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Xu L, Yu Z, Xu Y, Wang Q, Wang G, Li B, Weng Q, Yi Y, Li J. An mRNA vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses confers cross-protection against influenza a viruses in adult and aged mice. Hum Vaccin Immunother 2025; 21:2453304. [PMID: 39957235 PMCID: PMC11834421 DOI: 10.1080/21645515.2025.2453304] [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: 11/15/2024] [Revised: 01/03/2025] [Accepted: 01/10/2025] [Indexed: 02/18/2025] Open
Abstract
Currently, vaccination with influenza vaccines is still an effective strategy to prevent infection by seasonal influenza virus. However, seasonal influenza vaccines frequently fail to induce effective immune protection against rapidly changing seasonal influenza viruses and emerging zoonotic influenza viruses. In addition, seasonal influenza vaccines may not confer potent protection in elderly and immunocompromised individuals. There is an urgent need to develop potent broad-spectrum influenza vaccines to address this problem. Herein, we designed an mRNA-based broad-spectrum influenza vaccine candidate encoding cholera toxin subunit B and conserved antigens of influenza viruses. In both adult and aged mice, this universal influenza mRNA vaccine candidate stimulated robust T-cell and humoral immune responses and conferred effective protection against broad-spectrum influenza viruses in both adult and aged mice.
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Affiliation(s)
- Liang Xu
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhihao Yu
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yifan Xu
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Qin Wang
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Guiqin Wang
- Nanjing Advanced Academy of Life and Health, Nanjing, China
| | - Benchi Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Qian Weng
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Yongxiang Yi
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Junwei Li
- Department of Infectious Disease, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
- Medical Innovation Center for Infectious Disease of Jiangsu Province, Nanjing, China
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2
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Yao H, Zhang D, Jin H, Guo Y, Liu Y, Wang S, Li T, Yuan S, Lu G, Sun Y. RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation. BMC Biol 2025; 23:147. [PMID: 40437520 PMCID: PMC12121112 DOI: 10.1186/s12915-025-02250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Accepted: 05/16/2025] [Indexed: 06/01/2025] Open
Abstract
BACKGROUND Omics technologies are widely applied in assisted reproductive technology (ART), such as embryo selection, investigation of infertility causes, and mechanisms underlying reproductive cell development. While RNAomics has shown great potential in investigating the physiology and pathology in female reproductive system, its applications are still not fully developed. More studies on epitranscriptomic regulation mechanisms and novel sequencing methods are needed to advance the field. RESULTS Here, we developed a method named Cap to Tail sequencing application (C2T-APP) and simultaneously characterized the m7G cap, poly(A) tail structure, and gene expression level for the intact RNA molecules in single cells. C2T-APP distinguished the N6, 2'-O-dimethyladenosine modification (m6Am) from N6-methyladenosine (m6A) modification with our published single-cell m6A sequencing (scm6A-seq) data. During oocyte maturation, we found a positive correlation of m7G and m6Am with translation efficiency and finely dissected the step-wised maternal RNA de-capping and de-tailing of different types of genes. Strikingly, we uncovered a subtle structural mechanism regulating poly(A) tails in oocytes: maternal RNA translation is temporarily suppressed by removing the poly(A) tails without complete degradation, while the poly(A)-tail regulators themselves depend strictly on translation initiated after meiotic resumption. Furthermore, we profiled single-cell RNA-multi-omic features of human oocytes with different qualities during in vitro culture maturation (IVM). Defects of epi-transcriptome features, including m6A, m6Am, m7G, and poly(A) structure of maternal RNA in the oocytes with poor quality, were detected. CONCLUSIONS Our results provided a valuable tool for RNAomics research and data resources provided novel insights into human oocyte maturation, which is helpful for IVM and oocyte selection for ART.
