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Motorin Y, Helm M. General Principles and Limitations for Detection of RNA Modifications by Sequencing. Acc Chem Res 2024; 57:275-288. [PMID: 38065564 PMCID: PMC10851944 DOI: 10.1021/acs.accounts.3c00529] [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: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 02/07/2024]
Abstract
Among the many analytical methods applied to RNA modifications, a particularly pronounced surge has occurred in the past decade in the field of modification mapping. The occurrence of modifications such as m6A in mRNA, albeit known since the 1980s, became amenable to transcriptome-wide analyses through the advent of next-generation sequencing techniques in a rather sudden manner. The term "mapping" here refers to detection of RNA modifications in a sequence context, which has a dramatic impact on the interpretation of biological functions. As a consequence, an impressive number of mapping techniques were published, most in the perspective of what now has become known as "epitranscriptomics". While more and more different modifications were reported to occur in mRNA, conflicting reports and controversial results pointed to a number of technical and theoretical problems rooted in analytics, statistics, and reagents. Rather than finding the proverbial needle in a haystack, the tasks were to determine how many needles of what color in what size of a haystack one was looking at.As the authors of this Account, we think it important to outline the limitations of different mapping methods since many life scientists freshly entering the field confuse the accuracy and precision of modification mapping with that of normal sequencing, which already features numerous caveats by itself. Indeed, we propose here to qualify a specific mapping method by the size of the transcriptome that can be meaningfully analyzed with it.We here focus on high throughput sequencing by Illumina technology, referred to as RNA-Seq. We noted with interest the development of methods for modification detection by other high throughput sequencing platforms that act directly on RNA, e.g., PacBio SMRT and nanopore sequencing, but those are not considered here.In contrast to approaches relying on direct RNA sequencing, current Illumina RNA-Seq protocols require prior conversion of RNA into DNA. This conversion relies on reverse transcription (RT) to create cDNA; thereafter, the cDNA undergoes a sequencing-by-synthesis type of analysis. Thus, a particular behavior of RNA modified nucleotides during the RT-step is a prerequisite for their detection (and quantification) by deep sequencing, and RT properties have great influence on the detection efficiency and reliability. Moreover, the RT-step requires annealing of a synthetic primer, a prerequisite with a crucial impact on library preparation. Thus, all RNA-Seq protocols must feature steps for the introduction of primers, primer landing sites, or adapters on both the RNA 3'- and 5'-ends.
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Affiliation(s)
- Yuri Motorin
- Université
de Lorraine, UMR7365 IMoPA CNRS-UL
and UAR2008/US40 IBSLor CNRS-Inserm, Biopole UL, Nancy F54000, France
| | - Mark Helm
- Institute
of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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2
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Lechner A, Wolff P. In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA. Methods Mol Biol 2024; 2741:273-287. [PMID: 38217659 DOI: 10.1007/978-1-0716-3565-0_15] [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] [Indexed: 01/15/2024]
Abstract
Regulatory RNAs, as well as many RNA families, contain chemically modified nucleotides, including pseudouridines (ψ). To map nucleotide modifications, approaches based on enzymatic digestion of RNA followed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analysis were implemented several years ago. However, detection of ψ by mass spectrometry (MS) is challenging as ψ exhibits the same mass as uridine. Thus, a chemical labeling strategy using acrylonitrile was developed to detect this mass-silent modification. Acrylonitrile reacts specifically to ψ to form 1-cyanoethylpseudouridine (Ceψ), resulting in a mass shift of ψ detectable by MS. Here, a protocol detailing the steps from the purification of RNA by polyacrylamide gel electrophoresis, including in-gel labeling of ψ, to MS data interpretation to map ψ and other modifications is proposed. To demonstrate its efficiency, the protocol was applied to bacterial regulatory RNAs from E. coli: 6S RNA and transfer-messenger RNA (tmRNA, also known as 10Sa RNA). Moreover, ribonuclease P (RNase P) was also mapped using this approach. This method enabled the detection of several ψ at single nucleotide resolution.
