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Su F, Liu W, Gao K, Chen D, Cheng Y, Li Z. Specific quantitative detection of N 6-methyladenosine at single-base resolution by extension-based isothermal exponential amplification reaction (E-IEXPAR). Anal Chim Acta 2024; 1302:342474. [PMID: 38580403 DOI: 10.1016/j.aca.2024.342474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND N6-methyladenosine (m6A) is a common modification in RNA, crucial for various cellular functions and associated with human diseases. Quantification of m6A at single-base resolution is of great significance for exploring its biological roles and related disease research. However, existing analysis techniques, such as polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP), face challenges like the requirement for thermal cycling or intricate primer design. Therefore, it is urgent to establish a simple, non-thermal cycling and highly sensitive assay for m6A. RESULTS Leveraging the inhibitory effect of m6A on primer elongation and uncomplicated feature of the isothermal exponential amplification reaction (IEXPAR), we have developed an extension-based IEXPAR (E-IEXPAR). This approach requires just a single extension primer and one template, simplifying the design process in comparison to the more complex primer requirements of the LAMP methods. The reactions are conducted at constant temperatures, therby elimiating the use of thermal cycling that needed in PCR methods. By combining IEXPAR with an extension reaction, E-IEXPAR can identify m6A in RNA concentrations as low as 4 fM. We have also introduced a new analytical model to process E-IEXPAR results, which can aid to minimize the impact of unmodified adenine (A) on m6A measurements, enabling accurate m6A quantification in small mixed samples and cellular RNA specimens. SIGNIFICANCE AND NOVELTY E-IEXPAR streamlines m6A detection by eliminating the need for intricate primer design and thermal cycling, which are common in current analytical methods. Its utilization of an extension reaction for the initial identification of m6A, coupled with a novel calculation model tailored to E-IEXPAR outcomes, ensures accurate m6A selectivity in mixed samples. As a result, E-IEXPAR offers a reliable, straightforward, and potentially economical approach for specifically assaying m6A in both biological function studies and clinical research.
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Affiliation(s)
- Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Weiliang Liu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Kejian Gao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Desheng Chen
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis (Hebei University), Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding, 071002, Hebei, PR China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
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Zhang P, Qin K, Gao K, Su F, Wang H, Liu J, Li Z. Multiple thermocycles followed by LAMP with only two primers for ultrasensitive colorimetric viral RNA testing and tracking at single-base resolution. Anal Chim Acta 2023; 1276:341621. [PMID: 37573111 DOI: 10.1016/j.aca.2023.341621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
Rapid, accurate and high throughput measurement of infectious viruses is an urgent need to prevent viral transmission. Loop-mediated isothermal amplification (LAMP) is an attractive isothermal amplification method for nucleic acid detection, especially for point-of-care (POC) testing, but it needs at least four primers and its sensitivity is also limited when integrating with visual detection methods. Herein, by designing only two primers to precisely recognize the four regions of the target, we developed a multiple thermocycles-based LAMP method (MTC-LAMP) for sensitive and specific testing and tracking of viral RNA. We also introduced a novel SYBR Green I (SG)-assisted stable colorimetric assay induced by the amplification products through the charge neutralization effect of positively charged SG toward gold nanoparticles (AuNPs). The ultralow nonspecific background of the double exponential amplification improved the detection sensitivity to near single-molecule level (1 aM, 3 copies in 5 μL solution), which was higher than RT-PCR and RT-LAMP. After adding AuNPs, a significant color difference between target and blank was immediately observed by naked eye. By introducing a peptide nucleic acid (PNA) clamp into our colorimetric MTC-LAMP assay, the specific distinguish of virus variants at single-base resolution was observed without the requirement of any equipment. This assay shows great potential for large-scale screening and tracking of the threatening viruses with ultrahigh sensitivity and pronounced colorimetric output, which is of great importance for pandemic control.
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Affiliation(s)
- Pengbo Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Ke Qin
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Kejian Gao
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Fengxia Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Hui Wang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, China.