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Affiliation(s)
- Huan Yao
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
- CUHK-SDU Joint Laboratory On Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Ma Liu Shui, Hong Kong.
| | - Danru Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Haixia Jin
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Guo
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Liu
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shengnan Wang
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Li
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shenli Yuan
- CUHK-SDU Joint Laboratory On Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Ma Liu Shui, Hong Kong
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory On Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Ma Liu Shui, Hong Kong.
| | - Yingpu Sun
- Center for Reproductive Medicine, Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Camperi J, Chatla K, Freund E, Galan C, Lippold S, Guilbaud A. Current Analytical Strategies for mRNA-Based Therapeutics. Molecules 2025; 30:1629. [PMID: 40286229 PMCID: PMC11990077 DOI: 10.3390/molecules30071629] [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: 03/14/2025] [Revised: 04/02/2025] [Accepted: 04/03/2025] [Indexed: 04/29/2025] Open
Abstract
Recent advancements in mRNA technology, utilized in vaccines, immunotherapies, protein replacement therapies, and genome editing, have emerged as promising and increasingly viable treatments. The rapid, potent, and transient properties of mRNA-encoded proteins make them attractive tools for the effective treatment of a variety of conditions, ranging from infectious diseases to cancer and single-gene disorders. The capability for rapid and large-scale production of mRNA therapeutics fueled the global response to the COVID-19 pandemic. For effective clinical implementation, it is crucial to deeply characterize and control important mRNA attributes such as purity/integrity, identity, structural quality features, and functionality. This implies the use of powerful and advanced analytical techniques for quality control and characterization of mRNA. Improvements in analytical techniques such as electrophoresis, chromatography, mass spectrometry, sequencing, and functionality assessments have significantly enhanced the quality and detail of information available for product and process characterization, as well as for routine stability and release testing. Here, we review the latest advancements in analytical techniques for the characterization of mRNA-based therapeutics, typically employed by the biopharmaceutical industry for eventual market release.
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Affiliation(s)
- Julien Camperi
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Kamalakar Chatla
- Cell Therapy Engineering and Development, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Emily Freund
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (E.F.); (C.G.)
| | - Carolina Galan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA; (E.F.); (C.G.)
| | - Steffen Lippold
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
| | - Axel Guilbaud
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA;
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4
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Gao Y, Takenaka K, Xu SM, Cheng Y, Janitz M. Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis. Brief Funct Genomics 2025; 24:elaf005. [PMID: 40251826 PMCID: PMC12008121 DOI: 10.1093/bfgp/elaf005] [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: 12/07/2024] [Revised: 03/10/2025] [Accepted: 03/18/2025] [Indexed: 04/21/2025] Open
Abstract
Non-coding RNAs (ncRNAs) are RNA molecules that are transcribed from DNA but are not translated into proteins. Studies over the past decades have revealed that ncRNAs can be classified into small RNAs, long non-coding RNAs and circular RNAs by genomic size and structure. Accumulated evidences have eludicated the critical roles of these non-coding transcripts in regulating gene expression through transcription and translation, thereby shaping cellular function and disease pathogenesis. Notably, recent studies have investigated the function of ncRNAs as competitive endogenous RNAs (ceRNAs) that sequester miRNAs and modulate mRNAs expression. The ceRNAs network emerges as a pivotal regulatory function, with significant implications in various diseases such as cancer and neurodegenerative disease. Therefore, we highlighted multiple bioinformatics tools and databases that aim to predict ceRNAs interaction. Furthermore, we discussed limitations of using current technologies and potential improvement for ceRNAs network detection. Understanding of the dynamic interplay within ceRNAs may advance the biological comprehension, as well as providing potential targets for therapeutic intervention.
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Affiliation(s)
- Yulan Gao
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Gate 11 via Botany St, Sydney, NSW 2052, Australia
| | - Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Gate 11 via Botany St, Sydney, NSW 2052, Australia
| | - Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Gate 11 via Botany St, Sydney, NSW 2052, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Gate 11 via Botany St, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Gate 11 via Botany St, Sydney, NSW 2052, Australia
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5
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Zhu X, Han X, Li Z, Zhou X, Yoo SH, Chen Z, Ji Z. CircaKB: a comprehensive knowledgebase of circadian genes across multiple species. Nucleic Acids Res 2025; 53:D67-D78. [PMID: 39329269 PMCID: PMC11701547 DOI: 10.1093/nar/gkae817] [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: 07/27/2024] [Revised: 08/30/2024] [Accepted: 09/14/2024] [Indexed: 09/28/2024] Open
Abstract
Circadian rhythms, which are the natural cycles that dictate various physiological processes over a 24-h period, have been increasingly recognized as important in the management and treatment of various human diseases. However, the lack of sufficient data and reliable analysis methods have been a major obstacle to understanding the bidirectional interaction between circadian variation and human health. We have developed CircaKB, a comprehensive knowledgebase of circadian genes across multiple species. CircaKB is the first knowledgebase that provides systematic annotations of the oscillatory patterns of gene expression at a genome-wide level for 15 representative species. Currently, CircaKB contains 226 time-course transcriptome datasets, covering a wide variety of tissues, organs, and cell lines. In addition, CircaKB integrates 12 computational models to facilitate reliable data analysis and identify oscillatory patterns and their variations in gene expression. CircaKB also offers powerful functionalities to its users, including easy search, fast browsing, strong visualization, and custom upload. We believe that CircaKB will be a valuable tool and resource for the circadian research community, contributing to the identification of new targets for disease prevention and treatment. We have made CircaKB freely accessible at https://cdsic.njau.edu.cn/CircaKB.
