double-strand break repair in rice cells. Deep-sequencing analysis revealed that the frequency of all types of mutations, namely deletion, insertion, combination of insertion with deletion, and substitution, in lig4 null mutant calli was higher than that in a lig4 heterozygous mutant or the wild type. In addition, the ratio of large deletions (greater than 10 bp) and deletions repaired by microhomology-mediated end joining (MMEJ) to total deletion mutations in lig4 null mutant calli was higher than that in the lig4 heterozygous mutant or wild type. Furthermore, almost all insertions (2 bp or greater) were shown to be processed via copy and paste of one or more regions around the TALENs cleavage site and rejoined via MMEJ regardless of genetic background. Taken together, our findings indicate that the dysfunction of cNHEJ leads to a shift in the repair pathway from cNHEJ to altNHEJ or synthesis-dependent strand annealing.
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Affiliation(s)
- Ayako Nishizawa-Yokoi
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Tomas Cermak
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Tomoki Hoshino
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Kazuhiko Sugimoto
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Hiroaki Saika
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Akiko Mori
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Keishi Osakabe
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Masao Hamada
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Yuichi Katayose
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Colby Starker
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Daniel F Voytas
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Seiichi Toki
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
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Xu Q, Huang SQ, Ma F, Tang B, Zhang CY. Controllable Mismatched Ligation for Bioluminescence Screening of Known and Unknown Mutations. Anal Chem 2016; 88:2431-9. [DOI: 10.1021/acs.analchem.5b04540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Qinfeng Xu
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Si-qiang Huang
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Fei Ma
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Bo Tang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
| | - Chun-yang Zhang
- College
of Chemistry, Chemical Engineering and Materials Science, Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
Universities of Shandong, Key Laboratory of Molecular and Nano Probes,
Ministry of Education, Shandong Provincial Key Laboratory of Clean
Production of Fine Chemicals, Shandong Normal University, Jinan, Shandong 250014, China
- Single-Molecule
Detection and Imaging Laboratory, Shenzhen Institutes of Advanced
Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
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Okabe Y, Ariizumi T. Mutant Resources and TILLING Platforms in Tomato Research. BIOTECHNOLOGY IN AGRICULTURE AND FORESTRY 2016. [DOI: 10.1007/978-3-662-48535-4_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sertori R, Trengove M, Basheer F, Ward AC, Liongue C. Genome editing in zebrafish: a practical overview. Brief Funct Genomics 2015; 15:322-30. [DOI: 10.1093/bfgp/elv051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Zou J, Tran D, Baalbaki M, Tang LF, Poon A, Pelonero A, Titus EW, Yuan C, Shi C, Patchava S, Halper E, Garg J, Movsesyan I, Yin C, Wu R, Wilsbacher LD, Liu J, Hager RL, Coughlin SR, Jinek M, Pullinger CR, Kane JP, Hart DO, Kwok PY, Deo RC. An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish. eLife 2015; 4:e09406. [PMID: 26473617 PMCID: PMC4720518 DOI: 10.7554/elife.09406] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022] Open
Abstract
Truncating mutations in the giant sarcomeric protein Titin result in dilated cardiomyopathy and skeletal myopathy. The most severely affected dilated cardiomyopathy patients harbor Titin truncations in the C-terminal two-thirds of the protein, suggesting that mutation position might influence disease mechanism. Using CRISPR/Cas9 technology, we generated six zebrafish lines with Titin truncations in the N-terminal and C-terminal regions. Although all exons were constitutive, C-terminal mutations caused severe myopathy whereas N-terminal mutations demonstrated mild phenotypes. Surprisingly, neither mutation type acted as a dominant negative. Instead, we found a conserved internal promoter at the precise position where divergence in disease severity occurs, with the resulting protein product partially rescuing N-terminal truncations. In addition to its clinical implications, our work may shed light on a long-standing mystery regarding the architecture of the sarcomere. DOI:http://dx.doi.org/10.7554/eLife.09406.001 The heart is able to beat partly because of a large protein called Titin that helps to give heart muscle its elasticity. Mutations that shorten the gene that encodes Titin can cause part of the heart to become enlarged and weakened, a condition called dilated cardiomyopathy. Some people with shortened copies of this protein have a mild form of cardiomyopathy and are able to lead relatively normal lives. Others develop more severe symptoms that prevent the heart from pumping blood effectively and may even cause the individual to need a heart transplant. Genetic studies have revealed that mutations that shorten the Titin protein by disrupting the portion of the gene corresponding to the latter two-thirds of the protein (which encodes the so-called “C-terminal” end of the protein) cause more severe symptoms than mutations that occur near the start of the gene. But it is not clear why the location of the mutation matters. To investigate this problem, Zou et al. used a gene-editing tool called CRISPR to create genetically engineered zebrafish. These fish had mutations at one of six different points in the gene that encodes the zebrafish version of Titin. Just as with humans, mutations near the C-terminal end of the gene caused more severe muscle problems in the fish. Specifically, Zou et al. found that the worst disease was associated with mutations that occurred at or after a “promoter” region within the gene and near this C-terminal end. Normally, the promoter produces an independent smaller form of the Titin protein, which helps to reduce the severity of muscle problems in zebrafish that have mutations near the start of the gene. However, mutations near the C-terminal end of the gene also damage this smaller form, preventing this failsafe from working, and so lead to more severe symptoms. Zou et al. also found this promoter to be active in both mouse and human hearts. Future work will focus on learning how this smaller form of Titin works to help muscle develop and withstand stress and determine whether increasing its production can overcome the more severe forms of disease. DOI:http://dx.doi.org/10.7554/eLife.09406.002
