1
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Wang H, Yu R, Zhu Q, Tian Z, Li F. A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:263-276. [PMID: 38078656 DOI: 10.1111/tpj.16585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 04/02/2024]
Abstract
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as 32P-labeled probe in dot blot and small RNA northern blot experiments. Addition of locked nucleic acids in T4BC33 probe further enhanced its sensitivity in detecting low-abundance miRNAs. With newly developed northern blot method, expression of miR6027 and miR6149 family members was validated. Northern blot analysis also confirmed the successful application of virus-based miRNA silencing in pepper, knocking down accumulation of Can-miR6027a and Can-miR6149L. Importantly, further analysis showed that knocking-down Can-miR6027a led to upregulation of a nucleotide binding-leucine rich repeat domain protein coding gene (CaRLb1) and increased immunity against Phytophthora capsici in pepper leaves. Our study provided a highly sensitive and convenient method for sRNA research and identified new targets for genetic improvement of pepper immunity against P. capsici.
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Affiliation(s)
- Hongzheng Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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2
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Le MN, Le CT, Nguyen TA. Intramolecular ligation method (iLIME) for pre-miRNA quantification and sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1028-1038. [PMID: 35487691 PMCID: PMC9202589 DOI: 10.1261/rna.079101.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/12/2022] [Indexed: 06/04/2023]
Abstract
Hairpin-containing pre-miRNAs, produced from pri-miRNAs, are precursors of miRNAs (microRNAs) that play essential roles in gene expression and various human diseases. Current qPCR-based methods used to quantify pre-miRNAs are not effective to discriminate between pre-miRNAs and their parental pri-miRNAs. Here, we developed the intramolecular ligation method (iLIME) to quantify and sequence pre-miRNAs specifically. This method utilizes T4 RNA ligase 1 to convert pre-miRNAs into circularized RNAs, allowing us to design PCR primers to quantify pre-miRNAs, but not their parental pri-miRNAs. In addition, the iLIME also enables us to sequence the ends of pre-miRNAs using next-generation sequencing. Therefore, this method offers a simple and effective way to quantify and sequence pre-miRNAs, so it will be highly beneficial for investigating pre-miRNAs when addressing research questions and medical applications.
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Affiliation(s)
- Minh Ngoc Le
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Cong Truc Le
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tuan Anh Nguyen
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
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3
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Garafutdinov RR, Sakhabutdinova AR, Gilvanov AR, Chemeris AV. Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021; 47:1172-1189. [PMID: 34931113 PMCID: PMC8675116 DOI: 10.1134/s1068162021060078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 11/23/2022]
Abstract
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
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Affiliation(s)
- R. R. Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. R. Gilvanov
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
| | - A. V. Chemeris
- Institute of Biochemistry and Genetics, Ufa Federal Research Center, Russian Academy of Sciences, 450054 Ufa, Russia
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4
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Del Piano A, Kecman T, Schmid M, Barbieri R, Brocchieri L, Tornaletti S, Firrito C, Minati L, Bernabo P, Signoria I, Lauria F, Gillingwater TH, Viero G, Clamer M. Phospho-RNA sequencing with circAID-p-seq. Nucleic Acids Res 2021; 50:e23. [PMID: 34850942 PMCID: PMC8887461 DOI: 10.1093/nar/gkab1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/14/2022] Open
Abstract
Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3′ end. Unfortunately, current library preparation protocols rely only on a 3′ hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3′ phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3′-phospho RNA molecules.
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Affiliation(s)
- Alessia Del Piano
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tea Kecman
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | | | | | - Luciano Brocchieri
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | - Silvia Tornaletti
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | | | - Luca Minati
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Paola Bernabo
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Ilaria Signoria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - Gabriella Viero
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
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5
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Jet T, Gines G, Rondelez Y, Taly V. Advances in multiplexed techniques for the detection and quantification of microRNAs. Chem Soc Rev 2021; 50:4141-4161. [PMID: 33538706 DOI: 10.1039/d0cs00609b] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNA detection is currently a crucial analytical chemistry challenge: almost 2000 papers were referenced in PubMed in 2018 and 2019 for the keywords "miRNA detection method". MicroRNAs are potential biomarkers for multiple diseases including cancers, neurodegenerative and cardiovascular diseases. Since miRNAs are stably released in bodily fluids, they are of prime interest for the development of non-invasive diagnosis methods, such as liquid biopsies. Their detection is however challenging, as high levels of sensitivity, specificity and robustness are required. The analysis also needs to be quantitative, since the aim is to detect miRNA concentration changes. Moreover, a high multiplexing capability is also of crucial importance, since the clinical potential of miRNAs probably lays in our ability to perform parallel mapping of multiple miRNA concentrations and recognize typical disease signature from this profile. A plethora of biochemical innovative detection methods have been reported recently and some of them provide new solutions to the problem of sensitive multiplex detection. In this review, we propose to analyze in particular the new developments in multiplexed approaches to miRNA detection. The main aspects of these methods (including sensitivity and specificity) will be analyzed, with a particular focus on the demonstrated multiplexing capability and potential of each of these methods.