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Affiliation(s)
- Xingchen Zhu
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
- Center for Data Science and Intelligent Computing, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
| | - Xiao Han
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
- Center for Data Science and Intelligent Computing, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
| | - Zhijin Li
- Department of Neurosurgery, The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230036, China
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin Street, Houston, TX 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiwei Ji
- College of Artificial Intelligence, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
- Center for Data Science and Intelligent Computing, Nanjing Agricultural University, No. 1 Weigang Rd., Nanjing, Jiangsu 210095, China
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Al Turihi N, Allouche D, Quéré M, Scuiller M, Legastelois I. Characterization of poly(A) and poly(T) tail lengths in plasmid DNA by liquid chromatography high-resolution mass spectrometry. Anal Bioanal Chem 2025; 417:59-68. [PMID: 39547978 PMCID: PMC11695563 DOI: 10.1007/s00216-024-05654-6] [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: 07/23/2024] [Revised: 11/04/2024] [Accepted: 11/07/2024] [Indexed: 11/17/2024]
Abstract
Rapid advances in messenger RNA (mRNA) technology necessitate effective analytical methods. This study describes the development of a novel in vitro method using ion-pair reversed-phase liquid chromatography coupled to high-resolution mass spectrometry (IP-RP-LC-HRMS) for assessing the poly(A) and complementary poly(T) tail lengths directly into the DNA template used to manufacture mRNA. Briefly, after the validation of poly(A) tail length in the plasmid by Sanger sequencing, double-stranded DNA fragments containing these tails in the plasmid of interest were amplified by the polymerase chain reaction (PCR), purified on silica column, and digested with restriction enzymes ClaI and HindIII. Gel or capillary electrophoresis confirmed sample quality and enzymatic digestion efficiency. Subsequently, poly(A) and complementary poly(T) tails were extracted and analyzed by LC-MS to determine their length and heterogeneity at a single-nucleotide resolution. Three DNA templates containing poly(A) tail lengths of 60A-G, 95A, or 108A were studied. LC-MS results correlated well with Sanger sequencing, identifying major populations of 60A-G, 95A, or 108A. Surprisingly, unlike Sanger sequencing, LC-MS analysis revealed minor poly(A) populations with lengths longer or shorter than the theoretically encoded poly(A) tail length. This finding could be explained by (i) the slippage of bacterial DNA polymerase I during plasmid replication in bacterial culture, which occurs on repeat mononucleotide sequences, or (ii) the slippage of Q5® High-Fidelity DNA Polymerase during PCR amplification. In conclusion, the method is easy, rapid, and accurate and could replace Sanger sequencing to assess the poly(A) and complementary poly(T) tail lengths in plasmid DNA.
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Affiliation(s)
- Nour Al Turihi
- RNA Sciences, Sanofi, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France.