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Affiliation(s)
- Antony Lechner
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France.
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3
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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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4
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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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5
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Kallert E, Behrendt M, Frey A, Kersten C, Barthels F. Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications. Chem Sci 2023; 14:9827-9837. [PMID: 37736627 PMCID: PMC10510756 DOI: 10.1039/d3sc02993j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2023] [Indexed: 09/23/2023] Open
Abstract
Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches. This new approach has been successfully used to study the binding of ligands to RNA molecules (e.g., SAM- and PreQ1 riboswitches) and the identification of modifications (e.g., m6A) in short RNA oligos which can be written by the RNA methyltransferase METTL3/14.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Malte Behrendt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
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Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq. Methods Mol Biol 2023; 2624:207-223. [PMID: 36723818 DOI: 10.1007/978-1-0716-2962-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pseudouridine, a modified RNA residue formed by the isomerization of its parental U nucleotide, is prevalent in a majority of cellular RNAs; its presence was reported in tRNA, rRNA, and sn/snoRNA as well as in mRNA/lncRNA. Multiple analytical deep sequencing-based approaches have been proposed for pseudouridine detection and quantification, among which the most popular relies on the use of soluble carbodiimide (termed CMCT). Recently, we developed an alternative protocol for pseudouridine mapping and quantification. The principle is based on protection of pseudouridine against random RNA cleavage by hydrazine/aniline treatment (HydraPsiSeq protocol). This "negative" detection mode requires higher sequencing depth and provides a precise quantification of the pseudouridine content. All "wet-lab" technical details of the HydraPsiSeq protocol have been described in recent publications. Here, we describe all bioinformatics analysis steps required for data processing from raw reads to the pseudouridylation profile of known or unknown RNA.
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Kotammagari TK, Tähtinen P, Lönnberg T. Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences. Chemistry 2022; 28:e202202530. [PMID: 36108095 PMCID: PMC10092508 DOI: 10.1002/chem.202202530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Indexed: 12/14/2022]
Abstract
Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Petri Tähtinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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Henry BA, Marchand V, Schlegel BT, Helm M, Motorin Y, Lee N. Pseudouridylation of Epstein-Barr virus noncoding RNA EBER2 facilitates lytic replication. RNA (NEW YORK, N.Y.) 2022; 28:1542-1552. [PMID: 36100352 PMCID: PMC9745832 DOI: 10.1261/rna.079219.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Epstein-Barr virus (EBV) expresses two highly abundant noncoding RNAs called EBV-encoded RNA 1 (EBER1) and EBER2, which are preserved in all clinical isolates of EBV, thus underscoring their essential function in the viral life cycle. Recent epitranscriptomics studies have uncovered a vast array of distinct RNA modifications within cellular as well as viral noncoding RNAs that are instrumental in executing their function. Here we show that EBER2 is marked by pseudouridylation, and by using HydraPsiSeq the modification site was mapped to a single nucleotide within the 3' region of EBER2. The writer enzyme was identified to be the snoRNA-dependent pseudouridine synthase Dyskerin, which is the catalytic subunit of H/ACA small nucleolar ribonucleoprotein complexes, and is guided to EBER2 by SNORA22. Similar to other noncoding RNAs for which pseudouridylation has a positive effect on RNA stability, loss of EBER2 pseudouridylation results in a decrease in RNA levels. Furthermore, pseudouridylation of EBER2 is required for the prolific accumulation of progeny viral genomes, suggesting that this single modification in EBER2 is important for efficient viral lytic replication. Taken together, our findings add to the list of RNA modifications that are essential for noncoding RNAs to implement their physiological roles.
