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Debnath TK, Xhemalçe B. Deciphering RNA modifications at base resolution: from chemistry to biology. Brief Funct Genomics 2021; 20:77-85. [PMID: 33454749 DOI: 10.1093/bfgp/elaa024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 01/04/2023] Open
Abstract
Nearly 200 distinct chemical modifications of RNAs have been discovered to date. Their analysis via direct methods has been possible in abundant RNA species, such as ribosomal, transfer or viral RNA, since several decades. However, their analysis in less abundant RNAs species, especially cellular messenger RNAs, was rendered possible only recently with the advent of high throughput sequencing techniques. Given the growing biomedical interest of the proteins that write, erase and read RNA modifications, ingenious new methods to enrich and identify RNA modifications at base resolution have been implemented, and more efforts are underway to render them more quantitative. Here, we review several crucial modification-specific (bio)chemical approaches and discuss their advantages and shortcomings for exploring the epitranscriptome.
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Affiliation(s)
- Turja K Debnath
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712 Austin TX, USA
| | - Blerta Xhemalçe
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712 Austin TX, USA
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2
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Kang ASW, Bernasconi JG, Jack W, Kanavarioti A. Ready-to-use nanopore platform for the detection of any DNA/RNA oligo at attomole range using an Osmium tagged complementary probe. Sci Rep 2020; 10:19790. [PMID: 33188229 PMCID: PMC7666163 DOI: 10.1038/s41598-020-76667-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Nanopores can serve as single molecule sensors. We exploited the MinION, a portable nanopore device from Oxford Nanopore Technologies, and repurposed it to detect any DNA/RNA oligo (target) in a complex mixture by conducting voltage-driven ion-channel measurements. The detection and quantitation of the target is enabled by the use of a unique complementary probe. Using a validated labeling technology, probes are tagged with a bulky Osmium tag (Osmium tetroxide 2,2′-bipyridine), in a way that preserves strong hybridization between probe and target. Intact oligos traverse the MinION’s nanopore relatively quickly compared to the device’s acquisition rate, and exhibit count of events comparable to the baseline. Counts are reported by a publicly available software, OsBp_detect. Due to the presence of the bulky Osmium tag, probes traverse more slowly, produce multiple counts over the baseline, and are even detected at single digit attomole (amole) range. In the presence of the target the probe is “silenced”. Silencing is attributed to a 1:1 double stranded (ds) complex that does not fit and cannot traverse this nanopore. This ready-to-use platform can be tailored as a diagnostic test to meet the requirements for point-of-care cell-free tumor DNA (ctDNA) and microRNA (miRNA) detection and quantitation in body fluids.
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Affiliation(s)
- Albert S W Kang
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Janette G Bernasconi
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | | | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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3
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Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R. Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL). Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Isabel Delazer
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Katharina Pascher
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Karl Brillet
- Université de StrasbourgArchitecture et Réactivité de l'ARN—CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Sarah Klotz
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Lukas Trixl
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
| | - Eric Ennifar
- Université de StrasbourgArchitecture et Réactivité de l'ARN—CNRS UPR 9002Institut de Biologie Moléculaire et Cellulaire 67000 Strasbourg France
| | - Dietmar Rieder
- Institute of BioinformaticsBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Alexandra Lusser
- Institute of Molecular BiologyBiocenterMedical University of Innsbruck Innrain 82 6020 Innsbruck Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular BiosciencesLeopold-Franzens University Innrain 80 6020 Innsbruck Austria
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Gasser C, Delazer I, Neuner E, Pascher K, Brillet K, Klotz S, Trixl L, Himmelstoß M, Ennifar E, Rieder D, Lusser A, Micura R. Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL). Angew Chem Int Ed Engl 2020; 59:6881-6886. [PMID: 31999864 PMCID: PMC7186826 DOI: 10.1002/anie.201916272] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/24/2022]
Abstract
Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH4 Cl/OsO4 -based conversion of 6-thioguanosine (6sG) into A', where A' constitutes a 6-hydrazino purine derivative. A' retains the Watson-Crick base-pair mode and is efficiently decoded as adenosine in primer extension assays and in RNA sequencing. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4-thiouridine (4sU) into C, the combination of both modified nucleosides in dual-labeling setups enables high accuracy measurements of RNA decay. This approach, termed TUC-seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA-lifetime evaluation with unprecedented precision.
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Affiliation(s)
- Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Isabel Delazer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Eva Neuner
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Katharina Pascher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Karl Brillet
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 67000, Strasbourg, France
| | - Sarah Klotz
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Lukas Trixl
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 67000, Strasbourg, France
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, Leopold-Franzens University, Innrain 80, 6020, Innsbruck, Austria
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Sultan M, Kanavarioti A. Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag. Sci Rep 2019; 9:14180. [PMID: 31578367 PMCID: PMC6775150 DOI: 10.1038/s41598-019-50459-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/12/2019] [Indexed: 12/19/2022] Open
Abstract
Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2'-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.
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Affiliation(s)
- Madiha Sultan
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA
| | - Anastassia Kanavarioti
- Yenos Analytical LLC, 4659 Golden Foothill Pkwy, Suite 101, El Dorado Hills, CA, 95672, USA.
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