| | - Delphine Allouche
- RNA Sciences, Sanofi, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - Maëlle Quéré
- RNA Sciences, Sanofi, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
| | - Mathieu Scuiller
- RNA Sciences, Sanofi, 1541 av. Marcel Mérieux, 69280, Marcy l'Étoile, France
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7
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Mishra SK, Liu T, Wang H. Thousands of oscillating LncRNAs in the mouse testis. Comput Struct Biotechnol J 2024; 23:330-346. [PMID: 38205156 PMCID: PMC10776378 DOI: 10.1016/j.csbj.2023.11.046] [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: 09/20/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
The long noncoding RNAs (lncRNAs) are involved in numerous fundamental biological processes, including circadian regulation. Although recent studies have revealed insights into the functions of lncRNAs, how the lncRNAs regulate circadian rhythms still requires a deeper investigation. In this study, we generate two datasets of RNA-seq profiles of the mouse (Mus musculus) testis under light-dark (LD) cycle. The first dataset included 18,613 unannotated transcripts measured at 12 time points, each with duplicate samples, under LD conditions; while the second dataset included 21,414 unannotated transcripts measured at six time points, each with three replicates, under desynchronized and control conditions. We identified 5964 testicular lncRNAs in each dataset by BLASTing these transcripts against the known mouse lncRNAs from the NONCODE database. MetaCycle analyses were performed to identify 519, 475, and 494 rhythmically expressed mouse testicular lncRNAs in the 12-time-point dataset, the six-time-point control dataset, and the six-time-point desynchronized dataset, respectively. A comparison of the expression profiles of the lncRNAs under desynchronized and control conditions revealed that 427 rhythmically expressed lncRNAs from the control condition became arrhythmic under the desynchronized condition, suggesting a possible loss of rhythmicity. In contrast, 446 arrhythmic lncRNAs from the control condition became rhythmic under the desynchronized condition, suggesting a possible gain of rhythmicity. Interestingly, 48 lncRNAs were rhythmically expressed under both desynchronized and control conditions. These oscillating lncRNAs were divided into morning lncRNAs, evening lncRNAs, and night lncRNAs based on their time-course expression patterns. We interrogated the promoter regions of these rhythmically expressed mouse testicular lncRNAs to predict their possible regulation by the E-box, D-box, or RORE promoter motifs. GO and KEGG analyses were performed to identify the possible biological functions of these rhythmically expressed mouse testicular lncRNAs. Further, we conducted conservation analyses of the rhythmically expressed mouse testicular lncRNAs with lncRNAs from humans, rats, and zebrafish, and uncovered three mouse testicular lncRNAs conserved across these four species. Finally, we computationally predicted the conserved lncRNA-encoded peptides and their 3D structures from each of the four species. Taken together, our study revealed thousands of rhythmically expressed lncRNAs in the mouse testis, setting the stage for further computational and experimental validations.
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Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, Jiangsu, China
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8
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Liu Y, Lu F, Wang J. Sequencing of Transcriptome-Wide Poly(A) Tails by PAIso-seq. Methods Mol Biol 2024; 2723:215-232. [PMID: 37824073 DOI: 10.1007/978-1-0716-3481-3_13] [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: 10/13/2023]
Abstract
Poly(A) tails are added to most eukaryotic mRNA and have essential regulatory functions. However, due to its homopolymeric nature, the sequence information in poly(A) tails is challenging to obtain in transcriptome measurement studies. In this chapter, we describe the detailed procedures of poly(A) inclusive full-length RNA isoform-sequencing (PAIso-seq), a method that can measure transcriptome-wide poly(A) tails from as low as nanogram level of total RNA based on the PacBio HiFi sequencing platform. The accurate length and base composition of poly(A) tails can be obtained along with the full-length cDNA.
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Affiliation(s)
- Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
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Kelly D, Schratt G. Screening and Characterization of Functional circRNAs in Neuronal Cultures. Methods Mol Biol 2024; 2765:311-324. [PMID: 38381347 DOI: 10.1007/978-1-0716-3678-7_17] [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: 02/22/2024]
Abstract
This chapter describes a methodology for the screening and characterization of functional circRNAs, particularly in the context of neural circuit development. Taking advantage of a primary rat neuron culture model of synaptogenesis, we propose a means of selecting from the plethora of circRNA species based on their expression levels, dendritic localization, conservation, and activity regulation. These candidates are then knocked down with RNAi approaches in a functional screen for their potential role in the formation and maturation of excitatory synapses.Upon identification of top candidates regulating synaptogenesis, we tie together different "Omics" approaches to explore the molecular mechanisms underlying the phenotypes observed upon circRNA knockdown. We utilized our EnrichMir algorithm to identify overrepresented miRNA binding sites in differentially expressed genes from polyA-RNA-seq following circRNA knockdown. Furthermore, our ScanMiR web tool allows for the miRNA binding prediction of reconstructed internal circular RNA sequences. Small-RNA sequencing is used to monitor changes in miRNA levels in the circRNA knockdown to complement results obtained from EnrichMiR. Finally, the experimental validation of promising miRNA-circRNA pairs sets the stage for in-depth biochemical exploration of the circRNA interactome and mechanism of action.
