1
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Fang X, Zhao R, Wang Y, Sun M, Xu J, Long S, Mo J, Liu H, Li X, Wang F, Zhou X, Weng X. A bisulfite-assisted and ligation-based qPCR amplification technology for locus-specific pseudouridine detection at base resolution. Nucleic Acids Res 2024; 52:e49. [PMID: 38709875 PMCID: PMC11162771 DOI: 10.1093/nar/gkae344] [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: 08/25/2023] [Revised: 03/09/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
Over 150 types of chemical modifications have been identified in RNA to date, with pseudouridine (Ψ) being one of the most prevalent modifications in RNA. Ψ plays vital roles in various biological processes, and precise, base-resolution detection methods are fundamental for deep analysis of its distribution and function. In this study, we introduced a novel base-resolution Ψ detection method named pseU-TRACE. pseU-TRACE relied on the fact that RNA containing Ψ underwent a base deletion after treatment of bisulfite (BS) during reverse transcription, which enabled efficient ligation of two probes complementary to the cDNA sequence on either side of the Ψ site and successful amplification in subsequent real-time quantitative PCR (qPCR), thereby achieving selective and accurate Ψ detection. Our method accurately and sensitively detected several known Ψ sites in 28S, 18S, 5.8S, and even mRNA. Moreover, pseU-TRACE could be employed to measure the Ψ fraction in RNA and explore the Ψ metabolism of different pseudouridine synthases (PUSs), providing valuable insights into the function of Ψ. Overall, pseU-TRACE represents a reliable, time-efficient and sensitive Ψ detection method.
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Affiliation(s)
- Xin Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Ruiqi Zhao
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Mei Sun
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Jin Xu
- Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Shengrong Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Hudan Liu
- Medical Research Institute, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China
- Wuhan TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China
- Wuhan TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P. R. China
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2
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López J, Blanco S. Exploring the role of ribosomal RNA modifications in cancer. Curr Opin Genet Dev 2024; 86:102204. [PMID: 38759459 DOI: 10.1016/j.gde.2024.102204] [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: 02/16/2024] [Revised: 04/05/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024]
Abstract
Recent advances have highlighted the significant roles of post-transcriptional modifications in rRNA in various cancers. Evidence suggests that dysregulation of rRNA modifications acts as a common denominator in cancer development, with alterations in these modifications conferring competitive advantages to cancer cells. Specifically, rRNA modifications modulate protein synthesis and favor the specialized translation of oncogenic programs, thereby contributing to the formation of a protumorigenic proteome in cancer cells. These findings reveal a novel regulatory layer mediated by changes in the deposition of rRNA chemical modifications. Moreover, inhibition of these modifications in vitro and in preclinical studies demonstrates potential therapeutic applications. The recurrence of altered rRNA modification patterns across different types of cancer underscores their importance in cancer progression, proposing them as potential biomarkers and novel therapeutic targets. This review will highlight the latest insights into how post-transcriptional rRNA modifications contribute to cancer progression and summarize the main developments and ongoing challenges in this research area.
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Affiliation(s)
- Judith López
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain. https://twitter.com/@judithlopezluis
| | - Sandra Blanco
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC) - University of Salamanca, 37007 Salamanca, Spain; Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, 37007 Salamanca, Spain.
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3
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McCormick CA, Qiu Y, Fanari O, Liu Y, Bloch D, Klink IN, Meseonznik M, Jain M, Wanunu M, Rouhanifard SH. mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593203. [PMID: 38766185 PMCID: PMC11100687 DOI: 10.1101/2024.05.08.593203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Pseudouridine (psi) is one of the most abundant human mRNA modifications generated from the isomerization of uridine via psi synthases, including TRUB1 and PUS7 . Nanopore direct RNA sequencing combined with our recent tool, Mod- p ID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is sensitive for detecting changes in positional psi occupancies across cell types, which can inform our understanding of the impact on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, among a list of highly conserved sites across cell types, most are TRUB1 substrates and fall within the coding sequence. We find that these conserved psi positions correspond to higher levels of protein expression than expected, suggesting translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. We validate these sites by ruling out single-nucleotide variants, analyzing current traces, and performing enzymatic knockdowns of psi synthases. Finally, we characterize sites with multiple psi modifications on the same transcript (hypermodification type II) and found that these can be conserved or cell type specific. Among these, we discovered examples of multiple psi modifications within the same k-mer for the first time and analyzed the effect on current distribution. Our data support the hypothesis that motif sequence and the presence of psi synthase are insufficient to drive modifications, that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation.
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4
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Li Y, Wu S, Ye K. Landscape of RNA pseudouridylation in archaeon Sulfolobus islandicus. Nucleic Acids Res 2024; 52:4644-4658. [PMID: 38375885 PMCID: PMC11077068 DOI: 10.1093/nar/gkae096] [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: 08/03/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Pseudouridine, one of the most abundant RNA modifications, is synthesized by stand-alone or RNA-guided pseudouridine synthases. Here, we comprehensively mapped pseudouridines in rRNAs, tRNAs and small RNAs in the archaeon Sulfolobus islandicus and identified Cbf5-associated H/ACA RNAs. Through genetic deletion and in vitro modification assays, we determined the responsible enzymes for these modifications. The pseudouridylation machinery in S. islandicus consists of the stand-alone enzymes aPus7 and aPus10, and six H/ACA RNA-guided enzymes that account for all identified pseudouridines. These H/ACA RNAs guide the modification of all eleven sites in rRNAs, two sites in tRNAs, and two sites in CRISPR RNAs. One H/ACA RNA shows exceptional versatility by targeting eight different sites. aPus7 and aPus10 are responsible for modifying positions 13, 54 and 55 in tRNAs. We identified four atypical H/ACA RNAs that lack the lower stem and the ACA motif and confirmed their function both in vivo and in vitro. Intriguingly, atypical H/ACA RNAs can be modified by Cbf5 in a guide-independent manner. Our data provide the first global view of pseudouridylation in archaea and reveal unexpected structures, substrates, and activities of archaeal H/ACA RNPs.
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MESH Headings
- Pseudouridine/metabolism
- Sulfolobus/genetics
- Sulfolobus/metabolism
- RNA, Transfer/metabolism
- RNA, Transfer/genetics
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Archaeal/chemistry
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/genetics
- Archaeal Proteins/metabolism
- Archaeal Proteins/genetics
- RNA Processing, Post-Transcriptional
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Intramolecular Transferases/genetics
- Intramolecular Transferases/metabolism
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Affiliation(s)
- Yuqian Li
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Garcia-Campos MA, Schwartz S. txtools: an R package facilitating analysis of RNA modifications, structures, and interactions. Nucleic Acids Res 2024; 52:e42. [PMID: 38512053 PMCID: PMC11077046 DOI: 10.1093/nar/gkae203] [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: 09/15/2023] [Revised: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024] Open
Abstract
We present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with transcriptomic representation. txtools' main inputs are BAM files and a transcriptome annotation, and the main output is a table, capturing mismatches, deletions, and the number of reads beginning and ending at each nucleotide in the transcriptomic space. txtools further facilitates downstream visualization and analyses. We showcase, using examples from the epitranscriptomic field, how a few calls to txtools functions can yield insightful and ready-to-publish results. txtools is of broad utility also in the context of structural mapping and RNA:protein interaction mapping. By providing a simple and intuitive framework, we believe that txtools will be a useful and convenient tool and pave the path for future discovery. txtools is available for installation from its GitHub repository at https://github.com/AngelCampos/txtools.
