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Popitsch N, Neumann T, von Haeseler A, Ameres SL. Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework. Genome Biol 2024; 25:166. [PMID: 38918865 DOI: 10.1186/s13059-024-03313-8] [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: 03/17/2023] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases in mapping the resulting reads to reference genomes remain poorly understood. We present splice_sim, a splice-aware RNA-seq simulation and evaluation pipeline that introduces user-defined nucleotide conversions at set frequencies, creates mixture models of converted and unconverted reads, and calculates mapping accuracies per genomic annotation. By simulating nucleotide conversion RNA-seq datasets under realistic experimental conditions, including metabolic RNA labeling and RNA bisulfite sequencing, we measure mapping accuracies of state-of-the-art spliced-read mappers for mouse and human transcripts and derive strategies to prevent biases in the data interpretation.
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Affiliation(s)
- Niko Popitsch
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, A-1030, Austria.
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, A-1030, Austria.
| | - Tobias Neumann
- Quantro Therapeutics, Vienna, A-1030, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, A-1030, Austria
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, A-1030, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, A-1030, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, A-1090, Austria
| | - Stefan L Ameres
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, A-1030, Austria
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, A-1030, Austria
- Institute of Molecular Biotechnology, IMBA, Vienna Biocenter Campus (VBC), Vienna, A-1030, Austria
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Acera Mateos P, J Sethi A, Ravindran A, Srivastava A, Woodward K, Mahmud S, Kanchi M, Guarnacci M, Xu J, W S Yuen Z, Zhou Y, Sneddon A, Hamilton W, Gao J, M Starrs L, Hayashi R, Wickramasinghe V, Zarnack K, Preiss T, Burgio G, Dehorter N, E Shirokikh N, Eyras E. Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications. Nat Commun 2024; 15:3899. [PMID: 38724548 PMCID: PMC11082244 DOI: 10.1038/s41467-024-47953-7] [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: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
The epitranscriptome embodies many new and largely unexplored functions of RNA. A significant roadblock hindering progress in epitranscriptomics is the identification of more than one modification in individual transcript molecules. We address this with CHEUI (CH3 (methylation) Estimation Using Ionic current). CHEUI predicts N6-methyladenosine (m6A) and 5-methylcytosine (m5C) in individual molecules from the same sample, the stoichiometry at transcript reference sites, and differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals to achieve high single-molecule, transcript-site, and stoichiometry accuracies in multiple tests using synthetic RNA standards and cell line data. CHEUI's capability to identify two modification types in the same sample reveals a co-occurrence of m6A and m5C in individual mRNAs in cell line and tissue transcriptomes. CHEUI provides new avenues to discover and study the function of the epitranscriptome.
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Affiliation(s)
- P Acera Mateos
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A J Sethi
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A Ravindran
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - A Srivastava
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - K Woodward
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - S Mahmud
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - M Kanchi
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - M Guarnacci
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - J Xu
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
| | - Z W S Yuen
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - Y Zhou
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - A Sneddon
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - W Hamilton
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3052, Australia
| | - J Gao
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - L M Starrs
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - R Hayashi
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | | | - K Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - T Preiss
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- Victor Chang Cardiac Research Institute, Sydney, NSW, 2010, Australia
| | - G Burgio
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
| | - N Dehorter
- The Eccles Institute of Neuroscience, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
- The Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - N E Shirokikh
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
| | - E Eyras
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, 2601, Australia.