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Affiliation(s)
- Darren Kelly
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Swiss Federal Institute of Technology ETH, Zurich, Switzerland.
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Iben JR, Li T, Mattijssen S, Maraia RJ. Single-Molecule Poly(A) Tail Sequencing (SM-PATseq) Using the PacBio Platform. Methods Mol Biol 2024; 2723:285-301. [PMID: 37824077 DOI: 10.1007/978-1-0716-3481-3_17] [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: 10/13/2023]
Abstract
The polyadenylation of the 3' ends of messenger RNAs is an important regulator of stability and translation. We developed the single-molecule poly(A) tail sequencing method, SM-PATseq, to assay tail lengths of the whole transcriptome at nucleotide resolution using long-read sequencing. This method generates cDNA using an oligo-dT 3' splint adaptor ligation to prime first-strand cDNA synthesis, followed by random hexamer priming for second-strand synthesis. By directly sequencing the cDNA on long-read platforms, we can resolve tail lengths at nucleotide resolution, identify non-A bases within the tail, and quantify transcript abundance analogous to traditional RNAseq methods. Here, we discuss the method for generating, sequencing, and primary analysis of poly(A) tail data from total RNA using the Pacific Biosciences Sequel platform.
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Affiliation(s)
- James R Iben
- Molecular Genetics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Tianwei Li
- Molecular Genetics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sandy Mattijssen
- Section on Molecular and Cell Biology, NICHD, NIH, Bethesda, MD, USA
| | - Richard J Maraia
- Section on Molecular and Cell Biology, NICHD, NIH, Bethesda, MD, USA.
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11
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Vignon M, Bastide A, Attina A, David A, Bousquet P, Orti V, Vialaret J, Lehmann S, Periere DD, Hirtz C. Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis. J Periodontal Res 2023; 58:959-967. [PMID: 37349891 DOI: 10.1111/jre.13155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
OBJECTIVE To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS). BACKGROUND The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date. MATERIALS AND METHODS Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS. RESULTS Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary. CONCLUSION The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.
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Affiliation(s)
- Margaux Vignon
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Aurore Attina
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Philippe Bousquet
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Valérie Orti
- Department of Periodontology, Dental Faculty, University of Montpellier, Montpellier, France
| | - Jérôme Vialaret
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | - Sylvain Lehmann
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
| | | | - Christophe Hirtz
- INM, University of Montpellier, INSERM, Montpellier, France
- LBPC-PPC, University of Montpellier, CHU Montpellier, INM INSERM, Montpellier, France
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12
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Debelli A, Kienzle L, Khorami HH, Angers A, Breton S. Validation of the male-specific ORF of the paternally-transmitted mtDNA in Mytilus edulis as a protein-coding gene. Gene 2023; 879:147586. [PMID: 37356740 DOI: 10.1016/j.gene.2023.147586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/27/2023]
Abstract
There appears to be an additional set of sex-specific mtDNA-encoded proteins in bivalve species with doubly uniparental mitochondrial inheritance that may be involved in the transmission of the female and male mitogenomes. In the marine mussel Mytilus edulis, the translation of the female-specific open reading frame (F-ORF) was demonstrated but the translation of the male-specific ORF (M-ORF) remains to be shown. Here we validate the male-specific ORF of the paternal mitogenome in M. edulis as a protein-coding gene. The M-ORF protein was detected only in male gonads and localized in sperm mitochondria and acrosome, suggesting that it is involved in a key sperm function in Mytilus edulis.
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Affiliation(s)
- Alizée Debelli
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Laura Kienzle
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Hajar Hosseini Khorami
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Annie Angers
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Sophie Breton
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC H3C 3J7, Canada.
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13
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Vlasenok M, Margasyuk S, Pervouchine DD. Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation. NAR Genom Bioinform 2023; 5:lqad051. [PMID: 37260513 PMCID: PMC10227441 DOI: 10.1093/nargab/lqad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are two crucial steps in the post-transcriptional regulation of eukaryotic gene expression. Protocols capturing and sequencing RNA 3'-ends have uncovered widespread intronic polyadenylation (IPA) in normal and disease conditions, where it is currently attributed to stochastic variations in the pre-mRNA processing. Here, we took advantage of the massive amount of RNA-seq data generated by the Genotype Tissue Expression project (GTEx) to simultaneously identify and match tissue-specific expression of intronic polyadenylation sites with tissue-specific splicing. A combination of computational methods including the analysis of short reads with non-templated adenines revealed that APA events are more abundant in introns than in exons. While the rate of IPA in composite terminal exons and skipped terminal exons expectedly correlates with splicing, we observed a considerable fraction of IPA events that lack AS support and attributed them to spliced polyadenylated introns (SPI). We hypothesize that SPIs represent transient byproducts of a dynamic coupling between APA and AS, in which the spliceosome removes the intron while it is being cleaved and polyadenylated. These findings indicate that cotranscriptional pre-mRNA splicing could serve as a rescue mechanism to suppress premature transcription termination at intronic polyadenylation sites.