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Affiliation(s)
- Belle A Henry
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UAR2008/US40 IBSLor, F-54000 Nancy, France
| | - Brent T Schlegel
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
| | - Mark Helm
- Johannes Gutenberg University Mainz, Institute of Pharmacy and Biochemistry, 55128 Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, UAR2008/US40 IBSLor, F-54000 Nancy, France
- Université de Lorraine, CNRS, UMR7365 IMoPA, F-54000 Nancy, France
| | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, USA
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9
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Ye W, Wu Z, Gao P, Kang J, Xu Y, Wei C, Zhang M, Zhu X. Identified Gefitinib Metabolism-Related lncRNAs can be Applied to Predict Prognosis, Tumor Microenvironment, and Drug Sensitivity in Non-Small Cell Lung Cancer. Front Oncol 2022; 12:939021. [PMID: 35978819 PMCID: PMC9376789 DOI: 10.3389/fonc.2022.939021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/06/2022] [Indexed: 12/15/2022] Open
Abstract
Gefitinib has shown promising efficacy in the treatment of patients with locally advanced or metastatic EGFR-mutated non-small cell lung cancer (NSCLC). Molecular biomarkers for gefitinib metabolism-related lncRNAs have not yet been elucidated. Here, we downloaded relevant genes and matched them to relevant lncRNAs. We then used univariate, LASSO, and multivariate regression to screen for significant genes to construct prognostic models. We investigated TME and drug sensitivity by risk score data. All lncRNAs with differential expression were selected for GO/KEGG analysis. Imvigor210 cohort was used to validate the value of the prognostic model. Finally, we performed a stemness indices difference analysis. lncRNA-constructed prognostic models were significant in the high-risk and low-risk subgroups. Immune pathways were identified in both groups at low risk. The higher the risk score the greater the value of exclusion, MDSC, and CAF. PRRophetic algorithm screened a total of 58 compounds. In conclusion, the prognostic model we constructed can accurately predict OS in NSCLC patients. Two groups of low-risk immune pathways are beneficial to patients. Gefitinib metabolism was again validated to be related to cytochrome P450 and lipid metabolism. Finally, drugs that might be used to treat NSCLC patients were screened.
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Affiliation(s)
- Weilong Ye
- School of Laboratory Medicine and Biological Engineering, Hangzhou Medical College, Hangzhou, China
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
| | - Zhengguo Wu
- Department of Thoracic Surgery, Yantian District People’s Hospital, Shenzhen, China
| | - Pengbo Gao
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
| | - Jianhao Kang
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
| | - Yue Xu
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
| | - Chuzhong Wei
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
| | - Ming Zhang
- Department of Physical Medicine and Rehabilitation, Zibo Central Hospital, Zibo, China
- *Correspondence: Ming Zhang, ; Xiao Zhu,
| | - Xiao Zhu
- School of Laboratory Medicine and Biological Engineering, Hangzhou Medical College, Hangzhou, China
- Computational Oncology Laboratory, Guangdong Medical University, Zhanjiang, China
- *Correspondence: Ming Zhang, ; Xiao Zhu,
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Finet O, Yague-Sanz C, Marchand F, Hermand D. The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function. RNA Biol 2022; 19:735-750. [PMID: 35638108 PMCID: PMC9176250 DOI: 10.1080/15476286.2022.2078094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal dihydrouridine (D) epitranscriptomic mark results from a reduction of uridine by the Dus family of NADPH-dependent reductases and is typically found within the eponym D-loop of tRNAs. Despite its apparent simplicity, D is structurally unique, with the potential to deeply affect the RNA backbone and many, if not all, RNA-connected processes. The first landscape of its occupancy within the tRNAome was reported 20 years ago. Its potential biological significance was highlighted by observations ranging from a strong bias in its ecological distribution to the predictive nature of Dus enzymes overexpression for worse cancer patient outcomes. The exquisite specificity of the Dus enzymes revealed by a structure-function analyses and accumulating clues that the D distribution may expand beyond tRNAs recently led to the development of new high-resolution mapping methods, including Rho-seq that established the presence of D within mRNAs and led to the demonstration of its critical physiological relevance.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur, Belgium
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