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Yang P, Zhang Y, Xia L, Mei J, Fan R, Huang Y, Liu L, Chen W. [MinerVa: A high performance bioinformatic algorithm for the detection of minimal residual disease in solid tumors]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2023; 40:313-319. [PMID: 37139763 DOI: 10.7507/1001-5515.202303039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
How to improve the performance of circulating tumor DNA (ctDNA) signal acquisition and the accuracy to authenticate ultra low-frequency mutation are major challenges of minimal residual disease (MRD) detection in solid tumors. In this study, we developed a new MRD bioinformatics algorithm, namely multi-variant joint confidence analysis (MinerVa), and tested this algorithm both in contrived ctDNA standards and plasma DNA samples of patients with early non-small cell lung cancer (NSCLC). Our results showed that the specificity of multi-variant tracking of MinerVa algorithm ranged from 99.62% to 99.70%, and when tracking 30 variants, variant signals could be detected as low as 6.3 × 10 -5 variant abundance. Furthermore, in a cohort of 27 NSCLC patients, the specificity of ctDNA-MRD for recurrence monitoring was 100%, and the sensitivity was 78.6%. These findings indicate that the MinerVa algorithm can efficiently capture ctDNA signals in blood samples and exhibit high accuracy in MRD detection.
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Affiliation(s)
- Piao Yang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu 214000, P. R. China
| | - Yaxi Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu 214000, P. R. China
| | - Liang Xia
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Jiandong Mei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Rui Fan
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu 214000, P. R. China
| | - Yu Huang
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu 214000, P. R. China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Weizhi Chen
- Genecast Biotechnology Co., Ltd, Wuxi, Jiangsu 214000, P. R. China
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Robles-Remacho A, Luque-Gonzalez MA, López-Delgado FJ, Guardia-Monteagudo JJ, Fara MA, Pernagallo S, Sanchez-Martin RM, Diaz-Mochon JJ. Direct detection of alpha satellite DNA with single-base resolution by using abasic Peptide Nucleic Acids and Fluorescent in situ Hybridization. Biosens Bioelectron 2023; 219:114770. [PMID: 36270082 DOI: 10.1016/j.bios.2022.114770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
The detection of repetitive sequences with single-base resolution is becoming increasingly important aiming to understand the biological implications of genomic variation in these sequences. However, there is a lack of techniques to experimentally validate sequencing data from repetitive sequences obtained by Next-Generation Sequencing methods, especially in the case of Single-Nucleotide Variations (SNVs). That is one of the reasons why repetitive sequences have been poorly studied and excluded from most genomic studies. Therefore, in addition to sequencing data, there is an urgent need for efficient validation methods of genomic variation in these sequences. Herein we report the development of chemFISH, an alternative method for the detection of SNVs in repetitive sequences. ChemFISH is an innovative method based on dynamic chemistry labelling and abasic Peptide Nucleic Acid (PNA) probes to detect in situ the α-satellite DNA, organized in tandem repeats, with single-base resolution in a direct and rapid reaction. With this approach, we detected by microscopy the α-satellite DNA in a variety of human cell lines, we quantified the detection showing a low coefficient of variation among samples (13.16%-25.33%) and we detected single-base specificity with high sensitivity (82.41%-88.82%). These results indicate that chemFISH can serve as a rapid method to validate previously detected SNVs in sequencing data, as well as to find novel SNVs in repetitive sequences. Furthermore, the versatile chemistry behind chemFISH can lead to develop novel molecular assays for the in situ detection of nucleic acids.
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Affiliation(s)
- Agustín Robles-Remacho
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain
| | - M Angelica Luque-Gonzalez
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain
| | - F Javier López-Delgado
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Juan J Guardia-Monteagudo
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Mario Antonio Fara
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Salvatore Pernagallo
- DESTINA Genomica S.L, PTS Granada, Avenida de la Innovación 1, Edificio BIC, Armilla, 18100, Granada, Spain
| | - Rosario M Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain.
| | - Juan Jose Diaz-Mochon
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Avenida de la Ilustración, 114, 18016, Granada, Spain; Department of Medicinal and Organic Chemistry, School of Pharmacy, University of Granada, Campus Cartuja s/n, 18071, Granada, Spain; Biosanitary Research Institute of Granada (ibs.GRANADA), University Hospital of Granada/University of Granada, Avenida del Conocimiento, s/n, 18016, Granada, Spain.