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Affiliation(s)
- Thomas Jet
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, CNRS SNC5096, Equipe Labellisée Ligue Nationale Contre le Cancer, F-75006 Paris, France.
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6
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Song Y, Xu Z, Wang F. Genetically Encoded Reporter Genes for MicroRNA Imaging in Living Cells and Animals. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:555-567. [PMID: 32721876 PMCID: PMC7390858 DOI: 10.1016/j.omtn.2020.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/12/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by base paring with the complementary sequences of the target mRNAs, and then exert their function through degrading mRNA or inhibiting protein translation. They play a significant role as a regulatory factor in biological processes of organism development, cell proliferation, differentiation, and cell death. Some of the traditional methods for studying miRNAs, such as northern blot, real-time PCR, or microarray, have been extensively used to investigate the biological properties and expression patterns of miRNAs. However, these methods often require considerable time, cell samples, and the design of effective primers or specific probes. Therefore, in order to gain a deeper understanding of the role of miRNAs in biological processes and accelerate the clinical application of miRNAs in the field of disease treatment, non-invasive, sensitive, and efficient imaging methods are needed to visualize the dynamic expression of miRNAs in living cells and animals. In this study, we reviewed the recent progress in the genetically encoded reporter genes for miRNA imaging.
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Affiliation(s)
- Yingzhuang Song
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Zhijing Xu
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China
| | - Fu Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Engineering Research Center of Molecular and Neuro Imaging, Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710071, China.
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7
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Forero DA, González-Giraldo Y, Castro-Vega LJ, Barreto GE. qPCR-based methods for expression analysis of miRNAs. Biotechniques 2019; 67:192-199. [PMID: 31560239 DOI: 10.2144/btn-2019-0065] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
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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Affiliation(s)
- Diego A Forero
- Laboratory of NeuroPsychiatric Genetics, Biomedical Sciences Research Group, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia.,PhD Program in Health Sciences, School of Medicine, Universidad Antonio Nariño, Bogotá, Colombia
| | - Yeimy González-Giraldo
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Luis J Castro-Vega
- INSERM, UMR970, Paris-Cardiovascular Research Center, Equipe Labellisée par la Ligue contre le Cancer, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
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8
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Abstract
![]()
Nanopore
sequencing offers a portable and affordable alternative
to sequencing-by-synthesis methods but suffers from lower accuracy
and cannot sequence ultrashort DNA. This puts applications such as
molecular diagnostics based on the analysis of cell-free DNA or single-nucleotide
variants (SNVs) out of reach. To overcome these limitations, we report
a nanopore-based sequencing strategy in which short target sequences
are first circularized and then amplified via rolling-circle amplification
to produce long stretches of concatemeric repeats. After sequencing
on the Oxford Nanopore Technologies MinION platform, the resulting
repeat sequences can be aligned to produce a highly accurate consensus
that reduces the high error-rate present in the individual repeats.
Using this approach, we demonstrate for the first time the ability
to obtain unbiased and accurate nanopore data for target DNA sequences
<100 bp. Critically, this approach is sensitive enough to achieve
SNV discrimination in mixtures of sequences and even enables quantitative
detection of specific variants present at ratios of <10%. Our method
is simple, cost-effective, and only requires well-established processes.
It therefore expands the utility of nanopore sequencing for molecular
diagnostics and other applications, especially in resource-limited
settings.
