1
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Makhamreh A, Tavakoli S, Fallahi A, Kang X, Gamper H, Nabizadehmashhadtoroghi M, Jain M, Hou YM, Rouhanifard SH, Wanunu M. Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific: quantification requires dedicated synthetic controls. Sci Rep 2024; 14:22457. [PMID: 39341872 PMCID: PMC11438862 DOI: 10.1038/s41598-024-72994-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 09/11/2024] [Indexed: 10/01/2024] Open
Abstract
Chemical modifications to mRNA respond dynamically to environmental cues and are important modulators of gene expression. Nanopore direct RNA sequencing has been applied for assessing the presence of pseudouridine (ψ) modifications through basecalling errors and signal analysis. These approaches strongly depend on the sequence context around the modification, and the occupancies derived from these measurements are not quantitative. In this work, we combine direct RNA sequencing of synthetic RNAs bearing site-specific modifications and supervised machine learning models (ModQuant) to achieve near-analytical, site-specific ψ quantification. Our models demonstrate that the ionic current signal features important for accurate ψ classification are sequence dependent and encompass information extending beyond n + 2 and n - 2 nucleotides from the ψ site. This is contradictory to current models, which assume that accurate ψ classification can be achieved with signal information confined to the 5-nucleotide k-mer window (n + 2 and n - 2 nucleotides from the ψ site). We applied our models to quantitatively profile ψ occupancy in five mRNA sites in datasets from seven human cell lines, demonstrating conserved and variable sites. Our study motivates a wider pipeline that uses ground-truth RNA control sets with site-specific modifications for quantitative profiling of RNA modifications. The ModQuant pipeline and guide are freely available at https://github.com/wanunulab/ModQuant .
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Affiliation(s)
- Amr Makhamreh
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Sepideh Tavakoli
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Ali Fallahi
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Xinqi Kang
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Miten Jain
- Department of Bioengineering, Northeastern University, Boston, MA, USA
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Meni Wanunu
- Department of Bioengineering, Northeastern University, Boston, MA, USA.
- Department of Physics, Northeastern University, Boston, MA, USA.
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2
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Ali I, Ali MM, Liu Q, Hu L. Unraveling Clinical Glycoproteome by Integrating Affinity Enrichment with Nanopore Sequencing. Chembiochem 2024:e202400419. [PMID: 39234982 DOI: 10.1002/cbic.202400419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/28/2024] [Indexed: 09/06/2024]
Abstract
This prospect explores the integration of enrichment strategies with nanopore detection to advance clinical glycoproteomics. Glycoproteins, crucial for understanding biological processes, pose challenges due to their low abundance and structural diversity. Enrichment techniques using lectin affinity, boronate affinity, and hydrazide chemistry and especially molecular imprinted polymers may selectively and specifically isolate glycoproteins from complex samples, while nanopore technology enables label-free, real-time, and single-molecule analysis. This approach holds promise for disease-related glycosylation studies, biomarker discovery, personalized medicine, and streamlined clinical analysis. Standardization, optimization, and data analysis remain challenges, requiring interdisciplinary collaborations and technological advancements. Overall, this integration may offer transformative potential for clinical glycoproteomics and innovative diagnostic and therapeutic strategies.
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Affiliation(s)
- Irshad Ali
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, China
| | - Muhammad Mujahid Ali
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, China
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, US
| | - Quanjun Liu
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, China
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University, Changchun, 130012, China
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3
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Tan L, Guo Z, Shao Y, Ye L, Wang M, Deng X, Chen S, Li R. Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing. Nucleic Acids Res 2024; 52:8746-8762. [PMID: 39011882 PMCID: PMC11347139 DOI: 10.1093/nar/gkae601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Affiliation(s)
- Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yanwen Shao
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Miaomiao Wang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Deng
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong, China
| | - Runsheng Li
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, 518057, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
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4
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Gong B, Li D, Łabaj PP, Pan B, Novoradovskaya N, Thierry-Mieg D, Thierry-Mieg J, Chen G, Bergstrom Lucas A, LoCoco JS, Richmond TA, Tseng E, Kusko R, Happe S, Mercer TR, Pabón-Peña C, Salmans M, Tilgner HU, Xiao W, Johann DJ, Jones W, Tong W, Mason CE, Kreil DP, Xu J. Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing. Sci Data 2024; 11:892. [PMID: 39152166 PMCID: PMC11329654 DOI: 10.1038/s41597-024-03741-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
Next-generation sequencing (NGS) has revolutionized genomic research by enabling high-throughput, cost-effective genome and transcriptome sequencing accelerating personalized medicine for complex diseases, including cancer. Whole genome/transcriptome sequencing (WGS/WTS) provides comprehensive insights, while targeted sequencing is more cost-effective and sensitive. In comparison to short-read sequencing, which still dominates the field due to high speed and cost-effectiveness, long-read sequencing can overcome alignment limitations and better discriminate similar sequences from alternative transcripts or repetitive regions. Hybrid sequencing combines the best strengths of different technologies for a more comprehensive view of genomic/transcriptomic variations. Understanding each technology's strengths and limitations is critical for translating cutting-edge technologies into clinical applications. In this study, we sequenced DNA and RNA libraries of reference samples using various targeted DNA and RNA panels and the whole transcriptome on both short-read and long-read platforms. This study design enables a comprehensive analysis of sequencing technologies, targeting protocols, and library preparation methods. Our expanded profiling landscape establishes a reference point for assessing current sequencing technologies, facilitating informed decision-making in genomic research and precision medicine.
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Affiliation(s)
- Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | | | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, 5323 Harry Hine Blvd., Dallas, TX, 75390, USA
| | - Anne Bergstrom Lucas
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
| | | | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., 4300 Hacienda Dr., Pleasanton, CA, 94588, USA
| | | | - Rebecca Kusko
- Cellino Bio, 750 Main Street, Cambridge, MA, 02143, USA
| | - Scott Happe
- Agilent Technologies, Inc., 1834 State Hwy 71 West, Cedar Creek, TX, 78612, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Carlos Pabón-Peña
- Agilent Technologies, Inc., 5301 Stevens Creek Blvd., Santa Clara, CA, 95051, USA
| | | | - Hagen U Tilgner
- Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Donald J Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, 4301W Markham St., Little Rock, AR, 72205, USA
| | - Wendell Jones
- Q squared Solutions Genomics, 2400 Elis Road, Durham, NC, 27703, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| | - David P Kreil
- Bioinformatics Research, Institute of Molecular Biotechnology, Boku University Vienna, Vienna, Austria.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.
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5
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Sethi AJ, Acera Mateos P, Hayashi R, Shirokikh NE, Eyras E. R2Dtool: integration and visualization of isoform-resolved RNA features. Bioinformatics 2024; 40:btae495. [PMID: 39110520 PMCID: PMC11338438 DOI: 10.1093/bioinformatics/btae495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 07/06/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
MOTIVATION Long-read RNA sequencing enables the mapping of RNA modifications, structures, and protein-interaction sites at the resolution of individual transcript isoforms. To understand the functions of these RNA features, it is critical to analyze them in the context of transcriptomic and genomic annotations, such as open reading frames and splice junctions. RESULTS We have developed R2Dtool, a bioinformatics tool that integrates transcript-mapped information with transcript and genome annotations, allowing for the isoform-resolved analytics and graphical representation of RNA features in their genomic context. We illustrate R2Dtool's capability to integrate and expedite RNA feature analysis using epitranscriptomics data. R2Dtool facilitates the comprehensive analysis and interpretation of alternative transcript isoforms. AVAILABILITY AND IMPLEMENTATION R2Dtool is freely available under the MIT license at github.com/comprna/R2Dtool.