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Affiliation(s)
- Miguel Angel Garcia-Campos
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Central District, 761000, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Central District, 761000, Israel
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6
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Pan Y, Adachi H, He X, Chen JL, Yu YT, Boutz PL. Updated Pseudo-seq Protocol for Transcriptome-Wide Detection of Pseudouridines. Bio Protoc 2024; 14:e4985. [PMID: 38737508 PMCID: PMC11082786 DOI: 10.21769/bioprotoc.4985] [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: 01/15/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 05/14/2024] Open
Abstract
Pseudouridine (Ψ), the most prevalent modified base in cellular RNAs, has been mapped to numerous sites not only in rRNAs, tRNAs, and snRNAs but also mRNAs. Although there have been multiple techniques to identify Ψs, due to the recent development of sequencing technologies some reagents are not compatible with the current sequencer. Here, we show the updated Pseudo-seq, a technique enabling the genome-wide identification of pseudouridylation sites with single-nucleotide precision. We provide a comprehensive description of Pseudo-seq, covering protocols for RNA isolation from human cells, library preparation, and detailed data analysis procedures. The methodology presented is easily adaptable to any cell or tissue type with high-quality mRNA isolation. It can be used for discovering novel pseudouridylation sites, thus constituting a crucial initial step toward understanding the regulation and function of this modification. Key features • Identification of Ψ sites on mRNAs. • Updated Pseudo-seq provides precise positional and quantitative information of Ψ. • Uses a more efficient library preparation with the latest, currently available materials.
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Affiliation(s)
- Yi Pan
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
| | - Hironori Adachi
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
| | - Xueyang He
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
| | - Jonathan L. Chen
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
| | - Yi-Tao Yu
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
| | - Paul L. Boutz
- University of Rochester Medical Center, Department of Biochemistry and Biophysics, Center for RNA Biology, Rochester, NY, USA
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7
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 PMCID: PMC11075746 DOI: 10.1016/j.cels.2024.03.005] [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: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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8
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Zhang M, Zhang X, Ma Y, Yi C. New directions for Ψ and m 1A decoding in mRNA: deciphering the stoichiometry and function. RNA (NEW YORK, N.Y.) 2024; 30:537-547. [PMID: 38531648 PMCID: PMC11019747 DOI: 10.1261/rna.079950.124] [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: 01/15/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Over the past decade, advancements in epitranscriptomics have significantly enhanced our understanding of mRNA metabolism and its role in human development and diseases. This period has witnessed breakthroughs in sequencing technologies and the identification of key proteins involved in RNA modification processes. Alongside the well-studied m6A, Ψ and m1A have emerged as key epitranscriptomic markers. Initially identified through transcriptome-wide profiling, these modifications are now recognized for their broad impact on RNA metabolism and gene expression. In this Perspective, we focus on the detections and functions of Ψ and m1A modifications in mRNA and discuss previous discrepancies and future challenges. We summarize recent advances and highlight the latest sequencing technologies for stoichiometric detection and their mechanistic investigations for functional unveiling in mRNA as the new research directions.
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Affiliation(s)
- Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yichen Ma
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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9
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Gilbert WV. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA (NEW YORK, N.Y.) 2024; 30:530-536. [PMID: 38531650 PMCID: PMC11019745 DOI: 10.1261/rna.079975.124] [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: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Pseudouridine is an abundant mRNA modification found in diverse organisms ranging from bacteria and viruses to multicellular plants and humans. New developments in pseudouridine profiling provide quantitative tools to map mRNA pseudouridylation sites. Sparse biochemical studies establish the potential for mRNA pseudouridylation to affect most stages of the mRNA life cycle from birth to death. This recent progress sets the stage for deeper investigations into the molecular and cellular functions of specific mRNA pseudouridines, including in disease.
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Affiliation(s)
- Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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10
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Fanari O, Tavakoli S, Akeson S, Makhamreh A, Nian K, McCormick CA, Qiu Y, Bloch D, Jain M, Wanunu M, Rouhanifard SH. Probing enzyme-dependent pseudouridylation using direct RNA sequencing to assess neuronal epitranscriptome plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586895. [PMID: 38585714 PMCID: PMC10996719 DOI: 10.1101/2024.03.26.586895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Chemical modifications in mRNAs such as pseudouridine (psi) can regulate gene expression, although our understanding of the functional impact of individual psi modifications, especially in neuronal cells, is limited. We apply nanopore direct RNA sequencing to investigate psi dynamics under cellular perturbations in SH-SY5Y cells. We assign sites to psi synthases using siRNA-based knockdown. A steady-state enzyme-substrate model reveals a strong correlation between psi synthase and mRNA substrate levels and psi modification frequencies. Next, we performed either differentiation or lead-exposure to SH-SY5Y cells and found that, upon lead exposure, not differentiation, the modification frequency is less dependent on enzyme levels suggesting translational control. Finally, we compared the plasticity of psi sites across cellular states and found that plastic sites can be condition-dependent or condition-independent; several of these sites fall within transcripts encoding proteins involved in neuronal processes. Our psi analysis and validation enable investigations into the dynamics and plasticity of RNA modifications.
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Affiliation(s)
- Oleksandra Fanari
- Dept. of Bioengineering, Northeastern University, Boston, MA
- These authors contributed equally
| | - Sepideh Tavakoli
- Dept. of Bioengineering, Northeastern University, Boston, MA
- These authors contributed equally
| | - Stuart Akeson
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Amr Makhamreh
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Keqing Nian
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | | | - Yuchen Qiu
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Dylan Bloch
- Dept. of Bioengineering, Northeastern University, Boston, MA
| | - Miten Jain
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
| | - Meni Wanunu
- Dept. of Bioengineering, Northeastern University, Boston, MA
- Dept. of Physics, Northeastern University, Boston, MA
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11
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Sun M, Fang X, Lin B, Mo J, Wang F, Zhou X, Weng X. Locus-specific detection of pseudouridine with CRISPR-Cas13a. Chem Commun (Camb) 2024; 60:4088-4091. [PMID: 38511312 DOI: 10.1039/d4cc00179f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
We combined the CRISPR-Cas13a system with CMC chemical labeling, developing an approach that enables precise identification of pseudouridine (Ψ) sites at specific loci within ribosomal RNA (rRNA), messenger RNA (mRNA) and small nuclear RNAs (snRNA). This method, with good efficiency and simplicity, detects Ψ sites through fluorescence measurement, providing a straightforward and fast validation for targeted Ψ sites of interest.
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Affiliation(s)
- Mei Sun
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Xin Fang
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Bingqian Lin
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
| | - Fang Wang
- Wuhan University School of Pharmaceutical Sciences, Wuhan, 430071, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
- Wuhan TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, P. R. China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Department of Clinical Laboratory of Zhongnan Hospital, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan, Hubei, 430072, P. R. China.