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Ding JH, Chen MY, Xie NB, Xie C, Xiong N, He JG, Wang J, Guo C, Feng YQ, Yuan BF. Quantitative and site-specific detection of inosine modification in RNA by acrylonitrile labeling-mediated elongation stalling. Biosens Bioelectron 2023; 219:114821. [PMID: 36279821 DOI: 10.1016/j.bios.2022.114821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022]
Abstract
RNA molecules contain diverse modifications that play crucial roles in a wide variety of biological processes. Inosine is one of the most prevalent modifications in RNA and dysregulation of inosine is correlated with many human diseases. Herein, we established an acrylonitrile labeling-mediated elongation stalling (ALES) method for quantitative and site-specific detection of inosine in RNA from biological samples. In ALES method, inosine is selectively cyanoethylated with acrylonitrile to form N1-cyanoethylinosine (ce1I) through a Michael addition reaction. The N1-cyanoethyl group of ce1I compromises the hydrogen bond between ce1I and other nucleobases, leading to the stalling of reverse transcription at original inosine site. This specific property of stalling at inosine site could be evaluated by subsequent real-time quantitative PCR (qPCR). With the proposed ALES method, we found the significantly increased level of inosine at position Chr1:63117284 of Ino80dos RNA of multiple tissues from sleep-deprived mice compared to the control mice. This is the first report on the investigation of inosine modification in sleep-deprived mice, which may open up new direction for deciphering insomnia from RNA modifications. In addition, we found the decreased level of inosine at GluA2 Q/R site (Chr4:157336723) in glioma tissues, indicating the decreased level of inosine at GluA2 Q/R site may serve as potential indicator for the diagnosis of glioma. Taken together, the proposed ALES method is capable of quantitative and site-specific detection of inosine in RNA, which provides a valuable tool to uncover the functions of inosine in human diseases.
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Affiliation(s)
- Jiang-Hui Ding
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Meng-Yuan Chen
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Neng-Bin Xie
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Conghua Xie
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Nanxiang Xiong
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China
| | - Jin-Gang He
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, 430071, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, 430071, Wuhan, China; University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yu-Qi Feng
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Bi-Feng Yuan
- School of Public Health, College of Chemistry and Molecular Sciences, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China; Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan, 430071, China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, 430071, China.
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Zhang M, Sun H, Li K, Xiao Y, Yi C. m 6Am RNA modification detection by m 6Am-seq. Methods 2021; 203:242-248. [PMID: 34624505 DOI: 10.1016/j.ymeth.2021.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022] Open
Abstract
Reversible and dynamic RNA modifications play important roles in fine-tuning gene expression. N6, 2'-O-dimethyladenosine (m6Am), a terminal modification at mRNA cap, mediates various biological effects. However, limitations of the current m6Am detection methods lead to a lack of potential applications. Here, we describe a specific and sensitive method, termed m6Am-seq, that can detect m6Am at single-base resolution. m6Am-seq is based on optimized in-vitro demethylation assay and RNA immunoprecipitation, which can distinguish m6Am from 5'-UTR m6A. We provide a step by step protocol to perform m6Am-seq, including experimental procedures and sequencing data analysis. Collectively, we describe m6Am-seq, a robust tool to reveal both m6Am and 5'-UTR m6A methylome, enabling further functional and mechanistic study of m6Am modification.
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Affiliation(s)
- Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Ye Xiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Chen HX, Zhang Z, Ma DZ, Chen LQ, Luo GZ. Mapping single-nucleotide m 6A by m 6A-REF-seq. Methods 2021:S1046-2023(21)00175-4. [PMID: 34174388 DOI: 10.1016/j.ymeth.2021.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
The past few years have witnessed rapid progress in the field of RNA modifications. As the most prevailing modification on eukaryotic mRNA, m6A is characterized to play a vital role in various cellular activities. However, limitations of the detection method impede functional studies of m6A. Here we introduce m6A-REF-seq, a powerful and straightforward method to identify m6A at single-nucleotide resolution. m6A-REF-seq relies on the recognition of RNA endonuclease MazF towards m6A at the ACA motif, providing an orthogonal method independent of the m6A antibody being adopted by most of current methods. We describe a detailed protocol to perform m6A-REF-seq, including NGS library construction and sequencing data analysis. In particular, we describe an optimized assay to validate individual m6A sites identified by m6A-REF-seq, which can also be applied to detect any candidate m6A sites.