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Affiliation(s)
- Aditya J Sethi
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Acton ACT 2601, Australia
| | - Pablo Acera Mateos
- Children’s Cancer Institute, Lowy Cancer Centre, University of New South Wales, Sydney, Kensington NSW 2033, Australia
| | - Rippei Hayashi
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
| | - Nikolay E Shirokikh
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
| | - Eduardo Eyras
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- Centre for Computational Biomedical Sciences, John Curtin School of Medical Research, Australian National University, Canberra, Acton ACT 2601, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Acton ACT 2601, Australia
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6
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Samarakoon H, Liyanage K, Ferguson JM, Parameswaran S, Gamaarachchi H, Deveson IW. Interactive visualization of nanopore sequencing signal data with Squigualiser. Bioinformatics 2024; 40:btae501. [PMID: 39137136 PMCID: PMC11335371 DOI: 10.1093/bioinformatics/btae501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/11/2024] [Indexed: 08/15/2024] Open
Abstract
MOTIVATION Nanopore sequencing current signal data can be 'basecalled' into sequence information or analysed directly, with the capacity to identify diverse molecular features, such as DNA/RNA base modifications and secondary structures. However, raw signal data is large and complex, and there is a need for improved visualization strategies to facilitate signal analysis, exploration and tool development. RESULTS Squigualiser (Squiggle visualiser) is a toolkit for intuitive, interactive visualization of sequence-aligned signal data, which currently supports both DNA and RNA sequencing data from Oxford Nanopore Technologies instruments. Squigualiser is compatible with a wide range of alternative signal-alignment software packages and enables visualization of both signal-to-read and signal-to-reference aligned data at single-base resolution. Squigualiser generates an interactive signal browser view (HTML file), in which the user can navigate across a genome/transcriptome region and customize the display. Multiple independent reads are integrated into a 'signal pileup' format and different datasets can be displayed as parallel tracks. Although other methods exist, Squigualiser provides the community with a software package purpose-built for raw signal data visualization, incorporating a range of new and existing features into a unified platform. AVAILABILITY AND IMPLEMENTATION Squigualiser is an open-source package under an MIT licence: https://github.com/hiruna72/squigualiser. The software was developed using Python 3.8 and can be installed with pip or bioconda or executed directly using prebuilt binaries provided with each release.
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Affiliation(s)
- Hiruna Samarakoon
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Kisaru Liyanage
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - James M Ferguson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Sri Parameswaran
- School of Electrical and Information Engineering, University of Sydney, Sydney, NSW 2008, Australia
| | - Hasindu Gamaarachchi
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
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7
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White LK, Dobson K, del Pozo S, Bilodeaux JM, Andersen SE, Baldwin A, Barrington C, Körtel N, Martinez-Seidel F, Strugar SM, Watt KE, Mukherjee N, Hesselberth JR. Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604651. [PMID: 39091754 PMCID: PMC11291079 DOI: 10.1101/2024.07.23.604651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Transfer RNAs are the fundamental adapter molecules of protein synthesis and the most abundant and heterogeneous class of noncoding RNA molecules in cells. The study of tRNA repertoires remains challenging, complicated by the presence of dozens of post transcriptional modifications. Nanopore sequencing is an emerging technology with promise for both tRNA sequencing and the detection of RNA modifications; however, such studies have been limited by the throughput and accuracy of direct RNA sequencing methods. Moreover, detection of the complete set of tRNA modifications by nanopore sequencing remains challenging. Here we show that recent updates to nanopore direct RNA sequencing chemistry (RNA004) combined with our own optimizations to tRNA sequencing protocols and analysis workflows enable high throughput coverage of tRNA molecules and characterization of nanopore signals produced by 43 distinct RNA modifications. We share best practices and protocols for nanopore sequencing of tRNA and further report successful detection of low abundance mitochondrial and viral tRNAs, providing proof of concept for use of nanopore sequencing to study tRNA populations in the context of infection and organelle biology. This work provides a roadmap to guide future efforts towards de novo detection of RNA modifications across multiple organisms using nanopore sequencing.
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Affiliation(s)
- Laura K. White
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Kezia Dobson
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Samantha del Pozo
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Jill M. Bilodeaux
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Shelby E. Andersen
- Department of Microbiology and Immunology, University of Colorado School of Medicine, Aurora CO 80045
| | - Amber Baldwin
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Chloe Barrington
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Nadine Körtel
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Federico Martinez-Seidel
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Saylor M. Strugar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Kristin E.N. Watt
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora CO 80045
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora CO 80045
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8
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Wiswedel R, Bui ATN, Kim J, Lee MK. Beta-Barrel Nanopores as Diagnostic Sensors: An Engineering Perspective. BIOSENSORS 2024; 14:345. [PMID: 39056622 PMCID: PMC11274599 DOI: 10.3390/bios14070345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/13/2024] [Accepted: 07/14/2024] [Indexed: 07/28/2024]
Abstract
Biological nanopores are ultrasensitive and highly attractive platforms for disease diagnostics, including the sequencing of viral and microbial genes and the detection of biomarkers and pathogens. To utilize biological nanopores as diagnostic sensors, they have been engineered through various methods resulting in the accurate and highly sensitive detection of biomarkers and disease-related biomolecules. Among diverse biological nanopores, the β-barrel-containing nanopores have advantages in nanopore engineering because of their robust structure, making them well-suited for modifications. In this review, we highlight the engineering approaches for β-barrel-containing nanopores used in single-molecule sensing for applications in early diagnosis and prognosis. In the highlighted studies, β-barrel nanopores can be modified by genetic mutation to change the structure; alter charge distributions; or add enzymes, aptamers, and protein probes to enhance sensitivity and accuracy. Furthermore, this review discusses challenges and future perspectives for advancing nanopore-based diagnostic sensors.
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Affiliation(s)
- Rani Wiswedel
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Anh Thi Ngoc Bui
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
| | - Jinhyung Kim
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Mi-Kyung Lee
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; (R.W.); (A.T.N.B.); (J.K.)
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
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9
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Nova IC, Craig JM, Mazumder A, Laszlo AH, Derrington IM, Noakes MT, Brinkerhoff H, Yang S, Vahedian-Movahed H, Li L, Zhang Y, Bowman JL, Huang JR, Mount JW, Ebright RH, Gundlach JH. Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase. Proc Natl Acad Sci U S A 2024; 121:e2321017121. [PMID: 38990947 PMCID: PMC11260103 DOI: 10.1073/pnas.2321017121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/23/2024] [Indexed: 07/13/2024] Open
Abstract
RNA polymerases (RNAPs) carry out the first step in the central dogma of molecular biology by transcribing DNA into RNA. Despite their importance, much about how RNAPs work remains unclear, in part because the small (3.4 Angstrom) and fast (~40 ms/nt) steps during transcription were difficult to resolve. Here, we used high-resolution nanopore tweezers to observe the motion of single Escherichia coli RNAP molecules as it transcribes DNA ~1,000 times improved temporal resolution, resolving single-nucleotide and fractional-nucleotide steps of individual RNAPs at saturating nucleoside triphosphate concentrations. We analyzed RNAP during processive transcription elongation and sequence-dependent pausing at the yrbL elemental pause sequence. Each time RNAP encounters the yrbL elemental pause sequence, it rapidly interconverts between five translocational states, residing predominantly in a half-translocated state. The kinetics and force-dependence of this half-translocated state indicate it is a functional intermediate between pre- and post-translocated states. Using structural and kinetics data, we show that, in the half-translocated and post-translocated states, sequence-specific protein-DNA interaction occurs between RNAP and a guanine base at the downstream end of the transcription bubble (core recognition element). Kinetic data show that this interaction stabilizes the half-translocated and post-translocated states relative to the pre-translocated state. We develop a kinetic model for RNAP at the yrbL pause and discuss this in the context of key structural features.
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Affiliation(s)
- Ian C. Nova
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Abhishek Mazumder
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Andrew H. Laszlo
- Department of Physics, University of Washington, Seattle, WA98195
| | | | | | | | - Shuya Yang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | | | - Lingting Li
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai200032, China
| | | | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA98195
| | | | - Richard H. Ebright
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ08854
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA98195
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10
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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11
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Gribling-Burrer AS, Bohn P, Smyth RP. Isoform-specific RNA structure determination using Nano-DMS-MaP. Nat Protoc 2024; 19:1835-1865. [PMID: 38347203 DOI: 10.1038/s41596-024-00959-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/12/2023] [Indexed: 06/12/2024]
Abstract
RNA structure determination is essential to understand how RNA carries out its diverse biological functions. In cells, RNA isoforms are readily expressed with partial variations within their sequences due, for example, to alternative splicing, heterogeneity in the transcription start site, RNA processing or differential termination/polyadenylation. Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) is a method for in situ isoform-specific RNA structure determination. Unlike similar methods that rely on short sequencing reads, Nano-DMS-MaP employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules to reveal their previously hidden structural differences. This Protocol describes the development and applications of Nano-DMS-MaP and outlines the main considerations for designing and implementing a successful experiment: from bench to data analysis. In cell probing experiments can be carried out by an experienced molecular biologist in 3-4 d. Data analysis requires good knowledge of command line tools and Python scripts and requires a further 3-5 d.
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Affiliation(s)
- Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Faculty of Medicine, University of Würzburg, Würzburg, Germany.