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12
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Wang X, Li P, Wang R, Gao X. PseUpred-ELPSO Is an Ensemble Learning Predictor with Particle Swarm Optimizer for Improving the Prediction of RNA Pseudouridine Sites. BIOLOGY 2024; 13:248. [PMID: 38666860 PMCID: PMC11048358 DOI: 10.3390/biology13040248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
RNA pseudouridine modification exists in different RNA types of many species, and it has a significant role in regulating the expression of biological processes. To understand the functional mechanisms for RNA pseudouridine sites, the accurate identification of pseudouridine sites in RNA sequences is essential. Although several fast and inexpensive computational methods have been proposed, the challenge of improving recognition accuracy and generalization still exists. This study proposed a novel ensemble predictor called PseUpred-ELPSO for improved RNA pseudouridine site prediction. After analyzing the nucleotide composition preferences between RNA pseudouridine site sequences, two feature representations were determined and fed into the stacking ensemble framework. Then, using five tree-based machine learning classifiers as base classifiers, 30-dimensional RNA profiles are constructed to represent RNA sequences, and using the PSO algorithm, the weights of the RNA profiles were searched to further enhance the representation. A logistic regression classifier was used as a meta-classifier to complete the final predictions. Compared to the most advanced predictors, the performance of PseUpred-ELPSO is superior in both cross-validation and the independent test. Based on the PseUpred-ELPSO predictor, a free and easy-to-operate web server has been established, which will be a powerful tool for pseudouridine site identification.
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Affiliation(s)
- Xiao Wang
- School of Computer Science and Technology, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450002, China; (X.W.); (P.L.)
- Henan Provincial Key Laboratory of Data Intelligence for Food Safety, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450002, China
| | - Pengfei Li
- School of Computer Science and Technology, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450002, China; (X.W.); (P.L.)
| | - Rong Wang
- School of Electronic Information, Zhengzhou University of Light Industry, No. 136, Science Avenue, Zhengzhou 450002, China;
| | - Xu Gao
- National Supercomputing Center in Zhengzhou, School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou 450001, China
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13
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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
ConspectusAmong 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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14
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Zhang LS, Ye C, Ju CW, Gao B, Feng X, Sun HL, Wei J, Yang F, Dai Q, He C. BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution. Nat Protoc 2024; 19:517-538. [PMID: 37968414 PMCID: PMC11007761 DOI: 10.1038/s41596-023-00917-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 09/25/2023] [Indexed: 11/17/2023]
Abstract
Pseudouridine (Ψ) is an abundant RNA modification that is present in and affects the functions of diverse non-coding RNA species, including rRNA, tRNA and small nuclear RNA. Ψ also exists in mammalian mRNA and probably exhibits functional roles; however, functional investigations of mRNA Ψ modifications in mammals have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed bisulfite-induced deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol for mapping Ψ distribution across cellular mRNAs, which includes fast steps in both library preparation and data analysis. This protocol generates highly reproducible results by inducing high deletion ratios at Ψ modification within diverse sequence contexts, and meanwhile displayed almost zero background deletions at unmodified uridines. When used for transcriptome-wide Ψ profiling in mouse embryonic stem cells, the current protocol uncovered 8,407 Ψ sites from as little as 10 ng of polyA+ RNA input. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS) and data analysis. Library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe ( https://github.com/y9c/pseudoU-BIDseq ), a user-friendly data analysis pipeline for Ψ site detection and modification stoichiometry quantification, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from BID-seq data.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Chang Ye
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Cheng-Wei Ju
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | - Boyang Gao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xinran Feng
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Hui-Lung Sun
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Fan Yang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
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15
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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16
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Joshi K, Wang DO. epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation. Brief Bioinform 2024; 25:bbad521. [PMID: 38271482 PMCID: PMC10810334 DOI: 10.1093/bib/bbad521] [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: 07/13/2023] [Revised: 11/01/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Recent technological advances in sequencing DNA and RNA modifications using high-throughput platforms have generated vast epigenomic and epitranscriptomic datasets whose power in transforming life science is yet fully unleashed. Currently available in silico methods have facilitated the identification, positioning and quantitative comparisons of individual modification sites. However, the essential challenge to link specific 'epi-marks' to gene expression in the particular context of cellular and biological processes is unmet. To fast-track exploration, we generated epidecodeR implemented in R, which allows biologists to quickly survey whether an epigenomic or epitranscriptomic status of their interest potentially influences gene expression responses. The evaluation is based on the cumulative distribution function and the statistical significance in differential expression of genes grouped by the number of 'epi-marks'. This tool proves useful in predicting the role of H3K9ac and H3K27ac in associated gene expression after knocking down deacetylases FAM60A and SDS3 and N6-methyl-adenosine-associated gene expression after knocking out the reader proteins. We further used epidecodeR to explore the effectiveness of demethylase FTO inhibitors and histone-associated modifications in drug abuse in animals. epidecodeR is available for downloading as an R package at https://bioconductor.riken.jp/packages/3.13/bioc/html/epidecodeR.html.
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Affiliation(s)
- Kandarp Joshi
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Dan O Wang
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- New York University Abu Dhabi,Saadiyat Campus C1-031, Abu Dhabi, United Arab Emirates
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17
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Chen JL, Leeder WM, Morais P, Adachi H, Yu YT. Pseudouridylation-mediated gene expression modulation. Biochem J 2024; 481:1-16. [PMID: 38174858 DOI: 10.1042/bcj20230096] [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: 10/14/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.
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Affiliation(s)
- Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | | | | | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, U.S.A
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18
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Xuan J, Chen L, Chen Z, Pang J, Huang J, Lin J, Zheng L, Li B, Qu L, Yang J. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Res 2024; 52:D273-D284. [PMID: 37956310 PMCID: PMC10767931 DOI: 10.1093/nar/gkad1070] [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: 09/15/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.