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Affiliation(s)
- Brandon D Wilson
- Department of Chemical Engineering , Stanford University , Stanford , California 94305 , United States
| | - Michael Eisenstein
- Department of Electrical Engineering , Stanford University , Stanford , California 94305 , United States.,Department of Radiology , Stanford University , Stanford , California 94305 , United States
| | - H Tom Soh
- Department of Electrical Engineering , Stanford University , Stanford , California 94305 , United States.,Department of Radiology , Stanford University , Stanford , California 94305 , United States.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
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9
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Zhang Z, Wang Y, Li Y, Yu D, Chen H, Cai Y, Fang W, Yang Z, Ji Y, Guan Y, Chu Y, Xu C. Portable fluorescence-based microRNA detection system based on isothermal signal amplification technology. Biotechnol Appl Biochem 2018; 66:82-90. [PMID: 30311952 DOI: 10.1002/bab.1699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/07/2018] [Indexed: 01/01/2023]
Abstract
MicroRNAs (miRNAs) diagnostics can be useful for diagnosing or confirming miRNA abundance and are used in screening tests and to assess changes in miRNAs in vivo. At present, the use of traditional nucleic acid amplification assays to detect miRNAs has been limited in laboratory environment because of the time, equipment, and technical expertise required to perform these assays. A specialized, rapid affordable miRNA detection system is necessary when there are limited resources or point-of-care testing needs. We designed a portable and affordable fluorescence-based miRNA detection system based on isothermal signal amplification technology, using SYBR Green II as a fluorescent dye. To reduce costs, we chose LED as a light source and designed the corresponding optical path for LED. The portable detection system shows results consistent with those by real-time PCR, and can be used to detect miR-183 with a limit of detection of approximately 2 fmol. We used the system to detect miR-183 in tissues and blood from patients with hepatocellular carcinoma (HCC). The results from the portable detection device were compared with those from clinical trials and indicated that the miR-183 fluorescence signal could successfully identify HCC and provide information related to cancer progression.
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Affiliation(s)
- Zhanying Zhang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Yanfei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Yanlei Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Dongsheng Yu
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Haiyan Chen
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yi Cai
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Weikai Fang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Zhe Yang
- Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yufeng Ji
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Yifu Guan
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Yannan Chu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
| | - Chidong Xu
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China.,Anhui Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Hefei, Anhui, People's Republic of China
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10
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Barberán-Soler S, Vo JM, Hogans RE, Dallas A, Johnston BH, Kazakov SA. Decreasing miRNA sequencing bias using a single adapter and circularization approach. Genome Biol 2018; 19:105. [PMID: 30173660 PMCID: PMC6120088 DOI: 10.1186/s13059-018-1488-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 12/22/2022] Open
Abstract
The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for preparing miRNA sequencing libraries, RealSeq®-AC, that involves ligating the miRNAs with a single adapter and circularizing the ligation products. When compared to other methods, RealSeq®-AC provides greatly reduced miRNA sequencing bias and allows the identification of the largest variety of miRNAs in biological samples. This reduced bias also allows robust quantification of miRNAs present in samples across a wide range of RNA input levels.
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Affiliation(s)
| | - Jenny M. Vo
- SomaGenics, Inc., Santa Cruz, California, USA
| | | | - Anne Dallas
- SomaGenics, Inc., Santa Cruz, California, USA
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11
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Kim KJ, Kwak J, Lee JH, Lee SS. Real-time qRT-PCR assay for the detection of miRNAs using bi-directional extension sequences. Anal Biochem 2017; 536:32-35. [DOI: 10.1016/j.ab.2017.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/08/2017] [Accepted: 08/11/2017] [Indexed: 02/06/2023]
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12
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Sakhabutdinova AR, Maksimova MA, Garafutdinov RR. Synthesis of circular DNA templates with T4 RNA ligase for rolling circle amplification. Mol Biol 2017. [DOI: 10.1134/s0026893317040161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Dellett M, Simpson DA. Considerations for optimization of microRNA PCR assays for molecular diagnosis. Expert Rev Mol Diagn 2016; 16:407-14. [PMID: 26854938 DOI: 10.1586/14737159.2016.1152184] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The remarkable stability of microRNAs in biofluids underlies their potential as biomarkers, but their small size presents challenges for detection by RT-qPCR. The heterogeneity of microRNAs, with each one comprising a series of variants or 'isomiRs', adds additional complexity. Presented here are the key considerations for use of RT-qPCR to measure microRNAs and their isomiRs, with a focus on plasma. Modified nucleotides can be incorporated into primer sequences to enhance affinity and provide increased specificity and sensitivity for RT-qPCR assays. Approaches based upon polyA tailing and use of a common oligo(dT)-based reverse transcription oligonucleotide will detect most isomiRs. Conversely, stem-loop RT oligonucleotides and sequence specific probes can enable detection of specific isomiRs of interest. Next generation sequencing of all the products of a microRNA RT-PCR reaction is a promising new approach for both microRNA quantification and characterization.