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12
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Kumari P, Kaur M, Dindhoria K, Ashford B, Amarasinghe SL, Thind AS. Advances in long-read single-cell transcriptomics. Hum Genet 2024:10.1007/s00439-024-02678-x. [PMID: 38787419 DOI: 10.1007/s00439-024-02678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
Long-read single-cell transcriptomics (scRNA-Seq) is revolutionizing the way we profile heterogeneity in disease. Traditional short-read scRNA-Seq methods are limited in their ability to provide complete transcript coverage, resolve isoforms, and identify novel transcripts. The scRNA-Seq protocols developed for long-read sequencing platforms overcome these limitations by enabling the characterization of full-length transcripts. Long-read scRNA-Seq techniques initially suffered from comparatively poor accuracy compared to short read scRNA-Seq. However, with improvements in accuracy, accessibility, and cost efficiency, long-reads are gaining popularity in the field of scRNA-Seq. This review details the advances in long-read scRNA-Seq, with an emphasis on library preparation protocols and downstream bioinformatics analysis tools.
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Affiliation(s)
- Pallawi Kumari
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Manmeet Kaur
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Kiran Dindhoria
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Bruce Ashford
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia
| | - Shanika L Amarasinghe
- Monash Biomedical Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Walter and Eliza Hall Institute of Medical Research, 1G, Royal Parade, Parkville, VIC, 3025, Australia
| | - Amarinder Singh Thind
- Illawarra Shoalhaven Local Health District (ISLHD), NSW Health, Wollongong, NSW, Australia.
- The School of Chemistry and Molecular Bioscience (SCMB), University of Wollongong, Loftus St, Wollongong, NSW, 2500, Australia.
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13
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Wu Y, Shao W, Yan M, Wang Y, Xu P, Huang G, Li X, Gregory BD, Yang J, Wang H, Yu X. Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing. Nat Commun 2024; 15:4049. [PMID: 38744925 PMCID: PMC11094168 DOI: 10.1038/s41467-024-48437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m6A and m5C modification sites. Furthermore, we perform transfer learning for identifying other modifications such as m7G, Ψ, and inosine, significantly reducing training data size and running time without compromising performance. Finally, we apply TandemMod to identify 3 types of RNA modifications in rice grown in different environments, demonstrating its applicability across species and conditions. In summary, we provide a resource with ground-truth labels that can serve as benchmark datasets for nanopore-based modification identification methods, and TandemMod for identifying diverse RNA modifications using a single DRS sample.
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Affiliation(s)
- You Wu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenna Shao
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yuqin Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Pengfei Xu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqiang Huang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaofei Li
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Chenshan Scientific Research Center of CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China.
| | - Hongxia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
- Chenshan Scientific Research Center of CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 201602, China.
| | - Xiang Yu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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14
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Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m 6As. Nat Microbiol 2024; 9:1340-1355. [PMID: 38605174 PMCID: PMC11087264 DOI: 10.1038/s41564-024-01638-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 02/15/2024] [Indexed: 04/13/2024]
Abstract
Although the significance of chemical modifications on RNA is acknowledged, the evolutionary benefits and specific roles in human immunodeficiency virus (HIV-1) replication remain elusive. Most studies have provided only population-averaged values of modifications for fragmented RNAs at low resolution and have relied on indirect analyses of phenotypic effects by perturbing host effectors. Here we analysed chemical modifications on HIV-1 RNAs at the full-length, single RNA level and nucleotide resolution using direct RNA sequencing methods. Our data reveal an unexpectedly simple HIV-1 modification landscape, highlighting three predominant N6-methyladenosine (m6A) modifications near the 3' end. More densely installed in spliced viral messenger RNAs than in genomic RNAs, these m6As play a crucial role in maintaining normal levels of HIV-1 RNA splicing and translation. HIV-1 generates diverse RNA subspecies with distinct m6A ensembles, and maintaining multiple of these m6As on its RNAs provides additional stability and resilience to HIV-1 replication, suggesting an unexplored viral RNA-level evolutionary strategy.
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Affiliation(s)
- Alice Baek
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Ga-Eun Lee
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Sarah Golconda
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Asif Rayhan
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Anastasios A Manganaris
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
- Department of Computer Science and Engineering, Ohio State University, Columbus, OH, USA
| | - Shuliang Chen
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Nagaraja Tirumuru
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
| | - Hannah Yu
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Shihyoung Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Christopher Kimmel
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA
| | - Olivier Zablocki
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Matthew B Sullivan
- Center of Microbiome Science, Ohio State University, Columbus, OH, USA
- Department of Microbiology, Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA
| | - Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sanggu Kim
- Center for Retrovirus Research, Ohio State University, Columbus, OH, USA.
- Department of Veterinary Biosciences, Ohio State University, Columbus, OH, USA.
- Infectious Diseases Institute, Ohio State University, Columbus, OH, USA.
- Translational Data Analytics Institute, Ohio State University, Columbus, OH, USA.
- Center for RNA Biology, Ohio State University, Columbus, OH, USA.
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15
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Grasso L, Fonzino A, Manzari C, Leonardi T, Picardi E, Gissi C, Lazzaro F, Pesole G, Muzi-Falconi M. Detection of ribonucleotides embedded in DNA by Nanopore sequencing. Commun Biol 2024; 7:491. [PMID: 38654143 DOI: 10.1038/s42003-024-06077-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Ribonucleotides represent the most common non-canonical nucleotides found in eukaryotic genomes. The sources of chromosome-embedded ribonucleotides and the mechanisms by which unrepaired rNMPs trigger genome instability and human pathologies are not fully understood. The available sequencing technologies only allow to indirectly deduce the genomic location of rNMPs. Oxford Nanopore Technologies (ONT) may overcome such limitation, revealing the sites of rNMPs incorporation in genomic DNA directly from raw sequencing signals. We synthesized two types of DNA molecules containing rNMPs at known or random positions and we developed data analysis pipelines for DNA-embedded ribonucleotides detection by ONT. We report that ONT can identify all four ribonucleotides incorporated in DNA by capturing rNMPs-specific alterations in nucleotide alignment features, current intensity, and dwell time. We propose that ONT may be successfully employed to directly map rNMPs in genomic DNA and we suggest a strategy to build an ad hoc basecaller to analyse native genomes.
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Affiliation(s)
- Lavinia Grasso
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Adriano Fonzino
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
| | - Caterina Manzari
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso Leonardi
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Via Adamello 16, 20139, Milano, Italy
| | - Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy
| | - Carmela Gissi
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Ambiente, Università di Bari A. Moro, Via Orabona 4, 70126, Bari, Italy.
- Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, Consiglio Nazionale delle Ricerche, Via Amendola 122/O, 70126, Bari, Italy.
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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16
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Zhou KI, Pecot CV, Holley CL. 2'- O-methylation (Nm) in RNA: progress, challenges, and future directions. RNA (NEW YORK, N.Y.) 2024; 30:570-582. [PMID: 38531653 PMCID: PMC11019748 DOI: 10.1261/rna.079970.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
RNA 2'-O-methylation (Nm) is highly abundant in noncoding RNAs including ribosomal RNA (rRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA), and occurs in the 5' cap of virtually all messenger RNAs (mRNAs) in higher eukaryotes. More recently, Nm has also been reported to occur at internal sites in mRNA. High-throughput methods have been developed for the transcriptome-wide detection of Nm. However, these methods have mostly been applied to abundant RNAs such as rRNA, and the validity of the internal mRNA Nm sites detected with these approaches remains controversial. Nonetheless, Nm in both coding and noncoding RNAs has been demonstrated to impact cellular processes, including translation and splicing. In addition, Nm modifications at the 5' cap and possibly at internal sites in mRNA serve to prevent the binding of nucleic acid sensors, thus preventing the activation of the innate immune response by self-mRNAs. Finally, Nm has been implicated in a variety of diseases including cancer, cardiovascular diseases, and neurologic syndromes. In this review, we discuss current challenges in determining the distribution, regulation, function, and disease relevance of Nm, as well as potential future directions for the field.