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Affiliation(s)
- Jiajia Xuan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lifan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhirong Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinran Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Human Phenome Institute, Fudan University, 825 Zhangheng Road, Shanghai 201203, China
| | - Lingling Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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19
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Zhang LS, Dai Q, He C. Base-Resolution Sequencing Methods for Whole-Transcriptome Quantification of mRNA Modifications. Acc Chem Res 2024; 57:47-58. [PMID: 38079380 PMCID: PMC10765377 DOI: 10.1021/acs.accounts.3c00532] [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: 08/30/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
ConspectusRNA molecules are not merely a combination of four bases of A, C, G, and U. Chemical modifications occur in almost all RNA species and play diverse roles in gene expression regulation. The abundant cellular RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), are known to have the highest density of RNA modifications, which exert critical functions in rRNA and tRNA biogenesis, stability, and subsequent translation. In recent years, modifications on low-abundance RNA species in mammalian cells, such as messenger RNA (mRNA), regulatory noncoding RNA (ncRNA), and chromatin-associated RNA (caRNA), have been shown to contain multiple different chemical modifications with functional significance.As the most abundant mRNA modification in mammals, N6-methyladenosine (m6A) affects nearly every stage of mRNA processing and metabolism, with the antibody-based m6A-MeRIP-seq (methylated RNA immunoprecipitation sequencing) followed by high-throughput sequencing widely employed in mapping m6A distribution transcriptome-wide in diverse biological systems. In addition to m6A, other chemical modifications such as pseudouridine (Ψ), 2'-O-methylation (Nm), 5-methylcytidine (m5C), internal N7-methylguanosine (m7G), N1-methyladenosine (m1A), N4-acetylcytidine (ac4C), etc. also exist in polyA-tailed RNA in mammalian cells, requiring effective mapping approaches for whole-transcriptome profiling of these non-m6A mRNA modifications. Like m6A, the antibody-based enrichment followed by sequencing has been the primary method to study distributions of these modifications. Methods to more quantitatively map these modifications would dramatically improve our understanding of distributions and modification density of these chemical marks on RNA, thereby bettering informing functional implications. In this Account, aimed at both single-base resolution and modification fraction quantification, we summarize our recent advances in developing a series of chemistry- or biochemistry-based methods to quantitatively map RNA modifications, including m6A, Ψ, m5C, m1A, 2'-O-methylation (Nm), and internal m7G, in mammalian mRNA at base resolution. These new methods, including m6A-SAC-seq, eTAM-seq, BID-seq, UBS-seq, DAMM-seq, m1A-quant-seq, Nm-Mut-seq, and m7G-quant-seq, promise to conduct base-resolution mapping of most major mRNA modifications with low RNA input and uncover dynamic changes in modification stoichiometry during biological and physiological processes, facilitating future investigations on these RNA modifications in regulating cellular gene expression and as potential biomarkers for clinical diagnosis and prognosis. These quantitative sequencing methods allow the mapping of most mRNA modifications with limited input sample requirements. The same modifications on diverse RNA species, such as caRNA, ncRNA, nuclear nascent RNA, mitochondrial RNA, cell-free RNA (cfRNA), etc., could be sequenced using the same methods.
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Affiliation(s)
- Li-Sheng Zhang
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
- Department
of Chemistry, The Hong Kong University of
Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
- Division
of Life Science, The Hong Kong University
of Science and Technology (HKUST), Kowloon 999077, Hong
Kong SAR, China
| | - Qing Dai
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Howard
Hughes Medical Institute, The University
of Chicago, Chicago, Illinois 60637, United States
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20
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Rodell R, Robalin N, Martinez NM. Why U matters: detection and functions of pseudouridine modifications in mRNAs. Trends Biochem Sci 2024; 49:12-27. [PMID: 38097411 DOI: 10.1016/j.tibs.2023.10.008] [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: 08/02/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 01/07/2024]
Abstract
The uridine modifications pseudouridine (Ψ), dihydrouridine, and 5-methyluridine are present in eukaryotic mRNAs. Many uridine-modifying enzymes are associated with human disease, underscoring the importance of uncovering the functions of uridine modifications in mRNAs. These modified uridines have chemical properties distinct from those of canonical uridines, which impact RNA structure and RNA-protein interactions. Ψ, the most abundant of these uridine modifications, is present across (pre-)mRNAs. Recent work has shown that many Ψs are present at intermediate to high stoichiometries that are likely conducive to function and at locations that are poised to influence pre-/mRNA processing. Technological innovations and mechanistic investigations are unveiling the functions of uridine modifications in pre-mRNA splicing, translation, and mRNA stability, which are discussed in this review.
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Affiliation(s)
- Rebecca Rodell
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Nicolas Robalin
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Nicole M Martinez
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H Institute, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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21
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Gionco JT, Bernstein AI. Emerging Role of Environmental Epitranscriptomics and RNA Modifications in Parkinson's Disease. JOURNAL OF PARKINSON'S DISEASE 2024; 14:643-656. [PMID: 38578904 DOI: 10.3233/jpd-230457] [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] [Indexed: 04/07/2024]
Abstract
Environmental risk factors and gene-environment interactions play a critical role in Parkinson's disease (PD). However, the relatively large contribution of environmental risk factors in the overwhelming majority of PD cases has been widely neglected in the field. A "PD prevention agenda" proposed in this journal laid out a set of research priorities focused on preventing PD through modification of environmental risk factors. This agenda includes a call for preclinical studies to employ new high-throughput methods for analyzing transcriptomics and epigenomics to provide a deeper understanding of the effects of exposures linked to PD. Here, we focus on epitranscriptomics as a novel area of research with the potential to add to our understanding of the interplay between genes and environmental exposures in PD. Both epigenetics and epitranscriptomics have been recognized as potential mediators of the complex relationship between genes, environment, and disease. Multiple studies have identified epigenetic alterations, such as DNA methylation, associated with PD and PD-related exposures in human studies and preclinical models. In addition, recent technological advancements have made it possible to study epitranscriptomic RNA modifications, such as RNA N6-methyladenosine (m6A), and a handful of recent studies have begun to explore epitranscriptomics in PD-relevant exposure models. Continued exploration of epitranscriptomic mechanisms in environmentally relevant PD models offers the opportunity to identify biomarkers, pre-degenerative changes that precede symptom onset, and potential mitigation strategies for disease prevention and treatment.
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Affiliation(s)
- John T Gionco
- Graduate Program in Cell and Developmental Biology, Rutgers University, Piscataway, NJ, USA
| | - Alison I Bernstein
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, NJ, USA
- Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
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22
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Deng L, Kumar J, Rose R, McIntyre W, Fabris D. Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code. MASS SPECTROMETRY REVIEWS 2024; 43:5-38. [PMID: 36052666 DOI: 10.1002/mas.21798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
The discovery of RNA silencing has revealed that non-protein-coding sequences (ncRNAs) can cover essential roles in regulatory networks and their malfunction may result in severe consequences on human health. These findings have prompted a general reassessment of the significance of RNA as a key player in cellular processes. This reassessment, however, will not be complete without a greater understanding of the distribution and function of the over 170 variants of the canonical ribonucleotides, which contribute to the breathtaking structural diversity of natural RNA. This review surveys the analytical approaches employed for the identification, characterization, and detection of RNA posttranscriptional modifications (rPTMs). The merits of analyzing individual units after exhaustive hydrolysis of the initial biopolymer are outlined together with those of identifying their position in the sequence of parent strands. Approaches based on next generation sequencing and mass spectrometry technologies are covered in depth to provide a comprehensive view of their respective merits. Deciphering the epitranscriptomic code will require not only mapping the location of rPTMs in the various classes of RNAs, but also assessing the variations of expression levels under different experimental conditions. The fact that no individual platform is currently capable of meeting all such demands implies that it will be essential to capitalize on complementary approaches to obtain the desired information. For this reason, the review strived to cover the broadest possible range of techniques to provide readers with the fundamental elements necessary to make informed choices and design the most effective possible strategy to accomplish the task at hand.
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Affiliation(s)
- L Deng
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - J Kumar
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - R Rose
- Department of Advanced Research Technologies, New York University Langone Health Center, New York, USA
| | - W McIntyre
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Daniele Fabris
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
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23
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Pham CT, Rangan L, Schlenner S. RNA modifications-a regulatory dimension yet to be deciphered in immunity. Genes Immun 2023; 24:281-282. [PMID: 37985689 DOI: 10.1038/s41435-023-00228-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Affiliation(s)
- Cuong Thi Pham
- Department of Microbiology, Immunology and Transplantation, KU Leuven-University of Leuven, Leuven, Belgium
| | - Laurie Rangan
- Department of Microbiology, Immunology and Transplantation, KU Leuven-University of Leuven, Leuven, Belgium
| | - Susan Schlenner
- Department of Microbiology, Immunology and Transplantation, KU Leuven-University of Leuven, Leuven, Belgium.