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Affiliation(s)
- Margaret Dellett
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
| | - David Arthur Simpson
- a Centre for Experimental Medicine , Queen's University Belfast , Belfast , Northern Ireland , UK
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14
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Liu H, Bei X, Xia Q, Fu Y, Zhang S, Liu M, Fan K, Zhang M, Yang Y. Enzyme-free electrochemical detection of microRNA-21 using immobilized hairpin probes and a target-triggered hybridization chain reaction amplification strategy. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1636-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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16
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Chu Y, Wang T, Dodd D, Xie Y, Janowski BA, Corey DR. Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells. Nucleic Acids Res 2015; 43:e75. [PMID: 25813040 PMCID: PMC4477644 DOI: 10.1093/nar/gkv213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/03/2015] [Indexed: 12/21/2022] Open
Abstract
RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived from cultured human cells after crosslinking and immunoprecipitation (CLIP). Here, we report a method for obtaining strand-specific small RNA libraries for RNA sequencing that requires picograms of RNA. We employ an intramolecular circularization step that increases the efficiency of library preparation and avoids the need for intermolecular ligations of adaptor sequences. Other key features include random priming for full-length cDNA synthesis and gel-free library purification. Using our method, we generated CLIP-Seq libraries from nuclear RNA that had been UV-crosslinked and immunoprecipitated with anti-Argonaute 2 (Ago2) antibody. Computational protocols were developed to enable analysis of raw sequencing data and we observe substantial differences between recognition by Ago2 of RNA species in the nucleus relative to the cytoplasm. This RNA self-circularization approach to RNA sequencing (RC-Seq) allows data to be obtained using small amounts of input RNA that cannot be sequenced by standard methods.
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Affiliation(s)
- Yongjun Chu
- Departments of Pharmacology and Biochemistry, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Clinical Science, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David Dodd
- Departments of Pharmacology and Biochemistry, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Science, 6001 Forest Park Road, Dallas, TX 75390-9041, USA Simmons Cancer Center, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Bethany A Janowski
- Departments of Pharmacology and Biochemistry, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
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Hunt EA, Broyles D, Head T, Deo SK. MicroRNA Detection: Current Technology and Research Strategies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:217-37. [PMID: 25973944 DOI: 10.1146/annurev-anchem-071114-040343] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida 33136;
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18
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Jiang L, Wang Y, Rong Y, Xu L, Chu Y, Zhang Y, Yao Y. miR-1179 promotes cell invasion through SLIT2/ROBO1 axis in esophageal squamous cell carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:319-27. [PMID: 25755718 PMCID: PMC4348900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/24/2014] [Indexed: 06/04/2023]
Abstract
MiR-1179, a new identified miRNA highly associated with metastasis of colorectal cancer which was never reported in esophageal squamous cell carcinoma (ESCC). Here we measured the expression levels of miR-1179 and the candidate target gene in tissues from 40 patients with ESCC. Transwell, Dual-luciferase reporter assay and immunocytochemistry assay were employed to detect the function role of miR-1179 in vitro. We found that miR-1179 was up-regulated in human ESCC tumor tissues. Bioinformatics analysis indicated that SLIT2 acting as a new potential target of miR-1179 which was confirmed by luciferase reporter assay. Down-regulation of miR-1179 suppressed cell invasion in vitro with an increasing level of SLIT2 and ROBO1, besides, the up-regulation of SLIT2 decreased cell invasion through ROBO1. Taken together, these findings will shed light the role to mechanism of miR-1179 in regulating cell invasion via SLIT2/ROBO1 axis.