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Affiliation(s)
- Katherine I Zhou
- Division of Medical Oncology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
- University of North Carolina RNA Discovery Center, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christopher L Holley
- Division of Cardiology, Department of Medicine, Duke University, Durham, North Carolina 27710, USA
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17
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Sun G, DeFelice MM, Gillies TE, Ahn-Horst TA, Andrews CJ, Krummenacker M, Karp PD, Morrison JH, Covert MW. Cross-evaluation of E. coli's operon structures via a whole-cell model suggests alternative cellular benefits for low- versus high-expressing operons. Cell Syst 2024; 15:227-245.e7. [PMID: 38417437 PMCID: PMC10957310 DOI: 10.1016/j.cels.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/12/2023] [Accepted: 02/08/2024] [Indexed: 03/01/2024]
Abstract
Many bacteria use operons to coregulate genes, but it remains unclear how operons benefit bacteria. We integrated E. coli's 788 polycistronic operons and 1,231 transcription units into an existing whole-cell model and found inconsistencies between the proposed operon structures and the RNA-seq read counts that the model was parameterized from. We resolved these inconsistencies through iterative, model-guided corrections to both datasets, including the correction of RNA-seq counts of short genes that were misreported as zero by existing alignment algorithms. The resulting model suggested two main modes by which operons benefit bacteria. For 86% of low-expression operons, adding operons increased the co-expression probabilities of their constituent proteins, whereas for 92% of high-expression operons, adding operons resulted in more stable expression ratios between the proteins. These simulations underscored the need for further experimental work on how operons reduce noise and synchronize both the expression timing and the quantity of constituent genes. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Gwanggyu Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Mialy M DeFelice
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Taryn E Gillies
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Travis A Ahn-Horst
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cecelia J Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jerry H Morrison
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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18
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Tan L, Guo Z, Wang X, Kim DY, Li R. Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications. mSystems 2024; 9:e0116323. [PMID: 38294229 PMCID: PMC10878088 DOI: 10.1128/msystems.01163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Modifications on viral RNAs (vRNAs), either genomic RNAs or RNA transcripts, have complex effects on the viral life cycle and cellular responses to viral infection. The advent of Oxford Nanopore Technologies Direct RNA Sequencing provides a new strategy for studying RNA modifications. To this end, multiple computational tools have been developed, but a systemic evaluation of their performance in mapping vRNA modifications is lacking. Here, 10 computational tools were tested using the Sindbis virus (SINV) RNAs isolated from infected mammalian (BHK-21) or mosquito (C6/36) cells, with in vitro-transcribed RNAs serving as modification-free control. Three single-mode approaches were shown to be inapplicable in the viral context, and three out of seven comparative methods required cutoff adjustments to reduce false-positive predictions. Utilizing optimized cutoffs, an integrated analysis of comparative tools suggested that the intersected predictions of Tombo_com and xPore were significantly enriched compared with the background. Consequently, a pipeline integrating Tombo_com and xPore was proposed for vRNA modification detection; the performance of which was supported by N6-methyladenosine prediction in severe acute respiratory syndrome coronavirus 2 RNAs using publicly available data. When applied to SINV RNAs, this pipeline revealed more intensive modifications in subgenomic RNAs than in genomic RNAs. Modified uridines were frequently identified, exhibiting substantive overlapping between vRNAs generated in different cell lines. On the other hand, the interpretation of other modifications remained unclear, underlining the limitations of the current computational tools despite their notable potential.IMPORTANCEComputational approaches utilizing Oxford Nanopore Technologies Direct RNA Sequencing data were almost exclusively designed to map eukaryotic epitranscriptomes. Therefore, extra caution must be exercised when using these tools to detect vRNA modifications, as in most cases, vRNA modification profiles should be regarded as unknown epitranscriptomes without prior knowledge. Here, we comprehensively evaluated the performance of 10 computational tools in detecting vRNA modification sites. All tested single-mode methods failed to differentiate native and in vitro-transcribed samples. Using optimized cutoff values, seven tested comparative tools generated very different predictions. An integrated analysis showed significant enrichment of Tombo_com and xPore predictions against the background. A pipeline for vRNA modification detection was proposed accordingly and applied to Sindbis virus RNAs. In conclusion, our study underscores the need for the careful application of computational tools to analyze viral epitranscriptomics. It also offers insights into alphaviral RNA modifications, although further validation is required.
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Affiliation(s)
- Lu Tan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zhihao Guo
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiaoming Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Dal Young Kim
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
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19
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Lucas MC, Pryszcz LP, Medina R, Milenkovic I, Camacho N, Marchand V, Motorin Y, Ribas de Pouplana L, Novoa EM. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. Nat Biotechnol 2024; 42:72-86. [PMID: 37024678 DOI: 10.1038/s41587-023-01743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023]
Abstract
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. We show that default nanopore sequencing settings discard the vast majority of tRNA reads, leading to poor sequencing yields and biased representations of tRNA abundances based on their transcript length. Re-processing of raw nanopore current intensity signals leads to a 12-fold increase in the number of recovered tRNA reads and enables recapitulation of accurate tRNA abundances. We then apply Nano-tRNAseq to Saccharomyces cerevisiae tRNA populations, revealing crosstalks and interdependencies between different tRNA modification types within the same molecule and changes in tRNA populations in response to oxidative stress.
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Affiliation(s)
- Morghan C Lucas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Leszek P Pryszcz
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rebeca Medina
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivan Milenkovic
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Virginie Marchand
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR2008 IBSLor/UMR7365 IMoPA, Nancy, France
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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20
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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21
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Yang Y, Liu Z, Lu J, Sun Y, Fu Y, Pan M, Xie X, Ge Q. Analysis approaches for the identification and prediction of N6-methyladenosine sites. Epigenetics 2023; 18:2158284. [PMID: 36562485 PMCID: PMC9980620 DOI: 10.1080/15592294.2022.2158284] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The global dynamics in a variety of biological processes can be revealed by mapping transcriptional m6A sites, in particular full-transcriptome m6A. And individual m6A sites have contributed to biological function, which can be evaluated by stoichiometric information obtained from the single nucleotide resolution. Currently, the identification of m6A sites is mainly carried out by experiment and prediction methods, based on high-throughput sequencing and machine learning model respectively. This review summarizes the recent topics and progress made in bioinformatics methods of deciphering the m6A methylation, including the experimental detection of m6A methylation sites, techniques of data analysis, the way of predicting m6A methylation sites, m6A methylation databases, and detection of m6A modification in circRNA. At the end, the essay makes a brief discussion for the development perspective in this area.
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Affiliation(s)
- Yuwei Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Junru Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yuqing Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Yue Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Min Pan
- Department of Pathology and Pathophysiology School of Medicine, Southeast University, Nanjing, China
| | - Xueying Xie
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
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22
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Fleming AM, Zhu J, Done VK, Burrows CJ. Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications. RSC Chem Biol 2023; 4:952-964. [PMID: 37920399 PMCID: PMC10619145 DOI: 10.1039/d3cb00081h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 11/04/2023] Open
Abstract
Nanopore direct RNA sequencing is a technology that allows sequencing for epitranscriptomic modifications with the possibility of a quantitative assessment. In the present work, pseudouridine (Ψ) was sequenced with the nanopore before and after the pH 7 bisulfite reaction that yields stable ribose adducts at C1' of Ψ. The adducted sites produced greater base call errors in the form of deletion signatures compared to Ψ. Sequencing studies on E. coli rRNA and tmRNA before and after the pH 7 bisulfite reaction demonstrated that using chemically-assisted nanopore sequencing has distinct advantages for minimization of false positives and false negatives in the data. The rRNA from E. coli has 19 known U/C sequence variations that give similar base call signatures as Ψ, and therefore, are false positives when inspecting base call data; however, these sites are refractory to reacting with bisulfite as is easily observed in nanopore data. The E. coli tmRNA has a low occupancy Ψ in a pyrimidine-rich sequence context that is called a U representing a false negative; partial occupancy by Ψ is revealed after the bisulfite reaction. In a final study, 5-methylcytidine (m5C) in RNA can readily be observed after the pH 5 bisulfite reaction in which the parent C deaminates to U and the modified site does not react. This locates m5C when using bisulfite-assisted nanopore direct RNA sequencing, which is otherwise challenging to observe. The advantages and challenges of the overall approach are discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Judy Zhu
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Vilhelmina K Done
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah 315 S. 1400 East Salt Lake City UT 84112-0850 USA
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23
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Shaw A, Craig JM, Amiri H, Kim J, Upton HE, Pimentel SC, Huang JR, Marqusee S, Collins K, Gundlach JH, Bustamante CJ. Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535757. [PMID: 37066208 PMCID: PMC10104057 DOI: 10.1101/2023.04.05.535757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT from Bombyx mori with single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RT's dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.