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24
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Niu Y, Liu L. RNA pseudouridine modification in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6431-6447. [PMID: 37581601 DOI: 10.1093/jxb/erad323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Pseudouridine is one of the well-known chemical modifications in various RNA species. Current advances to detect pseudouridine show that the pseudouridine landscape is dynamic and affects multiple cellular processes. Although our understanding of this post-transcriptional modification mainly depends on yeast and human models, the recent findings provide strong evidence for the critical role of pseudouridine in plants. Here, we review the current knowledge of pseudouridine in plant RNAs, including its synthesis, degradation, regulatory mechanisms, and functions. Moreover, we propose future areas of research on pseudouridine modification in plants.
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Affiliation(s)
- Yanli Niu
- Laboratory of Cell Signal Transduction, School of Basic Medical Sciences, Henan University, Kaifeng 475001, China
| | - Lingyun Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
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25
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Rajan KS, Madmoni H, Bashan A, Taoka M, Aryal S, Nobe Y, Doniger T, Galili Kostin B, Blumberg A, Cohen-Chalamish S, Schwartz S, Rivalta A, Zimmerman E, Unger R, Isobe T, Yonath A, Michaeli S. A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei. Nat Commun 2023; 14:7462. [PMID: 37985661 PMCID: PMC10662448 DOI: 10.1038/s41467-023-43263-6] [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: 02/04/2022] [Accepted: 11/05/2023] [Indexed: 11/22/2023] Open
Abstract
Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.
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Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Saurav Aryal
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Beathrice Galili Kostin
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Amit Blumberg
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Andre Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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26
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Grünberg S, Doyle LA, Wolf EJ, Dai N, Corrêa IR, Yigit E, Stoddard BL. The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1. PLoS One 2023; 18:e0291267. [PMID: 37939088 PMCID: PMC10631681 DOI: 10.1371/journal.pone.0291267] [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: 05/05/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023] Open
Abstract
The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or 'PUS' enzymes include those that rely on guide RNA molecules and others that function as 'stand-alone' enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.
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Affiliation(s)
| | - Lindsey A. Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eric J. Wolf
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Nan Dai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Ivan R. Corrêa
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Erbay Yigit
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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27
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Zhang M, Xiao Y, Jiang Z, Yi C. Quantifying m 6A and Ψ Modifications in the Transcriptome via Chemical-Assisted Approaches. Acc Chem Res 2023; 56:2980-2991. [PMID: 37851547 DOI: 10.1021/acs.accounts.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Since the discovery of the first chemically modified RNA nucleotide in 1951, more than 170 types of chemical modifications have been characterized in RNA so far. Since the discovery of the reversible and dynamic nature of N6-methyladenosine (m6A) in mRNA modification, researchers have identified about ten modifications in eukaryotic mRNA; together with modifications on the noncoding RNAs, the term "epitranscriptome" has been coined to describe the ensemble of various chemical RNA modifications. The past decade has witnessed the discovery of many novel molecular functions of mRNA modifications, demonstrating their crucial roles in gene expression regulation. As the most abundant modifications in mRNA, the study of m6A and Ψ has been facilitated by innovative high-throughput sequencing technologies, which can be based on antibodies, enzymes, or novel chemistry. Among them, chemical-assisted methods utilize selective chemistry that can discriminate modified versus unmodified nucleotides, enabling the transcriptome-wide mapping of m6A and Ψ modifications and functional studies.Our group has developed several sequencing technologies to investigate these epitranscriptomic marks including m6A, Ψ, m1A, and m6Am. Among them, we have recently developed two methods for absolute quantification of m6A and Ψ in the transcriptome based on chemical reactivity to distinguish and measure the two modifications. In GLORI, we used glyoxal and nitrite to mediate efficient deamination of regular adenosine, while m6A remained unaffected, thereby enabling efficient and unbiased detection of single-base resolution and absolute quantification of m6A modification. In CeU-seq and PRAISE, we used different chemistry to achieve selective labeling and detection of transcriptome-wide Ψ. CeU-seq is based on an azido-derivatized carbodiimide compound, while PRAISE utilizes the unique activity of bisulfite to Ψ. PRAISE results in the formation of ring-opening Ψ-bisulfite adduct and quantitatively detects Ψ as 1-2 nt deletion signatures during sequencing. The resulting base-resolution and stoichiometric information expanded our understanding to the profiles of RNA modifications in the transcriptome. In particular, the quantitative information on RNA methylome is critical for characterizing the dynamic and reversible nature of RNA modifications, for instance, under environmental stress or during development. Additionally, base-resolution and stoichiometric information can greatly facilitate the analysis and characterization of functional modification sites that are important for gene expression regulation, especially when one modification type may have multiple or even opposing functions within a specific transcript. Together, the quantitative profiling methods provide the modification stoichiometry information, which is critical to study the regulatory roles of RNA modifications.In this Account, we will focus on the quantitative sequencing technologies of m6A and Ψ developed in our group, review recent advances in chemical-assisted reactions for m6A and Ψ detection, and discuss the challenges and future opportunities of transcriptome-wide mapping technologies for RNA modifications.
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Affiliation(s)
- Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ye Xiao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhe Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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28
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Herridge RP, Dolata J, Migliori V, de Santis Alves C, Borges F, Schorn AJ, Van Ex F, Parent JS, Lin A, Bajczyk M, Leonardi T, Hendrick A, Kouzarides T, Martienssen RA. Pseudouridine guides germline small RNA transport and epigenetic inheritance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.27.542553. [PMID: 37398006 PMCID: PMC10312437 DOI: 10.1101/2023.05.27.542553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes1. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation2,3. In C. elegans, these inherited small RNAs have poly (UG) tails4, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline.
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Affiliation(s)
- Rowan P Herridge
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jakub Dolata
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Valentina Migliori
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Andrea J Schorn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Frédéric Van Ex
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jean-Sebastien Parent
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Ann Lin
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Tommaso Leonardi
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Center for Genomic Science of IIT@SEMM, Instituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Alan Hendrick
- Storm Therapeutics, Ltd., Moneta Building (B280), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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29
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Yu Y, Liang C, Wang X, Shi Y, Shen L. The potential role of RNA modification in skin diseases, as well as the recent advances in its detection methods and therapeutic agents. Biomed Pharmacother 2023; 167:115524. [PMID: 37722194 DOI: 10.1016/j.biopha.2023.115524] [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: 07/04/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/20/2023] Open
Abstract
RNA modification is considered as an epigenetic modification that plays an indispensable role in biological processes such as gene expression and genome editing without altering nucleotide sequence, but the molecular mechanism of RNA modification has not been discussed systematically in the development of skin diseases. This article mainly presents the whole picture of theoretical achievements on the potential role of RNA modification in dermatology. Furthermore, this article summarizes the latest advances in clinical practice related with RNA modification, including its detection methods and drug development. Based on this comprehensive review, we aim to illustrate the current blind spots and future directions of RNA modification, which may provide new insights for researchers in this field.