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Affiliation(s)
- Maria Vlasenok
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Sergey Margasyuk
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
| | - Dmitri D Pervouchine
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Bulvar 30, Moscow 121205, Russia
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14
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Ramming A, Kappel C, Kanaoka MM, Higashiyama T, Lenhard M. Poly(A) polymerase 1 contributes to competence acquisition of pollen tubes growing through the style in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:651-667. [PMID: 36811355 DOI: 10.1111/tpj.16162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
Polyadenylation of mRNAs is critical for their export from the nucleus, stability, and efficient translation. The Arabidopsis thaliana genome encodes three isoforms of canonical nuclear poly(A) polymerase (PAPS) that redundantly polyadenylate the bulk of pre-mRNAs. However, previous studies have indicated that subsets of pre-mRNAs are preferentially polyadenylated by either PAPS1 or the other two isoforms. Such functional specialization raises the possibility of an additional level of gene-expression control in plants. Here we test this notion by studying the function of PAPS1 in pollen-tube growth and guidance. Pollen tubes growing through female tissue acquire the competence to find ovules efficiently and upregulate PAPS1 expression at the transcriptional, but not detectably at the protein level compared with in vitro grown pollen tubes. Using the temperature-sensitive paps1-1 allele we show that PAPS1 activity during pollen-tube growth is required for full acquisition of competence, resulting in inefficient fertilization by paps1-1 mutant pollen tubes. While these mutant pollen tubes grow almost at the wild-type rate, they are compromised in locating the micropyles of ovules. Previously identified competence-associated genes are less expressed in paps1-1 mutant than in wild-type pollen tubes. Estimating the poly(A) tail lengths of transcripts suggests that polyadenylation by PAPS1 is associated with reduced transcript abundance. Our results therefore suggest that PAPS1 plays a key role in the acquisition of competence and underline the importance of functional specialization between PAPS isoforms throughout different developmental stages.
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Affiliation(s)
- Anna Ramming
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Christian Kappel
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
| | - Masahiro M Kanaoka
- Prefectural University of Hiroshima, Faculty of Life and Environmental Sciences, Faculty of Bioresource Sciences, Shobara, Hiroshima, Japan
| | - Tetsuya Higashiyama
- The University of Tokyo Graduate School of Science, Faculty of Science, Bunkyo-ku, Tokyo, Japan
| | - Michael Lenhard
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam-Golm, Germany
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15
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Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: Methods for poly(A) tail profiling. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1737. [PMID: 35617484 PMCID: PMC10078590 DOI: 10.1002/wrna.1737] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 01/31/2023]
Abstract
The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). This epitranscriptomic regulation of mRNA recently became one of the most interesting aspects in the field. Advances in RNA sequencing technologies and software development have allowed the precise measurement of poly(A) tails, identification of new ncPAPs, expansion of the function of known enzymes, discovery and a better understanding of the physiological role of tail heterogeneity, and recognition of a correlation between tail length and RNA translatability. Here, we summarize the development of polyadenylation research methods, including classic low-throughput approaches, Illumina-based genome-wide analysis, and advanced state-of-art techniques that utilize long-read third-generation sequencing with Pacific Biosciences and Oxford Nanopore Technologies platforms. A boost in technical opportunities over recent decades has allowed a better understanding of the regulation of gene expression at the mRNA level. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Aleksandra Brouze
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Department of Embryology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Seweryn Mroczek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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16