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Affiliation(s)
- Alan Shaw
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
| | | | - Hossein Amiri
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
| | - Jeonghoon Kim
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Sydney C. Pimentel
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Present address: NYU Grossman School of Medicine 550 First Avenue New York, NY 10016
| | - Jesse R. Huang
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Susan Marqusee
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kathleen Collins
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Bakar Fellows Program, University of California, Berkeley, CA, 94720
| | - Jens H. Gundlach
- Department of Physics, University of Washington, Seattle, WA, 98195
| | - Carlos J. Bustamante
- Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720
- Biophysics Graduate Group, University of California, Berkeley, CA, 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Physics, University of California, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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24
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Burdick JT, Comai A, Bruzel A, Sun G, Dedon PC, Cheung VG. Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology. G3 (BETHESDA, MD.) 2023; 13:jkad200. [PMID: 37655917 PMCID: PMC10627276 DOI: 10.1093/g3journal/jkad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/14/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
RNA undergoes complex posttranscriptional processing including chemical modifications of the nucleotides. The resultant-modified nucleotides are an integral part of RNA sequences that must be considered in studying the biology of RNA and in the design of RNA therapeutics. However, the current "RNA-sequencing" methods primarily sequence complementary DNA rather than RNA itself, which means that the modifications present in RNA are not captured in the sequencing results. Emerging direct RNA-sequencing technologies, such as those offered by Oxford Nanopore, aim to address this limitation. In this study, we synthesized and used Nanopore technology to sequence RNA transcripts consisting of canonical nucleotides and 10 different modifications in various concentrations. The results show that direct RNA sequencing still has a baseline error rate of >10%, and although some modifications can be detected, many remain unidentified. Thus, there is a need to develop sequencing technologies and analysis methods that can comprehensively capture the total complexity of RNA. The RNA sequences obtained through this project are made available for benchmarking analysis methods.
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Affiliation(s)
- Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Annelise Comai
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109, USA
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25
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Lee SM, Koo B, Carré C, Fischer A, He C, Kumar A, Liu K, Meyer KD, Ming GL, Peng J, Roignant JY, Storkebaum E, Sun S, De Pietri Tonelli D, Wang Y, Weng YL, Pulvirenti L, Shi Y, Yoon KJ, Song H. Exploring the brain epitranscriptome: perspectives from the NSAS summit. Front Neurosci 2023; 17:1291446. [PMID: 37928731 PMCID: PMC10625424 DOI: 10.3389/fnins.2023.1291446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Increasing evidence reinforces the essential function of RNA modifications in development and diseases, especially in the nervous system. RNA modifications impact various processes in the brain, including neurodevelopment, neurogenesis, neuroplasticity, learning and memory, neural regeneration, neurodegeneration, and brain tumorigenesis, leading to the emergence of a new field termed neuroepitranscriptomics. Deficiency in machineries modulating RNA modifications has been implicated in a range of brain disorders from microcephaly, intellectual disability, seizures, and psychiatric disorders to brain cancers such as glioblastoma. The inaugural NSAS Challenge Workshop on Brain Epitranscriptomics hosted in Crans-Montana, Switzerland in 2023 assembled a group of experts from the field, to discuss the current state of the field and provide novel translational perspectives. A summary of the discussions at the workshop is presented here to simulate broader engagement from the general neuroscience field.
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Affiliation(s)
- Sung-Min Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Bonsang Koo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Sorbonne Université, Paris, France
| | - André Fischer
- Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Chuan He
- Department of Chemistry, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Ajeet Kumar
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kathy Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Kate D. Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, United States
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, TN, United States
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Danny Thomas Place, Memphis, TN, United States
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Staudingerweg, Germany
| | - Erik Storkebaum
- Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Shuying Sun
- Department of Physiology and Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, United States
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, TX, United States
| | | | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Ki-Jun Yoon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- KAIST Stem Cell Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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26
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Fleming AM, Bommisetti P, Xiao S, Bandarian V, Burrows CJ. Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes. ACS Chem Biol 2023; 18:2211-2223. [PMID: 37345867 PMCID: PMC10594579 DOI: 10.1021/acschembio.3c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/06/2023] [Indexed: 06/23/2023]
Abstract
The bacterium Escherichia coli possesses 16S and 23S rRNA strands that have 36 chemical modification sites with 17 different structures. Nanopore direct RNA sequencing using a protein nanopore sensor and helicase brake, which is also a sensor, was applied to the rRNAs. Nanopore current levels, base calling profile, and helicase dwell times for the modifications relative to unmodified synthetic rRNA controls found signatures for nearly all modifications. Signatures for clustered modifications were determined by selective sequencing of writer knockout E. coli and sequencing of synthetic RNAs utilizing some custom-synthesized nucleotide triphosphates for their preparation. The knowledge of each modification's signature, apart from 5-methylcytidine, was used to determine how metabolic and cold-shock stress impact rRNA modifications. Metabolic stress resulted in either no change or a decrease, and one site increased in modification occupancy, while cold-shock stress led to either no change or a decrease. The double modification m4Cm1402 resides in 16S rRNA, and it decreased with both stressors. Using the helicase dwell time, it was determined that the N4 methyl group is lost during both stressors, and the 2'-OMe group remained. In the ribosome, this modification stabilizes binding to the mRNA codon at the P-site resulting in increased translational fidelity that is lost during stress. The E. coli genome has seven rRNA operons (rrn), and the earlier studies aligned the nanopore reads to a single operon (rrnA). Here, the reads were aligned to all seven operons to identify operon-specific changes in the 11 pseudouridines. This study demonstrates that direct sequencing for >16 different RNA modifications in a strand is achievable.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Praneeth Bommisetti
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake
City, Utah 84112-0850, United States
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27
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Xiao L, Fang L, Kool ET. RNA Infrastructure Profiling Illuminates Transcriptome Structure in Crowded Spaces. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561413. [PMID: 37873487 PMCID: PMC10592667 DOI: 10.1101/2023.10.09.561413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
RNAs can fold into compact three-dimensional structures, and most RNAs undergo protein interactions in the cell. These compact and occluded environments can block the ability of structure-probing agents to provide useful data about the folding and modification of the underlying RNA. The development of probes that can analyze structure in crowded settings, and differentiate the proximity of interactions, can shed new light on RNA biology. To this end, here we employ 2'-OH-reactive probes that are small enough to access folded RNA structure underlying many close molecular contacts within cells, providing considerably broader coverage for intracellular RNA structural analysis. We compare reverse transcriptase stops in RNA-Seq data from probes of small and standard size to assess RNA-protein proximity and evaluate solvent-exposed tunnels adjacent to RNA. The data are analyzed first with structurally characterized complexes (human 18S and 28S RNA), and then applied transcriptome-wide to polyadenylated transcripts in HEK293 cells. In our transcriptome profile, the smallest probe acetylimidazole (AcIm) yields 80% greater structural coverage than larger conventional reagent NAIN3, providing enhanced structural information in hundreds of transcripts. We further show that acetyl probes provide superior signals for identifying m6A modification sites in transcripts, and provide information regarding methylation sites that are inaccessible to a larger standard probe. RNA infrastructure profiling (RISP) enables enhanced analysis of transcriptome structure, modification, and interactions in living cells, especially in spatially crowded settings.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, United States
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28
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Burrows CJ, Fleming AM. Bisulfite and Nanopore Sequencing for Pseudouridine in RNA. Acc Chem Res 2023; 56:2740-2751. [PMID: 37700703 PMCID: PMC10911771 DOI: 10.1021/acs.accounts.3c00458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Nucleophilic addition of bisulfite to pyrimidine bases has been known for a half century, and the reaction has been in use for at least a quarter of a century for identifying 5-methylcytidine in DNA. This account focuses on the chemistry of bisulfite with pseudouridine, an isomer of the RNA nucleoside uridine in which the uracil base is connected to C1' of ribose via C5 instead of N1. Pseudouridine, Ψ, is the most common nucleotide modification found in cellular RNA overall, in part due to its abundance in rRNAs and tRNAs. It has a stabilizing influence on RNA structure because N1 is now available for additional hydrogen bonding and because the heterocycle is slightly better at π stacking. The isomerization of U to Ψ in RNA strands is catalyzed by 13 different enzymes in humans and 11 in E. coli; some of these enzymes are implicated in disease states which is testament to the biological importance of pseudouridine in cells. Recently, pseudouridine came into the limelight as the key modification that, after N1 methylation, enables mRNA vaccines to be delivered efficiently into human tissue with minimal generation of a deleterious immunogenic response. Here we describe the bisulfite reaction with pseudouridine which gives rise to a chemical sequencing method to map the modified base in the epitranscriptome. Unlike the reaction with cytidine, the addition of bisulfite to Ψ leads irreversibly to form an adduct that is bypassed during cDNA synthesis by reverse transcriptases yielding a characteristic deletion signature. Although there were hints to the structure of the bisulfite adduct(s) 30 to 50 years ago, it took modern spectroscopic and computational methods to solve the mystery. Raman spectroscopy along with extensive NMR, ECD, and computational work led to the assignment of the major product as the (R) diastereomer of an oxygen adduct at C1' of a ring-opened pseudouridine. Mechanistically, this arose from a succession of conjugate addition, E2 elimination, and a [2,3] sigmatropic rearrangement, all of which are stereodefined reactions. A minor reaction with excess bisulfite led to the (S) isomer of a S-adducted SO3- group. Understanding structure and mechanism aided the design of a Ψ-specific sequencing reaction and guided attempts to improve the utility and specificity of the method. Separately, we have been investigating the use of nanopore direct RNA sequencing, a single-molecule method that directly analyzes RNA strands isolated from cells after end-ligation of adaptor sequences. By combining the electrical current and base-calling data from the nanopore with dwell-time analysis from the helicase employed to deliver RNA to the nanopore, we were able to map Ψ sites in nearly all sequence contexts. This analysis was employed to find Ψ residues in the SARS-CoV-2 vRNA, to analyze the sequence context effects of mRNA vaccine synthesis via in vitro transcription, and to evaluate the impact of stress on chemical modifications in the E. coli ribosome. Most recently, we found that bisulfite treatment of RNA leading to Ψ adducts could modulate the nanopore signal to help in mapping modifications of low occupancy.