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Affiliation(s)
- Jun Zou
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Diana Tran
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Mai Baalbaki
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Ling Fung Tang
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Annie Poon
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Angelo Pelonero
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Erron W Titus
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Christiana Yuan
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Chenxu Shi
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Shruthi Patchava
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Elizabeth Halper
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Jasmine Garg
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Irina Movsesyan
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
| | - Chaoying Yin
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Roland Wu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Lisa D Wilsbacher
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, United States.,McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Ronald L Hager
- Department of Exercise Sciences, Brigham Young University, Provo, United States
| | - Shaun R Coughlin
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California, San Francisco, San Francisco, United States
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Clive R Pullinger
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Physiological Nursing, University of California, San Francisco, San Francisco, United States
| | - John P Kane
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Daniel O Hart
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Dermatology, University of California, San Francisco, San Francisco, United States.,Institute for Human Genetics, University of California, San Francisco, United States
| | - Rahul C Deo
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Medicine, University of California, San Francisco, San Francisco, United States.,Institute for Human Genetics, University of California, San Francisco, United States.,California Institute for Quantitative Biosciences, San Francisco, United States
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Yazdi SMHT, Kiah HM, Garcia-Ruiz E, Ma J, Zhao H, Milenkovic O. DNA-Based Storage: Trends and Methods. ACTA ACUST UNITED AC 2015. [DOI: 10.1109/tmbmc.2016.2537305] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Bono JM, Olesnicky EC, Matzkin LM. Connecting genotypes, phenotypes and fitness: harnessing the power of CRISPR/Cas9 genome editing. Mol Ecol 2015; 24:3810-22. [PMID: 26033315 DOI: 10.1111/mec.13252] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/20/2015] [Accepted: 05/26/2015] [Indexed: 12/26/2022]
Abstract
One of the fundamental goals in evolution and ecology is to identify the genetic basis of adaptive phenotypes. Unfortunately, progress towards this goal has been hampered by a lack of genetic tools available for nonmodel organisms. The exciting new development of the CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 (CRISPR-associated nuclease 9) genome-editing system now promises to transform the field of molecular ecology by providing a versatile toolkit for manipulating the genome of a wide variety of organisms. Here, we review the numerous applications of this groundbreaking technology and provide a practical guide to the creation of genetic knockouts, transgenics and other related forms of gene manipulation in nonmodel organisms. We also specifically discuss the potential uses of the CRISPR/Cas9 system in ecological and evolutionary studies, which will further advance the field towards the long-standing goal of connecting genotypes, phenotypes and fitness.
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Affiliation(s)
- Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Eugenia C Olesnicky
- Department of Biology, University of Colorado Colorado Springs, 1420 Austin Bluffs Parkway, Colorado Springs, CO, 80918, USA
| | - Luciano M Matzkin
- Department of Biological Sciences, University of Alabama in Huntsville, 301 Sparkman Drive, Huntsville, AL, 35899, USA.,HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
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A Mutagenesis Assay for Reporter Gene Screening Using Partially Degenerate Oligonucleotides of the Tandems NNT and NNC. BIOMED RESEARCH INTERNATIONAL 2015; 2015:950873. [PMID: 26167508 PMCID: PMC4488517 DOI: 10.1155/2015/950873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/02/2015] [Indexed: 11/24/2022]
Abstract
Not all proteins are tolerable to mutations. Whether a specific protein can be a mutable target is of importance in the biotechnology and pharmaceutical industry. This study reported a novel mutagenesis assay using tandem NNT and NNC oligonucleotides to test the mutability of a candidate gene. These two tandem oligonucleotides avoid the risk of forming nonsense mutations and render flexibility of truncating or expanding the insertion size. As a reporter gene, ZeoR (zeocin resistance gene) was confirmed to have a high tolerance for mutagenesis by this new assay.