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Zhang N, Shi S, Yuan X, Ni W, Wang X, Yoo B, Jia TZ, Li W, Zhang S. A General LC-MS-Based Method for Direct and De Novo Sequencing of RNA Mixtures Containing both Canonical and Modified Nucleotides. Methods Mol Biol 2021; 2298:261-277. [PMID: 34085251 DOI: 10.1007/978-1-0716-1374-0_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry (MS)-based sequencing has advantages in direct sequencing of RNA, compared to cDNA-based RNA sequencing methods, as it is completely independent of enzymes and base complementarity errors in sample preparation. In addition, it allows for sequencing of different RNA modifications in a single study, rather than just one specific modification type per study. However, many technical challenges remain in de novo MS sequencing of RNA, making it difficult to MS sequence mixed RNAs or to differentiate isomeric modifications such as pseudouridine (Ψ) from uridine (U). Our recent study incorporates a two-dimensional hydrophobic end labeling strategy into MS-based sequencing (2D-HELS MS Seq) to systematically address the current challenges in MS sequencing of RNA, making it possible to directly and de novo sequence purified single RNA and mixed RNA containing both canonical and modified nucleotides. Here, we describe the method to sequence representative single-RNA and mixed-RNA oligonucleotides, each with a different sequence and/or containing modified nucleotides such as Ψ and 5-methylcytosine (m5C), using 2D-HELS MS Seq.
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Affiliation(s)
- Ning Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY, USA.,Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Shundi Shi
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Xiaohong Yuan
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY, USA
| | - Wenhao Ni
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY, USA
| | - Xuanting Wang
- Department of Chemical Engineering, Columbia University, New York, NY, USA
| | - Barney Yoo
- Department of Chemistry, Hunter College, City University of New York, New York, NY, USA
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - Wenjia Li
- Department of Computer Science, New York Institute of Technology, New York, NY, USA
| | - Shenglong Zhang
- Department of Biological and Chemical Sciences, New York Institute of Technology, New York, NY, USA.
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Jia Z, Shi Y, Zhang L, Ren Y, Wang T, Xing L, Zhang B, Gao G, Bu R. DNA methylome profiling at single-base resolution through bisulfite sequencing of 5mC-immunoprecipitated DNA. BMC Biotechnol 2018; 18:7. [PMID: 29409498 DOI: 10.1186/s12896-017-0409-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Abstract
Background Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as “junk DNA”. Methods In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment. Because many researchers are interested in investigating the methylation of functional regions such as promoters and gene bodies, we have also developed a novel alternative method named MRB-seq, which can be used to investigate the DNA methylation of functional regions by removing the repeats with Cot-1 DNA. Results In this study, we have developed MB-seq, a novel DNA methylome profiling technology combining MeDIP-seq with bisulfite conversion, which can precisely detect the 5mC sites and determine their DNA methylation level at single-base resolution in a cost-effective way. In addition, we have developed a new alternative method, MRB-seq (MeDIP-repetitive elements removal-bisulfite sequencing), which interrogates 5mCs in functional regions by depleting nearly half of repeat fragments enriched by MeDIP. Comparing MB-seq and MRB-seq to whole-genome BS-seq using the same batch of DNA from YH peripheral blood mononuclear cells. We found that the sequencing data of MB-seq and MRB-seq almost reaches saturation after generating 7–8 Gbp data, whereas BS-seq requires about 100 Gbp data to achieve the same effect. In comparison to MeDIP-seq and BS-seq, MB-seq offers several key advantages, including single-base resolution, discriminating the methylated sites within a CpG and non-CpG pattern and overcoming the false positive of MeDIP-seq due to the non-specific binding of 5-methylcytidine antibody to genomic fragments. Conclusion Our novel developed method MB-seq can accelerate the decoding process of DNA methylation mechanism in human diseases because it requires 7–8 Gbp data to measure human methylome with enough coverage and sequencing depth, affording it a direct and practical application in the study of multiple samples. In addition, we have also provided a novel alternative MRB-seq method, which removes most repetitive sequences and allows researchers to genome-wide characterize DNA methylation of functional regions. Electronic supplementary material The online version of this article (10.1186/s12896-017-0409-7) contains supplementary material, which is available to authorized users.
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Abstract
DNA methylation plays an important role in the regulation of the expression of transposons and genes. Various methods have been developed to assay DNA methylation levels. Bisulfite sequencing is considered to be the "gold standard" for single-base resolution measurement of DNA methylation levels. Coupled with next-generation sequencing, whole-genome bisulfite sequencing (WGBS) allows DNA methylation to be evaluated at a genome-wide scale. Here, we described a protocol for WGBS in plant species with large genomes. This protocol has been successfully applied to assay genome-wide DNA methylation levels in maize and barley. This protocol has also been successfully coupled with sequence capture technology to assay DNA methylation levels in a targeted set of genomic regions.
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Verga D, Welter M, Marx A. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides. Bioorg Med Chem Lett 2015; 26:841-844. [PMID: 26774580 DOI: 10.1016/j.bmcl.2015.12.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
Abstract
DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.
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Affiliation(s)
- Daniela Verga
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Moritz Welter
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
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