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Affiliation(s)
- Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112-0850, United States
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29
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Padilla JCA, Barutcu S, Malet L, Deschamps-Francoeur G, Calderon V, Kwon E, Lécuyer E. Profiling the polyadenylated transcriptome of extracellular vesicles with long-read nanopore sequencing. BMC Genomics 2023; 24:564. [PMID: 37736705 PMCID: PMC10514964 DOI: 10.1186/s12864-023-09552-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/03/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND While numerous studies have described the transcriptomes of extracellular vesicles (EVs) in different cellular contexts, these efforts have typically relied on sequencing methods requiring RNA fragmentation, which limits interpretations on the integrity and isoform diversity of EV-targeted RNA populations. It has been assumed that mRNA signatures in EVs are likely to be fragmentation products of the cellular mRNA material, and the extent to which full-length mRNAs are present within EVs remains to be clarified. RESULTS Using long-read nanopore RNA sequencing, we sought to characterize the full-length polyadenylated (poly-A) transcriptome of EVs released by human chronic myelogenous leukemia K562 cells. We detected 443 and 280 RNAs that were respectively enriched or depleted in EVs. EV-enriched poly-A transcripts consist of a variety of biotypes, including mRNAs, long non-coding RNAs, and pseudogenes. Our analysis revealed that 10.58% of all EV reads, and 18.67% of all cellular (WC) reads, corresponded to known full-length transcripts, with mRNAs representing the largest biotype for each group (EV = 58.13%, WC = 43.93%). We also observed that for many well-represented coding and non-coding genes, diverse full-length transcript isoforms were present in EV specimens, and these isoforms were reflective-of but often in different ratio compared to cellular samples. CONCLUSION This work provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs, while also underscoring the potential usefulness of nanopore sequencing to interrogate secreted RNA transcriptomes.
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Affiliation(s)
- Juan-Carlos A Padilla
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada
- Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Seda Barutcu
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada
| | - Ludovic Malet
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada
| | | | - Virginie Calderon
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada
| | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), 110 Avenue des Pins, Ouest, Montréal, QC, H2W 1R7, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Département de Biochimie et de Médecine Moléculaire, Université de Montréal, Montréal, QC, H3T 1J4, Canada.
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30
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Chen AY, Owens MC, Liu KF. Coordination of RNA modifications in the brain and beyond. Mol Psychiatry 2023; 28:2737-2749. [PMID: 37138184 DOI: 10.1038/s41380-023-02083-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Gene expression regulation is a critical process throughout the body, especially in the nervous system. One mechanism by which biological systems regulate gene expression is via enzyme-mediated RNA modifications, also known as epitranscriptomic regulation. RNA modifications, which have been found on nearly all RNA species across all domains of life, are chemically diverse covalent modifications of RNA nucleotides and represent a robust and rapid mechanism for the regulation of gene expression. Although numerous studies have been conducted regarding the impact that single modifications in single RNA molecules have on gene expression, emerging evidence highlights potential crosstalk between and coordination of modifications across RNA species. These potential coordination axes of RNA modifications have emerged as a new direction in the field of epitranscriptomic research. In this review, we will highlight several examples of gene regulation via RNA modification in the nervous system, followed by a summary of the current state of the field of RNA modification coordination axes. In doing so, we aim to inspire the field to gain a deeper understanding of the roles of RNA modifications and coordination of these modifications in the nervous system.
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Affiliation(s)
- Anthony Yulin Chen
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA, 19081, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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31
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White LK, Strugar SM, MacFadden A, Hesselberth JR. Nanopore sequencing of internal 2'-PO 4 modifications installed by RNA repair. RNA (NEW YORK, N.Y.) 2023; 29:847-861. [PMID: 36854608 PMCID: PMC10187680 DOI: 10.1261/rna.079290.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 02/09/2023] [Indexed: 05/18/2023]
Abstract
Ligation by plant and fungal RNA ligases yields an internal 2'-phosphate group on each RNA ligation product. In budding yeast, this covalent mark occurs at the splice junction of two targets of ligation: intron-containing tRNAs and the messenger RNA HAC1 The repertoire of RNA molecules repaired by RNA ligation has not been explored due to a lack of unbiased approaches for identifying RNA ligation products. Here, we define several unique signals produced by 2'-phosphorylated RNAs during nanopore sequencing. A 2'-phosphate at the splice junction of HAC1 mRNA inhibits 5' → 3' degradation, enabling detection of decay intermediates in yeast RNA repair mutants by nanopore sequencing. During direct RNA sequencing, intact 2'-phosphorylated RNAs on HAC1 and tRNAs produce diagnostic changes in nanopore current properties and base calling features, including stalls produced as the modified RNA translocates through the nanopore motor protein. These approaches enable directed studies to identify novel RNA repair events in other contexts.
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Affiliation(s)
- Laura K White
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Saylor M Strugar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jay R Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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32
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Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
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Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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33
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Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP. Nano-DMS-MaP allows isoform-specific RNA structure determination. Nat Methods 2023; 20:849-859. [PMID: 37106231 PMCID: PMC10250195 DOI: 10.1038/s41592-023-01862-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)-a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5' untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.
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Affiliation(s)
- Patrick Bohn
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Uddhav B Ambi
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research, Würzburg, Germany.
- Julius-Maximilians-Universität Würzburg, Faculty of Medicine, Würzburg, Germany.
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34
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Vaneev AN, Timoshenko RV, Gorelkin PV, Klyachko NL, Erofeev AS. Recent Advances in Nanopore Technology for Copper Detection and Their Potential Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13091573. [PMID: 37177118 PMCID: PMC10181076 DOI: 10.3390/nano13091573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
Recently, nanopore technology has emerged as a promising technique for the rapid, sensitive, and selective detection of various analytes. In particular, the use of nanopores for the detection of copper ions has attracted considerable attention due to their high sensitivity and selectivity. This review discusses the principles of nanopore technology and its advantages over conventional techniques for copper detection. It covers the different types of nanopores used for copper detection, including biological and synthetic nanopores, and the various mechanisms used to detect copper ions. Furthermore, this review provides an overview of the recent advancements in nanopore technology for copper detection, including the development of new nanopore materials, improvements in signal amplification, and the integration of nanopore technology with other analytical methods for enhanced detection sensitivity and accuracy. Finally, we summarize the extensive applications, current challenges, and future perspectives of using nanopore technology for copper detection, highlighting the need for further research in the field to optimize the performance and applicability of the technique.