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Ramarao KDR, Somasundram C, Razali Z, Kunasekaran W, Jin TL, Musa S, Achari VM. Antiproliferative effects of dried Moringa oleifera leaf extract on human Wharton's Jelly mesenchymal stem cells. PLoS One 2022; 17:e0274814. [PMID: 36197921 PMCID: PMC9534417 DOI: 10.1371/journal.pone.0274814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have seen an elevated use in clinical works like regenerative medicine. Its potential therapeutic properties increases when used in tandem with complementary agents like bio-based materials. Therefore, the present study is the first to investigate the cytotoxicity of a highly valued medicinal plant, Moringa oleifera, on human Wharton's Jelly mesenchymal stem cells (hWJMSCs) and its effects on the cells' gene expression when used as a pre-treatment agent in vitro. M. oleifera leaves (MOL) were dried and subjected to UHPLC-QTOF/MS analysis, revealing several major compounds like apigenin, kaempferol, and quercetin in the MOL, with various biological activities like antioxidant and anti-cancer properties. We then treated the hWJMSCs with MOL and noticed a dose-dependant inhibition on the cells' proliferation. RNA-sequencing was performed to explain the possible mechanism of action and revealed genes like PPP1R1C, SULT2B1, CDKN1A, mir-154 and CCNB1, whose expression patterns were closely associated with the negative cell cycle regulation and cell cycle arrest process. This is also evident from gene set enrichment analysis where the GO and KEGG terms for down-regulated pathways were closely related to the cell cycle regulation. The Ingenuity pathway analysis (IPA) software further predicted the significant activation of (p < 0.05, z-score > 2) of the G2/M DNA damage checkpoint regulation pathway. The present study suggests that MOL exhibits an antiproliferative effect on hWJMSCs via cell cycle arrest and apoptotic pathways. We believe that this study provides an important baseline reference for future works involving MOL's potential to accompany MSCs for clinical works. Future works can take advantage of the cell's strong anti-cancer gene expression found in this study, and evaluate our MOL treatment on various cancer cell lines.
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Affiliation(s)
- Kivaandra Dayaa Rao Ramarao
- Institute of Biological Sciences, Faculty of Science and The Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Chandran Somasundram
- Institute of Biological Sciences, Faculty of Science and The Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Zuliana Razali
- Institute of Biological Sciences, Faculty of Science and The Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | | | - Tan Li Jin
- Cytonex Sdn. Bhd., Menara UOA Bangsar, Bangsar, Kuala Lumpur, Malaysia
| | - Sabri Musa
- Department of Paediatric Dentistry & Orthodontics, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Vijayan Manickam Achari
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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17
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Liu Y, Zhang Y, Wang J, Lu F. Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nat Protoc 2022; 17:1980-2007. [PMID: 35831615 DOI: 10.1038/s41596-022-00704-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
Poly(A) tails are added to the 3' ends of most mRNAs in a non-templated manner and play essential roles in post-transcriptional regulation, including mRNA export, stability and translation. Measuring poly(A) tails is critical for understanding their regulatory roles in almost every aspect of biological and medical studies. Previous methods for analyzing poly(A) tails require large amounts of input RNA (microgram-level total RNA), which limits their application. We recently developed a poly(A) inclusive full-length RNA isoform-sequencing method (PAIso-seq) at single-oocyte-level sensitivity (a single mammalian oocyte contains ~0.5 ng of total RNA) based on PacBio sequencing that enabled accurate measurement of the poly(A) tail length and non-A residues within the body of poly(A) tails along with the full-length cDNA, providing the opportunity to study precious in vivo samples with very limited input material. Here, we describe a detailed protocol for PAIso-seq library preparation from single mouse oocytes or bulk oocyte samples. In addition, we provide a complete bioinformatic pipeline to perform the analysis from the raw data to downstream analysis. The minimum time required is ~14.5 h for PAIso-seq double-stranded cDNA preparation, 2 d for PacBio sequencing in HiFi mode and 8 h for the initial data analysis.