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Affiliation(s)
- Lixin Jiang
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Yongfang Wang
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Yaxiong Rong
- Department of General Surgery, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Lianhong Xu
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Ying Chu
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Ying Zhang
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
| | - Yonghua Yao
- Department of Clinical Laboratory, Wujin Hospital Affiliated to Jiangsu UniversityChangzhou, China
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Krysan K, Kusko R, Grogan T, O'Hearn J, Reckamp KL, Walser TC, Garon EB, Lenburg ME, Sharma S, Spira AE, Elashoff D, Dubinett SM. PGE2-driven expression of c-Myc and oncomiR-17-92 contributes to apoptosis resistance in NSCLC. Mol Cancer Res 2014; 12:765-74. [PMID: 24469837 DOI: 10.1158/1541-7786.mcr-13-0377] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UNLABELLED Aberrant expression of microRNAs (miRNA) with oncogenic capacities (oncomiRs) has been described for several different malignancies. The first identified oncomiR, miR-17-92, is frequently overexpressed in a variety of cancers and its targets include the tumor suppressor PTEN. The transcription factor c-Myc (MYC) plays a central role in proliferative control and is rapidly upregulated upon mitogenic stimulation. Expression of c-Myc is frequently deregulated in tumors, facilitating proliferation and inhibiting terminal differentiation. The c-Myc-regulated network comprises a large number of transcripts, including those encoding miRNAs. Here, prostaglandin E2 (PGE2) exposure rapidly upregulates the expression of the MYC gene followed by the elevation of miR-17-92 levels, which in turn suppresses PTEN expression, thus enhancing apoptosis resistance in non-small cell lung cancer (NSCLC) cells. Knockdown of MYC expression or the miR-17-92 cluster effectively reverses this outcome. Similarly, miR-17-92 levels are significantly elevated in NSCLC cells ectopically expressing COX-2. Importantly, circulating miR-17-92 was elevated in the blood of patients with lung cancer as compared with subjects at risk for developing lung cancer. Furthermore, in patients treated with celecoxib, miR-17-92 levels were significantly reduced. These data demonstrate that PGE2, abundantly produced by NSCLC and inflammatory cells in the tumor microenvironment, is able to stimulate cell proliferation and promote resistance to pharmacologically induced apoptosis in a c-Myc and miR-17-92-dependent manner. IMPLICATIONS This study describes a novel mechanism, involving c-Myc and miR-17-92, which integrates cell proliferation and apoptosis resistance.
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Affiliation(s)
- Kostyantyn Krysan
- Authors' Affiliations: Departments of Medicine, 2Pathology and Laboratory Medicine, 3Molecular and Medical Pharmacology, 4Anesthesiology, and 5Medicine Statistics Core, David Geffen School of Medicine, University of California, Los Angeles; 6UCLA Jonsson Comprehensive Cancer Center; 7West Los Angeles VA Healthcare System, Los Angeles; 8City of Hope Comprehensive Cancer Center, Duarte, California; and 9Boston University, Boston, Massachusetts
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20
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Abstract
MicroRNAs (miRNAs) are powerful regulators of gene expression at posttranscriptional level and play important roles in many biological processes and in disease. The rapid pace of the emerging field of miRNAs has opened new avenues for development of techniques to quantitatively determine miRNA expression levels in different systems. In this chapter we describe a PCR method for quantification of miRNAs based on a single reverse transcription reaction for all miRNAs combined with real-time PCR with two miRNA-specific DNA primers. This method quantifies synthetic templates over eight orders of magnitude and successfully discriminates miRNAs that differ by one single nucleotide. Due to the usage of DNA primers this method allows higher amplification efficiencies than a similar method based on locked nucleic acid-spiked primers. The high efficiency translates into higher sensitivity and precision in miRNA quantification. Furthermore, the method is easy to perform with common laboratory reagents, which allows miRNA quantification at low cost.
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Affiliation(s)
- Susanna Cirera
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 2., 1870, Frederiksberg, Denmark
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21
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Ma W, Yu C, Zhang W. Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell. Biol Direct 2013; 8:21. [PMID: 23971788 PMCID: PMC3765326 DOI: 10.1186/1745-6150-8-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 08/21/2013] [Indexed: 12/23/2022] Open
Abstract
Background It is now popularly accepted that an “RNA world” existed in early evolution. During division of RNA-based protocells, random distribution of individual genes (simultaneously as ribozymes) between offspring might have resulted in gene loss, especially when the number of gene types increased. Therefore, the emergence of a chromosome carrying linked genes was critical for the prosperity of the RNA world. However, there were quite a few immediate difficulties for this event to occur. For example, a chromosome would be much longer than individual genes, and thus more likely to degrade and less likely to replicate completely; the copying of the chromosome might start at middle sites and be only partial; and, without a complex transcription mechanism, the synthesis of distinct ribozymes would become problematic. Results Inspired by features of viroids, which have been suggested as “living fossils” of the RNA world, we supposed that these difficulties could have been overcome if the chromosome adopted a circular form and small, self-cleaving ribozymes (e.g. the hammer head ribozymes) resided at the sites between genes. Computer simulation using a Monte-Carlo method was conducted to investigate this hypothesis. The simulation shows that an RNA chromosome can spread (increase in quantity and be sustained) in the system if it is a circular one and its linear “transcripts” are readily broken at the sites between genes; the chromosome works as genetic material and ribozymes “coded” by it serve as functional molecules; and both circularity and self-cleavage are important for the spread of the chromosome. Conclusions In the RNA world, circularity and self-cleavage may have been adopted as a strategy to overcome the immediate difficulties for the emergence of a chromosome (with linked genes). The strategy suggested here is very simple and likely to have been used in this early stage of evolution. By demonstrating the possibility of the emergence of an RNA chromosome, this study opens on the prospect of a prosperous RNA world, populated by RNA-based protocells with a number of genes, showing complicated functions. Reviewers This article was reviewed by Sergei Kazakov (nominated by Laura Landweber), Nobuto Takeuchi (nominated by Anthony Poole), and Eugene Koonin.