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Affiliation(s)
- Alexander N Vaneev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Roman V Timoshenko
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Petr V Gorelkin
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
| | - Natalia L Klyachko
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexander S Erofeev
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
- Research Laboratory of Biophysics, National University of Science and Technology "MISIS", 119049 Moscow, Russia
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35
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Mustoe AM, Weidmann CA, Weeks KM. Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis. Acc Chem Res 2023; 56:763-775. [PMID: 36917683 PMCID: PMC10078950 DOI: 10.1021/acs.accounts.2c00782] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
RNA molecules convey biological information both in their linear sequence and in their base-paired secondary and tertiary structures. Chemical probing experiments, which involve treating an RNA with a reagent that modifies conformationally dynamic nucleotides, have broadly enabled examination of short- and long-range RNA structure in diverse contexts, including in living cells. For decades, chemical probing experiments have been interpreted in a per-nucleotide way, such that the reactivity measured at each nucleotide reports the average structure at a position over all RNA molecules within a sample. However, there are numerous important cases where per-nucleotide chemical probing falls short, including for RNAs that are bound by proteins, RNAs that form complex higher order structures, and RNAs that sample multiple conformations.Recent experimental and computational innovations have started a revolution in RNA structure analysis by transforming chemical probing into a massively parallel, single-molecule experiment. Enabled by a specialized reverse transcription strategy called mutational profiling (MaP), multiple chemical modification events can be measured within individual RNA molecules. Nucleotides that communicate structurally through direct base pairing or large-scale folding-unfolding transitions will react with chemical probes in a correlated manner, thereby revealing structural complexity hidden to conventional approaches. These single-molecule correlated chemical probing (smCCP) experiments can be interpreted to directly identify nucleotides that base pair (the PAIR-MaP strategy) and to reveal long-range, through-space structural communication (RING-MaP). Correlated probing can also define the thermodynamic populations of complex RNA ensembles (DANCE-MaP). Complex RNA-protein networks can be interrogated by cross-linking proteins to RNA and measuring correlations between cross-linked positions (RNP-MaP).smCCP thus visualizes RNA secondary and higher-order structure with unprecedented accuracy, defining novel structures, RNA-protein interaction networks, time-resolved dynamics, and allosteric structural switches. These strategies are not mutually exclusive; in favorable cases, multiple levels of RNA structure ─ base pairing, through-space structural communication, and equilibrium ensembles ─ can be resolved concurrently. The physical experimentation required for smCCP is profoundly simple, and experiments are readily performed in cells on RNAs of any size, including large noncoding RNAs and mRNAs. Single-molecule correlated chemical probing is paving the way for a new generation of biophysical studies on RNA in living systems.
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Affiliation(s)
- Anthony M. Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Department of Molecular and Human Genetics, and Therapeutic Innovation Center (THINC), One Baylor Plaza, Baylor College of Medicine, Houston, TX 77030
| | - Chase A. Weidmann
- Department of Biological Chemistry, Center for RNA Biomedicine, 1150 W. Medical Center Drive, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill NC 27599-3290
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36
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Spangenberg J, Zu Siederdissen CH, Žarković M, Triebel S, Rose R, Christophersen CM, Paltzow L, Hegab MM, Wansorra A, Srivastava A, Krumbholz A, Marz M. Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533105. [PMID: 36993667 PMCID: PMC10055291 DOI: 10.1101/2023.03.17.533105] [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] [Indexed: 06/19/2023]
Abstract
Oxford Nanopore Technologies (ONT) allows direct sequencing of ribonucleic acids (RNA) and, in addition, detection of possible RNA modifications due to deviations from the expected ONT signal. The software available so far for this purpose can only detect a small number of modifications. Alternatively, two samples can be compared for different RNA modifications. We present Magnipore, a novel tool to search for significant signal shifts between samples of Oxford Nanopore data from similar or related species. Magnipore classifies them into mutations and potential modifications. We use Magnipore to compare SARS-CoV-2 samples. Included were representatives of the early 2020s Pango lineages (n=6), samples from Pango lineages B.1.1.7 (n=2, Alpha), B.1.617.2 (n=1, Delta), and B.1.529 (n=7, Omicron). Magnipore utilizes position-wise Gaussian distribution models and a comprehensible significance threshold to find differential signals. In the case of Alpha and Delta, Magnipore identifies 55 detected mutations and 15 sites that hint at differential modifications. We predicted potential virus-variant and variant-group-specific differential modifications. Magnipore contributes to advancing RNA modification analysis in the context of viruses and virus variants.
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Affiliation(s)
- Jannes Spangenberg
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | | | - Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Sandra Triebel
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Ruben Rose
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 4, 24105 Kiel, Germany
| | | | - Lea Paltzow
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Mohsen M Hegab
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Anna Wansorra
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Andi Krumbholz
- Institute for Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 4, 24105 Kiel, Germany
- Labor Dr. Krause und Kollegen MVZ GmbH, Steenbeker Weg 23, 24106 Kiel, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
- European Virus Bioinformatics Center 2, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
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37
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Bruijnesteijn J. HLA/MHC and KIR characterization in humans and non-human primates using Oxford Nanopore Technologies and Pacific Biosciences sequencing platforms. HLA 2023; 101:205-221. [PMID: 36583332 DOI: 10.1111/tan.14957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
The gene products of the HLA/MHC and KIR multigene families are important modulators of the immune system and are associated with health and disease. Characterization of the genes encoding these receptors has been integrated into different biomedical applications, including transplantation and reproduction biology, immune therapies and in fundamental research into disease susceptibility or resistance. Conventional short-read sequencing strategies have shown their value in high throughput typing, but are insufficient to uncover the entire complexity of the highly polymorphic HLA/MHC and KIR gene systems. The implementation of single-molecule and real-time sequencing platforms, offered by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), revolutionized the fields of genomics and transcriptomics. Using fundamentally distinct principles, these platforms generate long-read data that can unwire the plasticity of the HLA/MHC and KIR genes, including high-resolution characterization of genes, alleles, phased haplotypes, transcription levels and epigenetics modification patterns. These insights might have profound clinical relevance, such as improved matching of donors and patients in clinical transplantation, but could also lift disease association studies to a higher level. Even more, a comprehensive characterization may refine animal models in preclinical studies. In this review, the different HLA/MHC and KIR characterization approaches using PacBio and ONT platforms are described and discussed.
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Affiliation(s)
- Jesse Bruijnesteijn
- Department of Comparative Genetics and Refinement, Biomedical Primate Research Centre, Rijswijk, The Netherlands
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38
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. MICROMACHINES 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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39
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Ueda H, Dasgupta B, Yu BY. RNA Modification Detection Using Nanopore Direct RNA Sequencing and nanoDoc2. Methods Mol Biol 2023; 2632:299-319. [PMID: 36781737 DOI: 10.1007/978-1-0716-2996-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
RNA modifications regulate multiple aspects of cellular function including RNA splicing, translation, export, decay, stability, and phase separation. One of the comprehensive ways to detect such modifications is by the recent advancement of direct RNA sequencing from Oxford Nanopore Technologies (ONT). However, this method obtains a large amount of data with high complexity in the form of raw current signal that poses a new informatics challenge to accurately detect those modifications. Here, we provide nanoDoc2, a software to detect multiple types of RNA modification from nanopore direct RNA sequencing data. The nanoDoc2 includes a novel signal segmentation algorithm based on the trace value-a base probability feature that is added by the Guppy basecalling program from ONT during processing of the raw signal. The core of nanoDoc2 includes a machine learning algorithm in which a 6-mer segmented raw current signal is analyzed by deep one-class classification using a WaveNet-based neural network. As an output, an RNA modification is detected by a statistical score in each candidate position. Herein, we describe the detailed instructions on how to use nanoDoc2 for signal segmentation, train/test the neural network, and finally predict RNA modifications present in nanopore direct RNA sequencing data.
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Affiliation(s)
- Hiroki Ueda
- Biological data Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan.