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Affiliation(s)
- Yue Yu
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Chen Liang
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xin Wang
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China
| | - Yuling Shi
- Department of Dermatology, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China; Institute of Psoriasis, School of Medicine, Tongji University, Shanghai, China.
| | - Liangliang Shen
- Department of Dermatology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
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30
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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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31
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Abstract
RNA modification is manifested as chemically altered nucleotides, widely exists in diverse natural RNAs, and is closely related to RNA structure and function. Currently, mRNA-based vaccines have received great attention and rapid development as novel and mighty fighters against various diseases including cancer. The achievement of RNA vaccines in clinical application is largely attributed to some methodological innovations including the incorporation of modified nucleotides into the synthetic RNA. The selection of optimal RNA modifications aimed at reducing the instability and immunogenicity of RNA molecules is a very critical task to improve the efficacy and safety of mRNA vaccines. This review summarizes the functions of RNA modifications and their application in mRNA vaccines, highlights recent advances of mRNA vaccines in cancer immunotherapy, and provides perspectives for future development of mRNA vaccines in the context of personalized tumor therapy.
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Affiliation(s)
- Yingxue Mei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xiang Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
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32
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Zhang M, Jiang Z, Ma Y, Liu W, Zhuang Y, Lu B, Li K, Peng J, Yi C. Quantitative profiling of pseudouridylation landscape in the human transcriptome. Nat Chem Biol 2023; 19:1185-1195. [PMID: 36997645 DOI: 10.1038/s41589-023-01304-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/02/2023] [Indexed: 04/07/2023]
Abstract
Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, stoichiometric measurement of individual Ψ sites in human transcriptome remains unaddressed. Here we develop 'PRAISE', via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional bisulfite treatment, our approach is based on quaternary base mapping and revealed an ~10% median modification level for 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1, with TRUB1 targets showing the highest modification stoichiometry. In addition, we quantified known and new Ψ sites in mitochondrial mRNA catalyzed by PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide Ψ; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.
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Affiliation(s)
- Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Zhe Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Yichen Ma
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wenqing Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuan Zhuang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Kai Li
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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33
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Sun H, Li K, Liu C, Yi C. Regulation and functions of non-m 6A mRNA modifications. Nat Rev Mol Cell Biol 2023; 24:714-731. [PMID: 37369853 DOI: 10.1038/s41580-023-00622-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.
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Affiliation(s)
- Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Kai Li
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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34
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Chen X, Xu H, Shu X, Song CX. Mapping epigenetic modifications by sequencing technologies. Cell Death Differ 2023:10.1038/s41418-023-01213-1. [PMID: 37658169 DOI: 10.1038/s41418-023-01213-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 09/03/2023] Open
Abstract
The "epigenetics" concept was first described in 1942. Thus far, chemical modifications on histones, DNA, and RNA have emerged as three important building blocks of epigenetic modifications. Many epigenetic modifications have been intensively studied and found to be involved in most essential biological processes as well as human diseases, including cancer. Precisely and quantitatively mapping over 100 [1], 17 [2], and 160 [3] different known types of epigenetic modifications in histone, DNA, and RNA is the key to understanding the role of epigenetic modifications in gene regulation in diverse biological processes. With the rapid development of sequencing technologies, scientists are able to detect specific epigenetic modifications with various quantitative, high-resolution, whole-genome/transcriptome approaches. Here, we summarize recent advances in epigenetic modification sequencing technologies, focusing on major histone, DNA, and RNA modifications in mammalian cells.
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Affiliation(s)
- Xiufei Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Haiqi Xu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Xiao Shu
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Chun-Xiao Song
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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35
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Ye Z, Harmon J, Ni W, Li Y, Wich D, Xu Q. The mRNA Vaccine Revolution: COVID-19 Has Launched the Future of Vaccinology. ACS NANO 2023; 17:15231-15253. [PMID: 37535899 DOI: 10.1021/acsnano.2c12584] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
During the COVID-19 pandemic, mRNA (mRNA) vaccines emerged as leading vaccine candidates in a record time. Nonreplicating mRNA (NRM) and self-amplifying mRNA (SAM) technologies have been developed into high-performing and clinically viable vaccines against a range of infectious agents, notably SARS-CoV-2. mRNA vaccines demonstrate efficient in vivo delivery, long-lasting stability, and nonexistent risk of infection. The stability and translational efficiency of in vitro transcription (IVT)-mRNA can be further increased by modulating its structural elements. In this review, we present a comprehensive overview of the recent advances, key applications, and future challenges in the field of mRNA-based vaccinology.
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Affiliation(s)
- Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Joseph Harmon
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Wei Ni
- Department of Medical Oncology, Dana-Farber Cancer Institute at Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Yamin Li
- Department of Pharmacology, State University of New York Upstate Medical University, Syracuse, New York 13210, United States
| | - Douglas Wich
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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36
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Pederiva C, Trevisan DM, Peirasmaki D, Chen S, Savage SA, Larsson O, Ule J, Baranello L, Agostini F, Farnebo M. Control of protein synthesis through mRNA pseudouridylation by dyskerin. SCIENCE ADVANCES 2023; 9:eadg1805. [PMID: 37506213 PMCID: PMC10381945 DOI: 10.1126/sciadv.adg1805] [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: 12/07/2022] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Posttranscriptional modifications of mRNA have emerged as regulators of gene expression. Although pseudouridylation is the most abundant, its biological role remains poorly understood. Here, we demonstrate that the pseudouridine synthase dyskerin associates with RNA polymerase II, binds to thousands of mRNAs, and is responsible for their pseudouridylation, an action that occurs in chromatin and does not appear to require a guide RNA with full complementarity. In cells lacking dyskerin, mRNA pseudouridylation is reduced, while at the same time, de novo protein synthesis is enhanced, indicating that this modification interferes with translation. Accordingly, mRNAs with fewer pseudouridines due to knockdown of dyskerin are translated more efficiently. Moreover, mRNA pseudouridylation is severely reduced in patients with dyskeratosis congenita caused by inherited mutations in the gene encoding dyskerin (i.e., DKC1). Our findings demonstrate that pseudouridylation by dyskerin modulates mRNA translatability, with important implications for both normal development and disease.
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Affiliation(s)
- Chiara Pederiva
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Davide M. Trevisan
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14152, Sweden
| | - Dimitra Peirasmaki
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Shan Chen
- Department of Oncology and Pathology, Karolinska Institutet, Solna 17165, Sweden
- Science for Life Laboratory, Stockholm 17165, Sweden
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20852, USA
| | - Ola Larsson
- Department of Oncology and Pathology, Karolinska Institutet, Solna 17165, Sweden
- Science for Life Laboratory, Stockholm 17165, Sweden
| | - Jernej Ule
- The Francis Crick Institute, London NW1 1AT, UK
- UK Dementia Research Institute, King’s College London, London W1T 7NF, UK
- National Institute of Chemistry, 1001 Ljubljana, Slovenia
| | - Laura Baranello
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
| | - Federico Agostini
- Science for Life Laboratory, Stockholm 17165, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna 17165, Sweden
| | - Marianne Farnebo
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna 17165, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge 14152, Sweden
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37
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548938. [PMID: 37503254 PMCID: PMC10369987 DOI: 10.1101/2023.07.13.548938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genome-wide measurements of ribosome occupancy on mRNA transcripts have enabled global empirical identification of translated regions. These approaches have revealed an unexpected diversity of protein products, but high-confidence identification of new coding regions that entirely overlap annotated coding regions - including those that encode truncated protein isoforms - has remained challenging. Here, we develop a sensitive and robust algorithm focused on identifying N-terminally truncated proteins genome-wide, identifying 388 truncated protein isoforms, a more than 30-fold increase in the number known in budding yeast. We perform extensive experimental validation of these truncated proteins and define two general classes. The first set lack large portions of the annotated protein sequence and tend to be produced from a truncated transcript. We show two such cases, Yap5 truncation and Pus1 truncation , to have condition-specific regulation and functions that appear distinct from their respective annotated isoforms. The second set of N-terminally truncated proteins lack only a small region of the annotated protein and are less likely to be regulated by an alternative transcript isoform. Many localize to different subcellular compartments than their annotated counterpart, representing a common strategy for achieving dual localization of otherwise functionally identical proteins.
