Evaluation of Three RT-qPCR-Based miRNA Detection Methods Using Seven Rice miRNAs

Mou, Guiping; Wang, Kang; Xu, Donglin; Zhou, Guohui

doi:10.1271/bbb.130192

Cited by 28 publications

(18 citation statements)

References 19 publications

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“…Mou et al compared three methods: stem-loop qPCR, poly(A) tailing and miQPCR, and found that the poly(A)-based method has a better ability to detect miRNAs with low expression levels [74]. …”

Section: Comparisons Of Available Methods For Expression Analysis Of mentioning

confidence: 99%

qPCR-Based Methods for Expression Analysis of miRNAs

et al. 2019

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Several approaches for miRNA expression analysis have been developed in recent years. In this article, we provide an updated and comprehensive review of available qPCR-based methods for miRNA expression analysis and discuss their advantages and disadvantages. Existing techniques involve the use of stem–loop reverse transcriptase–PCR, polyadenylation of RNAs, ligation of adapters or RT with complex primers, using universal or miRNA-specific qPCR primers and/or probes. Many of these methods are oriented towards the expression analysis of mature miRNAs and few are designed for the study of pre-miRNAs and pri-miRNAs. We also discuss findings from articles that compare results from existing methods. Finally, we suggest key points for the improvement of available techniques and for the future development of additional methods.

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Section: Comparisons Of Available Methods For Expression Analysis Of mentioning

confidence: 99%

qPCR-Based Methods for Expression Analysis of miRNAs

et al. 2019

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“…lncRNAs and miRNA-lncRNAs primers were designed using Oligo 7 software (Supplementary Tables S6 and S7) and the actin was applied as a housekeeping gene 155 . Mature miRNA expression analysis was done by stem-loop reverse transcription-qPCR method 156,157 . Supplementary Table S8 shows the sequences of RT primers and miRNA-specific PCR primers.…”

Section: Differential Expression Analysismentioning

confidence: 99%

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing

Jannesar

Seyedi

Jazi

et al. 2020

Sci Rep

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Long non-coding RNAs (lncRNAs) play crucial roles in regulating gene expression in response to plant stresses. Given the importance regulatory roles of lncRNAs, providing methods for predicting the function of these molecules, especially in non-model plants, is strongly demanded by researchers. Here, we constructed a reference sequence for lncRNAs in P. vera (Pistacia vera L.) with 53220 transcripts. In total, we identified 1909 and 2802 salt responsive lncRNAs in Ghazvini, a salt tolerant cultivar, after 6 and 24 h salt treatment, respectively and 1820 lncRNAs in Sarakhs, a salt sensitive cultivar, after 6 h salt treatment. Functional analysis of these lncRNAs by several hybrid methods, revealed that salt responsive NAT-related lncRNAs associated with transcription factors, CERK1, LEA, Laccase genes and several genes involved in the hormone signaling pathways. Moreover, gene ontology (GO) enrichment analysis of salt responsive target genes related to top five selected lncRNAs showed their involvement in the regulation of ATPase, cation transporter, kinase and UDP-glycosyltransferases genes. Quantitative real-time PCR (qRT-PCR) experiment results of lncRNAs, pre-miRNAs and mature miRNAs were in accordance with our RNA-seq analysis. In the present study, a comparative analysis of differentially expressed lncRNAs and microRNA precursors between salt tolerant and sensitive pistachio cultivars provides valuable knowledge on gene expression regulation under salt stress condition. Pistacia belongs to Anacardiaceae family and contains 13 or more species, which among them pistachio (Pistacia vera L.) is the only cultivated and economically important species that is called as the 'green gold tree'. The other species are used mainly as a rootstock for pistachio cultivation 1,2. Like many other fruit trees, P. vera is hard to root and thus requires a rootstock for vegetative propagation 3. Pistachio is a deciduous (2n = 30), wind-pollinated tree species 4,5. Studies indicate that pistachio probably originated in the Middle East 6-8. It has a long history of cultivation (3000-4000 years) in Iran 9. In 2017, Iran has been ranked first in area harvested (429535 ha) and production quantity (574987 tons) of pistachio among United States, Turkey, and Syria as biggest pistachio producer countries 10. According to the number of pistachio genotypes, Iran is one of the rich countries in the world 7,8,11. In addition to fruit, other parts of plant, including leaf, flower and resins, have pharmacological properties 12,13. Salinity is major and ever-increasing problem in arid and semi-arid regions that affect plant production and growth throughout the world 14. The cultivated areas of pistachio in Iran are often in arid and semi-arid regions that the most important problem for economic crop production in these areas is high concentration of ions

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“…In terms of detection methods, circulating miRNA is based on high-throughput sequencing, miRNA chips, northern blot, qRT-PCR, [110][111][112][113][114][115][116][117] modification, but the disadvantage is the cumbersome and expensive operation. 86,87 Furthermore, qRT-PCR is a gold standard for quantitative detection of miRNA, which can perform relative quantitative and absolute quantitative detection of miRNA and can detect the expression level of miRNA more intuitively.…”

Section: Challenges Of Circulating Mirna As a Biomarkermentioning

confidence: 99%

Circulating miRNA or circulating DNA—Potential biomarkers for organ transplant rejection

Huo

Zhou

Cooper

et al. 2018

Xenotransplantation

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Accurate and timely diagnosis of transplant rejection is essential for the long‐term survival of solid‐organ transplant recipients. Biopsy is the “gold standard” for the diagnosis of rejection, but this approach is a time‐consuming, expensive, and invasive process. An efficient, cheap, and noninvasive tool for monitoring of immune rejection is urgently needed. Circulating miRNA and circulating DNA can be easily amplified and quantified by PCR which could be potential biomarkers for monitoring organ survival and/or immune rejection. In this review, we briefly introduce the origins and characteristics of circulating miRNA and circulating DNA. Furthermore, we review their clinical application and potential as noninvasive biomarkers for rejection in organ transplantation. Finally, we sum up their potential as biomarkers, which may help scientists and surgeons choose the proper biomarker for routine assays.

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Evaluation of Three RT-qPCR-Based miRNA Detection Methods Using Seven Rice miRNAs

Cited by 28 publications

References 19 publications

qPCR-Based Methods for Expression Analysis of miRNAs

qPCR-Based Methods for Expression Analysis of miRNAs

A genome-wide identification, characterization and functional analysis of salt-related long non-coding RNAs in non-model plant Pistacia vera L. using transcriptome high throughput sequencing

Circulating miRNA or circulating DNA—Potential biomarkers for organ transplant rejection

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