| | - Bhaskar Dasgupta
- Biological data Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
| | - Bo-Yi Yu
- Biological data Science Division, Research Center for Advanced Science and Technologies, The University of Tokyo, Tokyo, Japan
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40
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Xiao L, Fang L, Chatterjee S, Kool ET. Diverse Reagent Scaffolds Provide Differential Selectivity of 2'-OH Acylation in RNA. J Am Chem Soc 2023; 145:143-151. [PMID: 36542611 DOI: 10.1021/jacs.2c09040] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA 2'-OH acylation is widely used both for mapping structure and for conjugating RNA, generally relying on selective reactions with unpaired nucleotides over paired ones. Common reagents for this acylation have been chiefly restricted to two similar aryl scaffolds, leaving open the question of how more broadly varied reagent structure might affect selectivity. Here, we prepared a set of 10 structurally diverse acylimidazole reagents and employed deep sequencing to profile their reactivity and selectivity in an RNA library of systematically varied structure. We show that structure-directed reactivity profiles vary significantly with the reagent scaffold, and we document new acylating agents that have altered selectivity profiles, including reagents that show elevated selectivity within loops, as well as compounds with reduced off-target reactivity in loop closing base pairs. Interestingly, we also show that the simplest reagent (acetylimidazole) is cell permeable and is small enough to map RNA structure in the presence of protein contacts that block other reagents. Finally, we describe reagents that show elevated selectivity within small loops, with applications in site-selective labeling. The results provide new tools for improved conjugation and mapping of RNA.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sayantan Chatterjee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California 94305, United States
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41
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Begik O, Mattick JS, Novoa EM. Exploring the epitranscriptome by native RNA sequencing. RNA (NEW YORK, N.Y.) 2022; 28:1430-1439. [PMID: 36104106 PMCID: PMC9745831 DOI: 10.1261/rna.079404.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). However, the signal modulations caused by most RNA modifications are yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
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Affiliation(s)
- Oguzhan Begik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Eva Maria Novoa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra, Barcelona 08002, Spain
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42
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White LK, Hesselberth JR. Modification mapping by nanopore sequencing. Front Genet 2022; 13:1037134. [PMID: 36386798 PMCID: PMC9650216 DOI: 10.3389/fgene.2022.1037134] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 06/26/2024] Open
Abstract
Next generation sequencing (NGS) has provided biologists with an unprecedented view into biological processes and their regulation over the past 2 decades, fueling a wave of development of high throughput methods based on short read DNA and RNA sequencing. For nucleic acid modifications, NGS has been coupled with immunoprecipitation, chemical treatment, enzymatic treatment, and/or the use of reverse transcriptase enzymes with fortuitous activities to enrich for and to identify covalent modifications of RNA and DNA. However, the majority of nucleic acid modifications lack commercial monoclonal antibodies, and mapping techniques that rely on chemical or enzymatic treatments to manipulate modification signatures add additional technical complexities to library preparation. Moreover, such approaches tend to be specific to a single class of RNA or DNA modification, and generate only indirect readouts of modification status. Third generation sequencing technologies such as the commercially available "long read" platforms from Pacific Biosciences and Oxford Nanopore Technologies are an attractive alternative for high throughput detection of nucleic acid modifications. While the former can indirectly sense modified nucleotides through changes in the kinetics of reverse transcription reactions, nanopore sequencing can in principle directly detect any nucleic acid modification that produces a signal distortion as the nucleic acid passes through a nanopore sensor embedded within a charged membrane. To date, more than a dozen endogenous DNA and RNA modifications have been interrogated by nanopore sequencing, as well as a number of synthetic nucleic acid modifications used in metabolic labeling, structure probing, and other emerging applications. This review is intended to introduce the reader to nanopore sequencing and key principles underlying its use in direct detection of nucleic acid modifications in unamplified DNA or RNA samples, and outline current approaches for detecting and quantifying nucleic acid modifications by nanopore sequencing. As this technology matures, we anticipate advances in both sequencing chemistry and analysis methods will lead to rapid improvements in the identification and quantification of these epigenetic marks.
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Affiliation(s)
| | - Jay R. Hesselberth
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, United States
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Caldwell RM, Flynn RA. Discovering glycoRNA: Traditional and Non‐Canonical Approaches to Studying RNA Modifications. Isr J Chem 2022. [DOI: 10.1002/ijch.202200059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Reese M. Caldwell
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
| | - Ryan A. Flynn
- Stem Cell Program, Boston Children's Hospital Boston 02115 Massachusetts United States
- Stem Cell and Regenerative Biology Department, Harvard University Cambridage 02138 Massachusetts United States
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Bizuayehu TT, Labun K, Jakubec M, Jefimov K, Niazi A, Valen E. Long-read single-molecule RNA structure sequencing using nanopore. Nucleic Acids Res 2022; 50:e120. [PMID: 36166000 PMCID: PMC9723614 DOI: 10.1093/nar/gkac775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/16/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
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Affiliation(s)
- Teshome Tilahun Bizuayehu
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
- Sars International Center for Marine Molecular Biology, University of Bergen, Norway
| | - Kornel Labun
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | | | - Kirill Jefimov
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Adnan Muhammad Niazi
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
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Hong A, Kim D, Kim VN, Chang H. Analyzing viral epitranscriptomes using nanopore direct RNA sequencing. J Microbiol 2022; 60:867-876. [PMID: 36001233 PMCID: PMC9400574 DOI: 10.1007/s12275-022-2324-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/24/2022]
Abstract
RNA modifications are a common occurrence across all domains of life. Several chemical modifications, including N6-methyladenosine, have also been found in viral transcripts and viral RNA genomes. Some of the modifications increase the viral replication efficiency while also helping the virus to evade the host immune system. Nonetheless, there are numerous examples in which the host's RNA modification enzymes function as antiviral factors. Although established methods like MeRIP-seq and miCLIP can provide a transcriptome- wide overview of how viral RNA is modified, it is difficult to distinguish between the complex overlapping viral transcript isoforms using the short read-based techniques. Nanopore direct RNA sequencing (DRS) provides both long reads and direct signal readings, which may carry information about the modifications. Here, we describe a refined protocol for analyzing the RNA modifications in viral transcriptomes using nanopore technology.
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Affiliation(s)
- Ari Hong
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongwan Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeshik Chang
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Morreel K, t’Kindt R, Debyser G, Jonckheere S, Sandra P. Diving into the Structural Details of In Vitro Transcribed mRNA Using Liquid Chromatography–Mass Spectrometry-Based Oligonucleotide Profiling. LCGC EUROPE 2022. [DOI: 10.56530/lcgc.eu.jk3969w4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The production process of in vitro transcribed messenger RNA (IVT-mRNA)-based vaccines has matured in recent years, partly due to the fight against infectious diseases such as COVID-19. One key to success has been the use of modified, next to canonical, nucleotides and the efficient addition of a Cap-structure and poly A tail to the 5’ and 3’ end, respectively, of this massive biomolecule. These important features affect mRNA stability and impact translation efficiency, consequently boosting the optimization and implementation of liquid chromatography–mass spectrometry (LC–MS)-based oligonucleotide profiling methods for their characterization. This article will provide an overview of these LC–MS methods at a fundamental and application level. It will be shown how LC–MS is implemented in mRNA-based vaccine analysis to determine the capping efficiency and the poly A tail length, and how it allows, via RNA mapping, (i) to determine the mRNA sequence, (ii) to screen the fidelity of the manufactured modifications, and (iii) to identify and quantify unwanted modifications resulting from manufacturing or storage, and sequence variants resulting from mutation or transcription errors.
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Barozzi C, Zacchini F, Asghar S, Montanaro L. Ribosomal RNA Pseudouridylation: Will Newly Available Methods Finally Define the Contribution of This Modification to Human Ribosome Plasticity? Front Genet 2022; 13:920987. [PMID: 35719370 PMCID: PMC9198423 DOI: 10.3389/fgene.2022.920987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
In human rRNA, at least 104 specific uridine residues are modified to pseudouridine. Many of these pseudouridylation sites are located within functionally important ribosomal domains and can influence ribosomal functional features. Until recently, available methods failed to reliably quantify the level of modification at each specific rRNA site. Therefore, information obtained so far only partially explained the degree of regulation of pseudouridylation in different physiological and pathological conditions. In this focused review, we provide a summary of the methods that are now available for the study of rRNA pseudouridylation, discussing the perspectives that newly developed approaches are offering.
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Affiliation(s)
- Chiara Barozzi
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Federico Zacchini
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Sidra Asghar
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
| | - Lorenzo Montanaro
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale (DIMES), Alma Mater Studiorum—Università di Bologna, Bologna, Italy
- Centro di Ricerca Biomedica Applicata, CRBA, Universita di Bologna, Policlinico di Sant’Orsola, Bologna, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Bhatti H, Lu Z, Liu Q. Nanopore Detection of Cancer Biomarkers: A Challenge to Science. Technol Cancer Res Treat 2022; 21:15330338221076669. [PMID: 35229683 PMCID: PMC8891933 DOI: 10.1177/15330338221076669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/02/2022] Open
Abstract
Cancer is the most complex and leading cause of fatality worldwide. Despite meritorious research in the field of cancer, it is still a substantial threat to human life. In this article, we address a question on the present strategies and manifest the importance of critical biomarkers for cancer screening and early diagnosis before the symptoms appear. However, this goal can only be achieved if scientists will focus on ultra-sensitive detection techniques such as "Nanopore." Nanopore sensing is a simple and rapid single-molecule detection technique that can detect multiple cancer biomarkers in femto-Molar concentrations in real time. Last but not least, we propose a systematic policy to win the war against cancer that is a big challenge to science.
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Affiliation(s)
- Huma Bhatti
- Southeast University, Nanjing, People’s Republic of China
| | - Zuhong Lu
- Southeast University, Nanjing, People’s Republic of China
| | - Quanjun Liu
- Southeast University, Nanjing, People’s Republic of China
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