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38
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Zhang LS, Dai Q, He C. Quantitative base-resolution sequencing technology for mapping pseudouridines in mammalian mRNA. Methods Enzymol 2023; 692:23-38. [PMID: 37925181 PMCID: PMC10880115 DOI: 10.1016/bs.mie.2023.06.005] [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] [Indexed: 11/06/2023]
Abstract
Posttranscriptional RNA modifications occur in almost all types of RNA in all life forms. As an abundant RNA modification in mammals, pseudouridine (Ψ) regulates diverse biological functions of different RNA species such as ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), etc. However, the functional investigation of mRNA pseudouridine (Ψ) has been hampered by the lack of a quantitative method that can efficiently map Ψ transcriptome-wide. We developed bisulfite-induced deletion sequencing (BID-seq), with the optimized bisulfite-based chemical reaction to convert pseudouridine selectively and completely into Ψ-BS adduct without cytosine deamination. The Ψ-BS adduct can be further read out as deletion signatures during reverse transcription. The deletion ratios induced by Ψ sites were used for estimating the modification stoichiometry at each modified site. BID-seq starts with 10-20 ng polyA+ RNA and detects thousands of mRNA Ψ sites with stoichiometry information in cell lines and tissues. We uncovered consensus motifs for Ψ in mammalian mRNA and assigned specific 'writer' proteins to individual Ψ deposition. BID-seq also confirmed the presence of Ψ within stop codons of mammalian mRNA. BID-seq set the stage for future investigations of Ψ functions in diverse biological processes.
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Affiliation(s)
- Li-Sheng Zhang
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Hong Kong, SAR, P.R. China; Department of Chemistry, The Hong Kong University of Science and Technology (HKUST), Hong Kong, SAR, P.R. China.
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, United States; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, United States
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39
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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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40
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Jalan A, Jayasree PJ, Karemore P, Narayan KP, Khandelia P. Decoding the 'Fifth' Nucleotide: Impact of RNA Pseudouridylation on Gene Expression and Human Disease. Mol Biotechnol 2023:10.1007/s12033-023-00792-1. [PMID: 37341888 DOI: 10.1007/s12033-023-00792-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023]
Abstract
Cellular RNAs, both coding and noncoding are adorned by > 100 chemical modifications, which impact various facets of RNA metabolism and gene expression. Very often derailments in these modifications are associated with a plethora of human diseases. One of the most oldest of such modification is pseudouridylation of RNA, wherein uridine is converted to a pseudouridine (Ψ) via an isomerization reaction. When discovered, Ψ was referred to as the 'fifth nucleotide' and is chemically distinct from uridine and any other known nucleotides. Experimental evidence accumulated over the past six decades, coupled together with the recent technological advances in pseudouridine detection, suggest the presence of pseudouridine on messenger RNA, as well as on diverse classes of non-coding RNA in human cells. RNA pseudouridylation has widespread effects on cellular RNA metabolism and gene expression, primarily via stabilizing RNA conformations and destabilizing interactions with RNA-binding proteins. However, much remains to be understood about the RNA targets and their recognition by the pseudouridylation machinery, the regulation of RNA pseudouridylation, and its crosstalk with other RNA modifications and gene regulatory processes. In this review, we summarize the mechanism and molecular machinery involved in depositing pseudouridine on target RNAs, molecular functions of RNA pseudouridylation, tools to detect pseudouridines, the role of RNA pseudouridylation in human diseases like cancer, and finally, the potential of pseudouridine to serve as a biomarker and as an attractive therapeutic target.
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Affiliation(s)
- Abhishek Jalan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - P J Jayasree
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Pragati Karemore
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Kumar Pranav Narayan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India
| | - Piyush Khandelia
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani - Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Medchal-Malkajgiri District, Telangana, 500078, India.
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41
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Chen ZB, He M, Li JYS, Shyy JYJ, Chien S. Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering. Annu Rev Biomed Eng 2023; 25:157-184. [PMID: 36913673 DOI: 10.1146/annurev-bioeng-081922-021233] [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] [Indexed: 03/11/2023]
Abstract
The central dogma of gene expression involves DNA transcription to RNA and RNA translation into protein. As key intermediaries and modifiers, RNAs undergo various forms of modifications such as methylation, pseudouridylation, deamination, and hydroxylation. These modifications, termed epitranscriptional regulations, lead to functional changes in RNAs. Recent studies have demonstrated crucial roles for RNA modifications in gene translation, DNA damage response, and cell fate regulation. Epitranscriptional modifications play an essential role in development, mechanosensing, atherogenesis, and regeneration in the cardiovascular (CV) system, and their elucidation is critically important to understanding the molecular mechanisms underlying CV physiology and pathophysiology. This review aims at providing biomedical engineers with an overview of the epitranscriptome landscape, related key concepts, recent findings in epitranscriptional regulations, and tools for epitranscriptome analysis. The potential applications of this important field in biomedical engineering research are discussed.
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Affiliation(s)
- Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Ming He
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Julie Yi-Shuan Li
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
| | - John Y-J Shyy
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Shu Chien
- Department of Medicine, University of California, San Diego, La Jolla, California, USA;
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA;
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42
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Barozzi C, Zacchini F, Corradini AG, Morara M, Serra M, De Sanctis V, Bertorelli R, Dassi E, Montanaro L. Alterations of ribosomal RNA pseudouridylation in human breast cancer. NAR Cancer 2023; 5:zcad026. [PMID: 37260601 PMCID: PMC10227372 DOI: 10.1093/narcan/zcad026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2'O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and they are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.
