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Relier S, Schiffers S, Beiki H, Oberdoerffer S. Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs. RNA 2024:rna.079863.123. [PMID: 38697668 DOI: 10.1261/rna.079863.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/04/2024] [Indexed: 05/05/2024]
Abstract
The functional analysis of epitranscriptomic modifications in RNA is constrained by a lack of methods that accurately capture their locations and levels. We previously demonstrated that the RNA modification N4-acetylcytidine (ac4C) can be mapped at base-resolution through sodium borohydride reduction to tetrahydroacetylcytidine (tetrahydro-ac4C), followed by cDNA synthesis to misincorporate adenosine opposite reduced ac4C sites, culminating in C:T mismatches at acetylated cytidines (RedaC:T). However, this process is relatively inefficient, resulting in less than 20% C:T mismatches at a fully modified ac4C site in 18S rRNA. Considering that ac4C locations in other substrates including mRNA are unlikely to reach full penetrance, this method is not ideal for comprehensive mapping. Here, we introduce "RetraC:T" (reduction to tetrahydro-ac4C and reverse transcription with amino-dATP to induce C:T mismatches) as a method with enhanced ability to detect ac4C in cellular RNA. In brief, RNA is reduced through NaBH4 or the closely related reagent sodium cyanoborohydride (NaCNBH3) followed by cDNA synthesis in the presence of a modified DNA nucleotide, 2-amino-dATP, that preferentially binds to tetrahydro-ac4C. Incorporation of the modified dNTP substantially improved C:T mismatch rates, reaching stoichiometric detection of ac4C in 18S rRNA. Importantly, 2-amino-dATP did not result in truncated cDNA products nor increase mismatches at other locations. Thus, modified dNTPs are introduced as a new addition to the toolbox for detecting ac4C at base resolution.
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Beiki H, Sturgill D, Arango D, Relier S, Schiffers S, Oberdoerffer S. Detection of ac4C in human mRNA is preserved upon data reassessment. Mol Cell 2024; 84:1611-1625.e3. [PMID: 38640896 DOI: 10.1016/j.molcel.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/19/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
We recently reported the distribution of N4-acetylcytidine (ac4C) in HeLa mRNA at base resolution through chemical reduction and the induction of C:T mismatches in sequencing (RedaC:T-seq). Our results contradicted an earlier report from Schwartz and colleagues utilizing a similar method termed ac4C-seq. Here, we revisit both datasets and reaffirm our findings. Through RedaC:T-seq reanalysis, we establish a low basal error rate at unmodified nucleotides that is not skewed to any specific mismatch type and a prominent increase in C:T substitutions as the dominant mismatch type in both treated wild-type replicates, with a high degree of reproducibility across replicates. In contrast, through ac4C-seq reanalysis, we uncover significant data quality issues including insufficient depth, with one wild-type replicate yielding 2.7 million reads, inconsistencies in reduction efficiencies between replicates, and an overall increase in mismatches involving thymine that could obscure ac4C detection. These analyses bolster the detection of ac4C in HeLa mRNA through RedaC:T-seq.
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Affiliation(s)
- Hamid Beiki
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Sturgill
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Daniel Arango
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sebastien Relier
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sarah Schiffers
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shalini Oberdoerffer
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Relier S, Amalric A, Attina A, Koumare IB, Rigau V, Burel Vandenbos F, Fontaine D, Baroncini M, Hugnot JP, Duffau H, Bauchet L, Hirtz C, Rivals E, David A. Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics. Anal Chem 2022; 94:11967-11972. [PMID: 35998076 PMCID: PMC9453740 DOI: 10.1021/acs.analchem.2c01526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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One of the main challenges in cancer management relates
to the
discovery of reliable biomarkers, which could guide decision-making
and predict treatment outcome. In particular, the rise and democratization
of high-throughput molecular profiling technologies bolstered the
discovery of “biomarker signatures” that could maximize
the prediction performance. Such an approach was largely employed
from diverse OMICs data (i.e., genomics, transcriptomics, proteomics,
metabolomics) but not from epitranscriptomics, which encompasses more
than 100 biochemical modifications driving the post-transcriptional
fate of RNA: stability, splicing, storage, and translation. We and
others have studied chemical marks in isolation and associated them
with cancer evolution, adaptation, as well as the response to conventional
therapy. In this study, we have designed a unique pipeline combining
multiplex analysis of the epitranscriptomic landscape by high-performance
liquid chromatography coupled to tandem mass spectrometry with statistical
multivariate analysis and machine learning approaches in order to
identify biomarker signatures that could guide precision medicine
and improve disease diagnosis. We applied this approach to analyze
a cohort of adult diffuse glioma patients and demonstrate the existence
of an “epitranscriptomics-based signature” that permits
glioma grades to be discriminated and predicted with unmet accuracy.
This study demonstrates that epitranscriptomics (co)evolves along
cancer progression and opens new prospects in the field of omics molecular
profiling and personalized medicine.
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Affiliation(s)
- S Relier
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - A Amalric
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - A Attina
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - I B Koumare
- Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France.,Neurosurgery Department, CHU Gabriel Toure, Bamako, Mali
| | - V Rigau
- Department of Pathology and Oncobiology, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - F Burel Vandenbos
- Central Laboratory of Pathology, Univ. Côte d'Azur, CHU Nice, CNRS, INSERM, Nice, Alpes-Maritimes 06000, France
| | - D Fontaine
- Neurosurgery Department, Univ. Côte d'Azur, CHU Nice, Nice, Alpes-Maritimes 06000, France
| | - M Baroncini
- Neurosurgery Department, CHU Lille, Univ. of Lille, Lille, Nord 59037, France
| | - J P Hugnot
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - H Duffau
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - L Bauchet
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - C Hirtz
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - E Rivals
- LIRMM, Univ. Montpellier, CNRS, Montpellier, Hérault 34095, France
| | - A David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
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