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Galindo-González L, Pinzón-Latorre D, Bergen EA, Jensen DC, Deyholos MK. Ion Torrent sequencing as a tool for mutation discovery in the flax (Linum usitatissimum L.) genome. PLANT METHODS 2015; 11:19. [PMID: 25788971 PMCID: PMC4363359 DOI: 10.1186/s13007-015-0062-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 03/02/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Detection of induced mutations is valuable for inferring gene function and for developing novel germplasm for crop improvement. Many reverse genetics approaches have been developed to identify mutations in genes of interest within a mutagenized population, including some approaches that rely on next-generation sequencing (e.g. exome capture, whole genome resequencing). As an alternative to these genome or exome-scale methods, we sought to develop a scalable and efficient method for detection of induced mutations that could be applied to a small number of target genes, using Ion Torrent technology. We developed this method in flax (Linum usitatissimum), to demonstrate its utility in a crop species. RESULTS We used an amplicon-based approach in which DNA samples from an ethyl methanesulfonate (EMS)-mutagenized population were pooled and used as template in PCR reactions to amplify a region of each gene of interest. Barcodes were incorporated during PCR, and the pooled amplicons were sequenced using an Ion Torrent PGM. A pilot experiment with known SNPs showed that they could be detected at a frequency > 0.3% within the pools. We then selected eight genes for which we wanted to discover novel mutations, and applied our approach to screen 768 individuals from the EMS population, using either the Ion 314 or Ion 316 chips. Out of 29 potential mutations identified after processing the NGS reads, 16 mutations were confirmed using Sanger sequencing. CONCLUSIONS The methodology presented here demonstrates the utility of Ion Torrent technology in detecting mutation variants in specific genome regions for large populations of a species such as flax. The methodology could be scaled-up to test >100 genes using the higher capacity chips now available from Ion Torrent.
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Affiliation(s)
| | - David Pinzón-Latorre
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Erik A Bergen
- />Department of Biological Sciences, University of Alberta, Edmonton, AB Canada T6G 2E9
| | - Dustin C Jensen
- />Department of Computing Sciences, Kings University College, Edmonton, AB Canada T6B 2H3
| | - Michael K Deyholos
- />IK Barber School of Arts & Sciences, University of British Columbia, Okanagan campus, Kelowna, BC Canada V1V 1 V7
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Guo Y, Abernathy B, Zeng Y, Ozias-Akins P. TILLING by sequencing to identify induced mutations in stress resistance genes of peanut (Arachis hypogaea). BMC Genomics 2015; 16:157. [PMID: 25881128 PMCID: PMC4369367 DOI: 10.1186/s12864-015-1348-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/16/2015] [Indexed: 11/28/2022] Open
Abstract
Background Targeting Induced Local Lesions in Genomes (TILLING) is a powerful reverse genetics approach for functional genomics studies. We used high-throughput sequencing, combined with a two-dimensional pooling strategy, with either minimum read percentage with non-reference nucleotide or minimum variance multiplier as mutation prediction parameters, to detect genes related to abiotic and biotic stress resistances. In peanut, lipoxygenase genes were reported to be highly induced in mature seeds infected with Aspergillus spp., indicating their importance in plant-fungus interactions. Recent studies showed that phospholipase D (PLD) expression was elevated more quickly in drought sensitive lines than in drought tolerant lines of peanut. A newly discovered lipoxygenase (LOX) gene in peanut, along with two peanut PLD genes from previous publications were selected for TILLING. Additionally, two major allergen genes Ara h 1 and Ara h 2, and fatty acid desaturase AhFAD2, a gene which controls the ratio of oleic to linoleic acid in the seed, were also used in our study. The objectives of this research were to develop a suitable TILLING by sequencing method for this allotetraploid, and use this method to identify mutations induced in stress related genes. Results We screened a peanut root cDNA library and identified three candidate LOX genes. The gene AhLOX7 was selected for TILLING due to its high expression in seeds and roots. By screening 768 M2 lines from the TILLING population, four missense mutations were identified for AhLOX7, three missense mutations were identified for AhPLD, one missense and two silent mutations were identified for Ara h 1.01, three silent and five missense mutations were identified for Ara h 1.02, one missense mutation was identified for AhFAD2B, and one silent mutation was identified for Ara h 2.02. The overall mutation frequency was 1 SNP/1,066 kb. The SNP detection frequency for single copy genes was 1 SNP/344 kb and 1 SNP/3,028 kb for multiple copy genes. Conclusions Our TILLING by sequencing approach is efficient to identify mutations in single and multi-copy genes. The mutations identified in our study can be used to further study gene function and have potential usefulness in breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1348-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
| | - Yajuan Zeng
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
| | - Peggy Ozias-Akins
- Department of Horticulture, University of Georgia -Tifton Campus, 2360 Rainwater Rd, Tifton, GA, 31793-5766, USA.