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Affiliation(s)
- Chiara Barozzi
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Federico Zacchini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Centre for Applied Biomedical Research – CRBA, University of Bologna, Sant’Orsola Hospital, Bologna I-40138, Italy
| | - Angelo Gianluca Corradini
- Unit of Pathology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Monica Morara
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Margherita Serra
- Unit of Breast Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Povo (TN) I-38123, Italy
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum - University of Bologna, Bologna I-40138, Italy
- Departmental Program in Laboratory Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy
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43
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Vögele J, Duchardt-Ferner E, Kruse H, Zhang Z, Sponer J, Krepl M, Wöhnert J. Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA. RNA (NEW YORK, N.Y.) 2023; 29:790-807. [PMID: 36868785 PMCID: PMC10187676 DOI: 10.1261/rna.079506.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/10/2023] [Indexed: 05/18/2023]
Abstract
Pseudouridine is the most frequently naturally occurring RNA modification, found in all classes of biologically functional RNAs. Compared to uridine, pseudouridine contains an additional hydrogen bond donor group and is therefore widely regarded as a structure stabilizing modification. However, the effects of pseudouridine modifications on the structure and dynamics of RNAs have so far only been investigated in a limited number of different structural contexts. Here, we introduced pseudouridine modifications into the U-turn motif and the adjacent U:U closing base pair of the neomycin-sensing riboswitch (NSR)-an extensively characterized model system for RNA structure, ligand binding, and dynamics. We show that the effects of replacing specific uridines with pseudouridines on RNA dynamics crucially depend on the exact location of the replacement site and can range from destabilizing to locally or even globally stabilizing. By using a combination of NMR spectroscopy, MD simulations and QM calculations, we rationalize the observed effects on a structural and dynamical level. Our results will help to better understand and predict the consequences of pseudouridine modifications on the structure and function of biologically important RNAs.
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Affiliation(s)
- Jennifer Vögele
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Zhengyue Zhang
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, 60438 Frankfurt, Germany
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44
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Keszthelyi TM, Tory K. The importance of pseudouridylation: human disorders related to the fifth nucleoside. Biol Futur 2023:10.1007/s42977-023-00158-3. [PMID: 37000312 DOI: 10.1007/s42977-023-00158-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Pseudouridylation is one of the most abundant RNA modifications in eukaryotes, making pseudouridine known as the "fifth nucleoside." This highly conserved alteration affects all non-coding and coding RNA types. Its role and importance have been increasingly widely researched, especially considering that its absence or damage leads to serious hereditary diseases. Here, we summarize the human genetic disorders described to date that are related to the participants of the pseudouridylation process.
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Affiliation(s)
| | - Kálmán Tory
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
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45
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Yamagami R, Hori H. Functional analysis of tRNA modification enzymes using mutational profiling. Methods Enzymol 2023; 692:69-101. [PMID: 37925188 DOI: 10.1016/bs.mie.2023.02.021] [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: 11/06/2023]
Abstract
Transfer RNA (tRNA) delivers amino acids to the ribosome and functions as an essential adapter molecule for decoding codons on the messenger RNA (mRNA) during protein synthesis. Before attaining their proper activity, tRNAs undergo multiple post-transcriptional modifications with highly diversified roles such as stabilization of the tRNA structure, recognition of aminoacyl tRNA synthetases, precise codon-anticodon recognition, support of viral replication and onset of immune responses. The synthesis of the majority of modified nucleosides is catalyzed by a site-specific tRNA modification enzyme. This chapter provides a detailed protocol for using mutational profiling to analyze the enzymatic function of a tRNA methyltransferase in a high-throughput manner. In a previous study, we took tRNA m1A22 methyltransferase TrmK from Geobacillus stearothermophilus as a model tRNA methyltransferase and applied this protocol to gain mechanistic insights into how TrmK recognizes the substrate tRNAs. In theory, this protocol can be used unaltered for studying enzymes that catalyze modifications at the Watson-Crick face such as 1-methyladenosine (m1A), 3-methylcytosine (m3C), 3-methyluridine (m3U), 1-methylguanosine (m1G), and N2,N2-dimethylguanosine (m22G).
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Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
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46
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Song W, Podicheti R, Rusch DB, Tracey WD. Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster. G3 (BETHESDA, MD.) 2023; 13:jkac333. [PMID: 36534986 PMCID: PMC9997552 DOI: 10.1093/g3journal/jkac333] [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: 10/03/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, and non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Drosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The 3 mRNAs most enriched for Psi encode highly expressed yolk proteins (Yp1, Yp2, and Yp3). By comparing the pseudouridine profiles in the RluA-2 mutant and the w1118 control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.
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Affiliation(s)
- Wan Song
- Gill Center for Biomolecular Research, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - William Daniel Tracey
- Gill Center for Biomolecular Research, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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47
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Bao Z, Li T, Liu J. Determining RNA Natural Modifications and Nucleoside Analog-Labeled Sites by a Chemical/Enzyme-Induced Base Mutation Principle. Molecules 2023; 28:1517. [PMID: 36838506 PMCID: PMC9958784 DOI: 10.3390/molecules28041517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The natural chemical modifications of messenger RNA (mRNA) in living organisms have shown essential roles in both physiology and pathology. The mapping of mRNA modifications is critical for interpreting their biological functions. In another dimension, the synthesized nucleoside analogs can enable chemical labeling of cellular mRNA through a metabolic pathway, which facilitates the study of RNA dynamics in a pulse-chase manner. In this regard, the sequencing tools for mapping both natural modifications and nucleoside tags on mRNA at single base resolution are highly necessary. In this work, we review the progress of chemical sequencing technology for determining both a variety of naturally occurring base modifications mainly on mRNA and a few on transfer RNA and metabolically incorporated artificial base analogs on mRNA, and further discuss the problems and prospects in the field.
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Affiliation(s)
- Ziming Bao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310058, China
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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48
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Zhang LS, Dai Q, He C. BID-seq: The Quantitative and Base-Resolution Sequencing Method for RNA Pseudouridine. ACS Chem Biol 2023; 18:4-6. [PMID: 36525588 DOI: 10.1021/acschembio.2c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Quantitative and base-resolution sequencing methods are critical to investigations of the biological functions of diverse RNA modifications. These methods may also be employed for clinical studies and clinical applications in the future. In this In Focus article, we introduce and discuss the development of Bisulfite-Induced Deletion sequencing (BID-seq) for quantitatively detecting mRNA pseudouridine (Ψ) modifications at base resolution.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry and the Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department of Chemistry and the Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry and the Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
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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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Yao J, Hao C, Chen K, Meng J, Song B. Pseudouridine Identification and Functional Annotation with PIANO. Methods Mol Biol 2023; 2624:153-162. [PMID: 36723815 DOI: 10.1007/978-1-0716-2962-8_11] [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: 02/02/2023]
Abstract
Pseudouridine (Ψ) is the first-discovered RNA modification abundantly present in many classes of RNAs, which plays a pivotal role in a series of biological processes. Accurately identifying the location of Ψ sites is helpful for relevant downstream researches. In this chapter, we introduce a website PIANO-for pseudouridine site (Ψ) identification and functional annotation, which enables researchers to predict human putative Ψ sites with a high-accuracy (average AUC of 0.955 under the full transcript model and 0.838 under the mature mRNA model when testing on six independent datasets). The posttranscriptional regulatory mechanisms of putative Ψ sites including miRNA-targets, RBP-binding regions, and splicing sites were also annotated. A comprehensive query database was also provided to deposit over 4300 human Ψ modifications, which is currently the most complete collection of experimental-derived Ψ sites. The PIANO website is freely accessible at: http://piano.rnamd.com or http://180.208.58.19/Ψ-WHISTLE .
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Affiliation(s)
- Jiahui Yao
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Cuiyueyue Hao
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
| | - Kunqi Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Jia Meng
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- AI University Research Centre, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Bowen Song
- Department of Mathematical Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, China.
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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