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Affiliation(s)
- Wentao Ma
- College of Life Sciences, Wuhan University, Wuhan 430072, P,R, China.
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22
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Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X. MicroRNA: Function, Detection, and Bioanalysis. Chem Rev 2013; 113:6207-33. [PMID: 23697835 DOI: 10.1021/cr300362f] [Citation(s) in RCA: 836] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Jianping Lei
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Lin Ding
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqiang Wen
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
| | - Huangxian Ju
- State Key Laboratory of Analytical
Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing 100083, P. R. China
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Kou SJ, Wu XM, Liu Z, Liu YL, Xu Q, Guo WW. Selection and validation of suitable reference genes for miRNA expression normalization by quantitative RT-PCR in citrus somatic embryogenic and adult tissues. PLANT CELL REPORTS 2012; 31:2151-63. [PMID: 22865195 DOI: 10.1007/s00299-012-1325-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 05/09/2023]
Abstract
UNLABELLED miRNAs have recently been reported to modulate somatic embryogenesis (SE), a key pathway of plant regeneration in vitro. For expression level detection and subsequent function dissection of miRNAs in certain biological processes, qRT-PCR is one of the most effective and sensitive techniques, for which suitable reference gene selection is a prerequisite. In this study, three miRNAs and eight non-coding RNAs (ncRNA) were selected as reference candidates, and their expression stability was inspected in developing citrus SE tissues cultured at 20, 25, and 30 °C. Stability of the eight non-miRNA ncRNAs was further validated in five adult tissues without temperature treatment. The best single reference gene for SE tissues was snoR14 or snoRD25, while for the adult tissues the best one was U4; although they were not as stable as the optimal multiple references snoR14 + U6 for SE tissues and snoR14 + U5 for adult tissues. For expression normalization of less abundant miRNAs in SE tissues, miR3954 was assessed as a viable reference. Single reference gene snoR14 outperformed multiple references for the overall SE and adult tissues. As one of the pioneer systematic studies on reference gene identification for plant miRNA normalization, this study benefits future exploration on miRNA function in citrus and provides valuable information for similar studies in other higher plants. KEY MESSAGE Three miRNAs and eight non-coding RNAs were tested as reference candidates on developing citrus SE tissues. Best single references snoR14 or snoRD25 and optimal multiple references snoR14 + U6, snoR14 + U5 were identified.
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Affiliation(s)
- Shu-Jun Kou
- Key Laboratory of Horticultural Plant Biology Ministry of Education, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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24
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Kang K, Zhang X, Liu H, Wang Z, Zhong J, Huang Z, Peng X, Zeng Y, Wang Y, Yang Y, Luo J, Gou D. A novel real-time PCR assay of microRNAs using S-Poly(T), a specific oligo(dT) reverse transcription primer with excellent sensitivity and specificity. PLoS One 2012; 7:e48536. [PMID: 23152780 PMCID: PMC3496722 DOI: 10.1371/journal.pone.0048536] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 09/26/2012] [Indexed: 01/08/2023] Open
Abstract
Background MicroRNAs (miRNAs) are small, non-coding RNAs capable of postranscriptionally regulating gene expression. Accurate expression profiling is crucial for understanding the biological roles of miRNAs, and exploring them as biomarkers of diseases. Methodology/Principal Findings A novel, highly sensitive, and reliable miRNA quantification approach,termed S-Poly(T) miRNA assay, is designed. In this assay, miRNAs are subjected to polyadenylation and reverse transcription with a S-Poly(T) primer that contains a universal reverse primer, a universal Taqman probe, an oligo(dT)11 sequence and six miRNA-specific bases. Individual miRNAs are then amplified by a specific forward primer and a universal reverse primer, and the PCR products are detected by a universal Taqman probe. The S-Poly(T) assay showed a minimum of 4-fold increase in sensitivity as compared with the stem-loop or poly(A)-based methods. A remarkable specificity in discriminating among miRNAs with high sequence similarity was also obtained with this approach. Using this method, we profiled miRNAs in human pulmonary arterial smooth muscle cells (HPASMC) and identified 9 differentially expressed miRNAs associated with hypoxia treatment. Due to its outstanding sensitivity, the number of circulating miRNAs from normal human serum was significantly expanded from 368 to 518. Conclusions/Significance With excellent sensitivity, specificity, and high-throughput, the S-Poly(T) method provides a powerful tool for miRNAs quantification and identification of tissue- or disease-specific miRNA biomarkers.