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Labuschagne C, Kotzé A, Paul Grobler J, Dalton DL. Endonuclease V digestion for SNP discovery and marker development in South African white rhinoceros (Ceratotherium simum). CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-014-0358-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (BETHESDA, MD.) 2015. [PMID: 25566793 DOI: 10.1534/g3.114.015834.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genome editing using engineered nucleases is used for targeted mutagenesis. But because genome editing does not target all loci with similar efficiencies, the mutation hit-rate at a given locus needs to be evaluated. The analysis of mutants obtained using engineered nucleases requires specific methods for mutation detection, and the enzyme mismatch cleavage method is used commonly for this purpose. This method uses enzymes that cleave heteroduplex DNA at mismatches and extrahelical loops formed by single or multiple nucleotides. Bacteriophage resolvases and single-stranded nucleases are used commonly in the assay but have not been compared side-by-side on mutations obtained by engineered nucleases. We present the first comparison of the sensitivity of T7E1 and Surveyor EMC assays on deletions and point mutations obtained by zinc finger nuclease targeting in frog embryos. We report the mutation detection limits and efficiencies of T7E1 and Surveyor. In addition, we find that T7E1 outperforms the Surveyor nuclease in terms of sensitivity with deletion substrates, whereas Surveyor is better for detecting single nucleotide changes. We conclude that T7E1 is the preferred enzyme to scan mutations triggered by engineered nucleases.
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Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3-GENES GENOMES GENETICS 2015; 5:407-15. [PMID: 25566793 PMCID: PMC4349094 DOI: 10.1534/g3.114.015834] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Genome editing using engineered nucleases is used for targeted mutagenesis. But because genome editing does not target all loci with similar efficiencies, the mutation hit-rate at a given locus needs to be evaluated. The analysis of mutants obtained using engineered nucleases requires specific methods for mutation detection, and the enzyme mismatch cleavage method is used commonly for this purpose. This method uses enzymes that cleave heteroduplex DNA at mismatches and extrahelical loops formed by single or multiple nucleotides. Bacteriophage resolvases and single-stranded nucleases are used commonly in the assay but have not been compared side-by-side on mutations obtained by engineered nucleases. We present the first comparison of the sensitivity of T7E1 and Surveyor EMC assays on deletions and point mutations obtained by zinc finger nuclease targeting in frog embryos. We report the mutation detection limits and efficiencies of T7E1 and Surveyor. In addition, we find that T7E1 outperforms the Surveyor nuclease in terms of sensitivity with deletion substrates, whereas Surveyor is better for detecting single nucleotide changes. We conclude that T7E1 is the preferred enzyme to scan mutations triggered by engineered nucleases.
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Li T, Wright DA, Spalding MH, Yang B. TALEN-Based Genome Editing in Yeast. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Abstract
TILLING is a method to find mutations in a gene of interest by scanning amplicons from a mutagenized population for sequence changes, commonly a single nucleotide. In the past 5 years, mutation detection by sequencing has become increasingly popular. This chapter details the experimental flow for TILLING-by-Sequencing, highlighting the critical steps involved in tridimensional pooling of genomic DNA templates, preparation of libraries for high-throughput sequencing, and bioinformatic processing of the sequence data.
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Affiliation(s)
- Helen Tsai
- Department of Plant Biology and Genome Center, University of California at Davis, One Shields Avenue, Davis, CA, 95616, USA
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