- The Shine-Dalgarno Centre for RNA Innovation, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
- The Centre for Computational Biomedical Sciences, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
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Xu X, Johnson Z, Wang A, Padget RL, Smyth JW, Xie H. Folate regulates RNA m 5C modification and translation in neural stem cells. BMC Biol 2022; 20:261. [PMID: 36424632 PMCID: PMC9686110 DOI: 10.1186/s12915-022-01467-0] [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] [Received: 04/15/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Folate is an essential B-group vitamin and a key methyl donor with important biological functions including DNA methylation regulation. Normal neurodevelopment and physiology are sensitive to the cellular folate levels. Either deficiency or excess of folate may lead to neurological disorders. Recently, folate has been linked to tRNA cytosine-5 methylation (m5C) and translation in mammalian mitochondria. However, the influence of folate intake on neuronal mRNA m5C modification and translation remains largely unknown. Here, we provide transcriptome-wide landscapes of m5C modification in poly(A)-enriched RNAs together with mRNA transcription and translation profiles for mouse neural stem cells (NSCs) cultured in three different concentrations of folate. RESULTS NSCs cultured in three different concentrations of folate showed distinct mRNA methylation profiles. Despite uncovering only a few differentially expressed genes, hundreds of differentially translated genes were identified in NSCs with folate deficiency or supplementation. The differentially translated genes induced by low folate are associated with cytoplasmic translation and mitochondrial function, while the differentially translated genes induced by high folate are associated with increased neural stem cell proliferation. Interestingly, compared to total mRNAs, polysome mRNAs contained high levels of m5C. Furthermore, an integrative analysis indicated a transcript-specific relationship between RNA m5C methylation and mRNA translation efficiency. CONCLUSIONS Altogether, our study reports a transcriptome-wide influence of folate on mRNA m5C methylation and translation in NSCs and reveals a potential link between mRNA m5C methylation and mRNA translation.
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Affiliation(s)
- Xiguang Xu
- grid.438526.e0000 0001 0694 4940Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061 USA ,grid.470073.70000 0001 2178 7701Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061 USA
| | - Zachary Johnson
- grid.438526.e0000 0001 0694 4940Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA
| | - Amanda Wang
- grid.438526.e0000 0001 0694 4940Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Rachel L. Padget
- grid.438526.e0000 0001 0694 4940Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016 USA
| | - James W. Smyth
- grid.438526.e0000 0001 0694 4940Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA 24016 USA ,grid.438526.e0000 0001 0694 4940Virginia Tech Carilion School of Medicine, Roanoke, VA 24016 USA
| | - Hehuang Xie
- grid.438526.e0000 0001 0694 4940Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061 USA ,grid.470073.70000 0001 2178 7701Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061 USA ,grid.438526.e0000 0001 0694 4940Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061 USA
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Xu X, Johnson Z, Xie H. Neuronal Depolarization Induced RNA m5C Methylation Changes in Mouse Cortical Neurons. BIOLOGY 2022; 11:biology11070988. [PMID: 36101370 PMCID: PMC9311806 DOI: 10.3390/biology11070988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
Neuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m5C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of neuronal mRNA m5C modification in response to environmental stimuli has not been explored. Here, we provide transcriptome-wide maps of m5C modification, together with gene expression profiles, for mouse cortical neurons at 0 h, 2 h, and 6 h upon membrane depolarization. Thousands of differentially expressed genes (DEGs) were identified during the neuronal depolarization process. In stimulated neurons, the majority of early response genes were found to serve as expression regulators of late response genes, which are involved in signaling pathways and diverse synaptic functions. With RNA bisulfite sequencing data, a union set of 439 m5C sites was identified with high confidence, and approximately 30% of them were shared by neurons at all three time points. Interestingly, over 41% of the m5C sites showed increased methylation upon neuronal activation and were enriched in transcripts coding for proteins with synaptic functions. In addition, a modest negative correlation was observed between RNA expression and methylation. In summary, our study provided dynamic transcriptome-wide landscapes of RNA m5C methylation in neurons, and revealed that mRNA m5C methylation is associated with the regulation of gene expression.
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Affiliation(s)
- Xiguang Xu
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061, USA
| | - Zachary Johnson
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
| | - Hehuang Xie
- Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA; (X.X.); (Z.J.)
- Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA 24061, USA
- Genetics, Bioinformatics and Computational Biology Program, Virginia Tech, Blacksburg, VA 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
- Translational Biology, Medicine and Health Program, Virginia Tech, Blacksburg, VA 24061, USA
- Correspondence:
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