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Affiliation(s)
- Kang Kang
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People’s Republic of China
| | - Xiaoying Zhang
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Hongtao Liu
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Zhiwei Wang
- Department of Cardiovascular Surgery, Shenzhen Sun Yat-Sen Cardiovascular Hospital, Shenzhen, Guangdong, People’s Republic of China
| | - Jiasheng Zhong
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Zhenting Huang
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Xiao Peng
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yan Zeng
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yuna Wang
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Yi Yang
- School of Medicine, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
| | - Jun Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People’s Republic of China
| | - Deming Gou
- College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, People’s Republic of China
- * E-mail:
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25
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Dallas A, Ilves H, Ge Q, Kumar P, Shorenstein J, Kazakov SA, Cuellar TL, McManus MT, Behlke MA, Johnston BH. Right- and left-loop short shRNAs have distinct and unusual mechanisms of gene silencing. Nucleic Acids Res 2012; 40:9255-71. [PMID: 22810205 PMCID: PMC3467060 DOI: 10.1093/nar/gks662] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Small hairpin RNAs (shRNAs) having duplex lengths of 25–29 bp are normally processed by Dicer into short interfering RNAs (siRNAs) before incorporation into the RNA-induced silencing complex (RISC). However, shRNAs of ≤19 bp [short shRNAs (sshRNAs)] are too short for Dicer to excise their loops, raising questions about their mechanism of action. sshRNAs are designated as L-type or R-type according to whether the loop is positioned 3′ or 5′ to the guide sequence, respectively. Using nucleotide modifications that inhibit RNA cleavage, we show that R- but not L-sshRNAs require loop cleavage for optimum activity. Passenger-arm slicing was found to be important for optimal functioning of L-sshRNAs but much less important for R-sshRNAs that have a cleavable loop. R-sshRNAs could be immunoprecipitated by antibodies to Argonaute-1 (Ago1); complexes with Ago1 contained both intact and loop-cleaved sshRNAs. In contrast, L-sshRNAs were immunoprecipitated with either Ago1 or Ago2 and were predominantly sliced in the passenger arm of the hairpin. However, ‘pre-sliced’ L-sshRNAs were inactive. We conclude that active L-sshRNAs depend on slicing of the passenger arm to facilitate opening of the duplex, whereas R-sshRNAs primarily act via loop cleavage to generate a 5′-phosphate at the 5′-end of the guide strand.
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Affiliation(s)
- Anne Dallas
- SomaGenics, Inc., 2161 Delaware Avenue, Santa Cruz, CA 95060, USA
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26
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Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B. MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci U S A 2012; 109:1790-5. [PMID: 22307647 PMCID: PMC3277104 DOI: 10.1073/pnas.1118282109] [Citation(s) in RCA: 433] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant genomes contain large numbers of cell surface leucine-rich repeat (LRR) and intracellular nucleotide binding (NB)-LRR immune receptors encoded by resistance (R) genes that recognize specific pathogen effectors and trigger resistance responses. The unregulated expression of NB-LRR genes can trigger autoimmunity in the absence of pathogen infection and inhibit plant growth. Despite the potential serious consequence on agricultural production, the mechanisms regulating R-gene expression are not well understood. We identified microRNA (miRNA) progenitor genes precursor transcripts, and two miRNAs [nta-miR6019 (22-nt) and nta-miR6020 (21-nt)] that guide cleavage of transcripts of the Toll and Interleukin-1 receptor-NB-LRR immune receptor N from tobacco that confers resistance to tobacco mosaic virus (TMV). We further showed that cleavage by nta-miR6019 triggers RNA-dependent RNA polymerase 6- and ribonuclease Dicer-like 4-dependent biogenesis of 21-nt secondary siRNAs "in phase" with the 22-nt miR6019 cleavage site. Furthermore, we found that processing of the 22-nt nta-miR6019 depended on an asymmetric bulge caused by mismatch in the nta-miR6019 precursor. Interestingly, coexpression of N with nta-miR6019 and nta-miR6020 resulted in attenuation of N-mediated resistance to TMV, indicating that these miRNAs have functional roles in NB-LRR regulation. Using a bioinformatics approach, we identified six additional 22-nt miRNA and two 21-nt miRNA families from three Solanaceae species-tobacco, tomato, and potato. We show that members of these miRNA families cleave transcripts of predicted functional R genes and trigger production of phased secondary 21-nt siRNAs. Our results demonstrate a conserved role for miRNAs and secondary siRNAs in NB-LRR/LRR immune receptor gene regulation and pathogen resistance in Solanaceae.
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Affiliation(s)
- Feng Li
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
| | - Daniela Pignatta
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
| | - Claire Bendix
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
| | - Jacob O. Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Megan M. Cohn
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Jeffery Tung
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
| | - Haoyu Sun
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
| | | | - Barbara Baker
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
- Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA 94710; and
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27
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Balcells I, Cirera S, Busk PK. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol 2011; 11:70. [PMID: 21702990 PMCID: PMC3135530 DOI: 10.1186/1472-6750-11-70] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 06/25/2011] [Indexed: 01/16/2023] Open
Abstract
Background MicroRNAs are important regulators of gene expression at the post-transcriptional level and play an important role in many biological processes. Due to the important biological role it is of great interest to quantitatively determine their expression level in different biological settings. Results We describe a PCR method for quantification of microRNAs based on a single reverse transcription reaction for all microRNAs combined with real-time PCR with two, microRNA-specific DNA primers. Primer annealing temperatures were optimized by adding a DNA tail to the primers and could be designed with a success rate of 94%. The method was able to quantify synthetic templates over eight orders of magnitude and readily discriminated between microRNAs with single nucleotide differences. Importantly, PCR with DNA primers yielded significantly higher amplification efficiencies of biological samples than a similar method based on locked nucleic acids-spiked primers, which is in agreement with the observation that locked nucleic acid interferes with efficient amplification of short templates. The higher amplification efficiency of DNA primers translates into higher sensitivity and precision in microRNA quantification. Conclusions MiR-specific quantitative RT-PCR with DNA primers is a highly specific, sensitive and accurate method for microRNA quantification.
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Affiliation(s)
- Ingrid Balcells
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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28
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Genome-wide profiling of microRNAs in adipose mesenchymal stem cell differentiation and mouse models of obesity. PLoS One 2011; 6:e21305. [PMID: 21731698 PMCID: PMC3121761 DOI: 10.1371/journal.pone.0021305] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 05/25/2011] [Indexed: 01/14/2023] Open
Abstract
In recent years, there has been accumulating evidence that microRNAs are key regulator molecules of gene expression. The cellular processes that are regulated by microRNAs include e.g. cell proliferation, programmed cell death and cell differentiation. Adipocyte differentiation is a highly regulated cellular process for which several important regulating factors have been discovered, but still not all are known to fully understand the underlying mechanisms. In the present study, we analyzed the expression of 597 microRNAs during the differentiation of mouse mesenchymal stem cells into terminally differentiated adipocytes by real-time RT-PCR. In total, 66 miRNAs were differentially expressed in mesenchymal stem cell-derived adipocytes compared to the undifferentiated progenitor cells. To further study the regulation of these 66 miRNAs in white adipose tissue in vivo and their dependence on PPARγ activity, mouse models of genetically or diet induced obesity as well as a mouse line expressing a dominant negative PPARγ mutant were employed.
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Ciesla M, Skrzypek K, Kozakowska M, Loboda A, Jozkowicz A, Dulak J. MicroRNAs as biomarkers of disease onset. Anal Bioanal Chem 2011; 401:2051-61. [PMID: 21544542 DOI: 10.1007/s00216-011-5001-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/24/2011] [Accepted: 04/08/2011] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNA molecules with the ability to posttranscriptionally regulate gene expression via targeting the 3' untranslated region of messenger RNAs. miRNAs are critical for normal cellular functions such as the regulation of the cell cycle, differentiation, and apoptosis, and they target genes during embryonal and postnatal development, whereas their expression is unbalanced in various pathological states. Importantly, miRNAs are abundantly present in body fluids (e.g., blood), which are routinely examined in patients. These molecules circulate in free and exosome encapsulated forms, and can be efficiently detected and amplified by means of molecular biology tools such as real-time PCR. Together with relative stability, specificity, and reproducibility, they are seen as good candidates for early recognition of the onset of disease. Thus, miRNAs might be considered as biomarkers for many pathological states.
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Affiliation(s)
- Maciej Ciesla
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
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