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Affiliation(s)
- Yusheng Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
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18
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Liu M, Hao L, Yang S, Wu X. PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data. Brief Bioinform 2022; 23:6620877. [PMID: 35769001 DOI: 10.1093/bib/bbac271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 12/18/2022] Open
Abstract
The poly(A) tail is a dynamic addition to the eukaryotic mRNA and the change in its length plays an essential role in regulating gene expression through affecting nuclear export, mRNA stability and translation. Only recently high-throughput sequencing strategies began to emerge for transcriptome-wide profiling of poly(A) tail length in diverse developmental stages and organisms. However, there is currently no easy-to-use and universal tool for measuring poly(A) tails in sequencing data from different sequencing protocols. Here we established PolyAtailor, a unified and efficient framework, for identifying and analyzing poly(A) tails from PacBio-based long reads or next generation short reads. PolyAtailor provides two core functions for measuring poly(A) tails, namely Tail_map and Tail_scan, which can be used for profiling tails with or without using a reference genome. Particularly, PolyAtailor can identify all potential tails in a read, providing users with detailed information such as tail position, tail length, tail sequence and tail type. Moreover, PolyAtailor integrates rich functions for poly(A) tail and poly(A) site analyses, such as differential poly(A) length analysis, poly(A) site identification and annotation, and statistics and visualization of base composition in tails. We compared PolyAtailor with three latest methods, FLAMAnalysis, FLEPSeq and PAIsoSeqAnalysis, using data from three sequencing protocols in HeLa samples and Arabidopsis. Results show that PolyAtailor is effective in measuring poly(A) tail length and detecting significance of differential poly(A) length, which achieves much higher sensitivity and accuracy than competing methods. PolyAtailor is available at https://github.com/BMILAB/PolyAtailor.
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Affiliation(s)
- Mengfei Liu
- Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China.,Department of Automation, Xiamen University, Xiamen, Fujian 361005, China
| | - Linlin Hao
- Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Sien Yang
- Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Xiaohui Wu
- Pasteurien College, Soochow University, Suzhou, Jiangsu 215000, China
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19
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Bilodeau DY, Sheridan RM, Balan B, Jex AR, Rissland OS. Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia. RNA (NEW YORK, N.Y.) 2022; 28:668-682. [PMID: 35110372 PMCID: PMC9014877 DOI: 10.1261/rna.078793.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript. The location of this cleavage event establishes the length and sequence of the 3' UTR of an mRNA, thus determining much of its post-transcriptional fate. Using long-read sequencing, we characterize the polyadenylation signal and related sequences surrounding Giardia lamblia cleavage sites for over 2600 genes. We find that G. lamblia uses an AGURAA poly(A) signal, which differs from the mammalian AAUAAA. We also describe how G. lamblia lacks common auxiliary elements found in other eukaryotes, along with the proteins that recognize them. Further, we identify 133 genes with evidence of alternative polyadenylation. These results suggest that despite pared-down cleavage and polyadenylation machinery, 3' end formation still appears to be an important regulatory step for gene expression in G. lamblia.
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Affiliation(s)
- Danielle Y Bilodeau
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Ryan M Sheridan
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC 3052, Australia
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Olivia S Rissland
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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20
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Hundreds of LncRNAs Display Circadian Rhythmicity in Zebrafish Larvae. Cells 2021; 10:cells10113173. [PMID: 34831396 PMCID: PMC8620895 DOI: 10.3390/cells10113173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/06/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in various life processes, including circadian rhythms. Although next generation sequencing technologies have facilitated faster profiling of lncRNAs, the resulting datasets require sophisticated computational analyses. In particular, the regulatory roles of lncRNAs in circadian clocks are far from being completely understood. In this study, we conducted RNA-seq-based transcriptome analysis of zebrafish larvae under both constant darkness (DD) and constant light (LL) conditions in a circadian manner, employing state-of-the-art computational approaches to identify approximately 3220 lncRNAs from zebrafish larvae, and then uncovered 269 and 309 lncRNAs displaying circadian rhythmicity under DD and LL conditions, respectively, with 30 of them are coexpressed under both DD and LL conditions. Subsequently, GO, COG, and KEGG pathway enrichment analyses of all these circadianly expressed lncRNAs suggested their potential involvement in numerous biological processes. Comparison of these circadianly expressed zebrafish larval lncRNAs, with rhythmically expressed lncRNAs in the zebrafish pineal gland and zebrafish testis, revealed that nine (DD) and twelve (LL) larval lncRNAs are coexpressed in the zebrafish pineal gland and testis, respectively. Intriguingly, among peptides encoded by these coexpressing circadianly expressed lncRNAs, three peptides (DD) and one peptide (LL) were found to have the known domains from the Protein Data Bank. Further, the conservation analysis of these circadianly expressed zebrafish larval lncRNAs with human and mouse genomes uncovered one lncRNA and four lncRNAs shared by all three species under DD and LL conditions, respectively. We also investigated the conserved lncRNA-encoded peptides and found one peptide under DD condition conserved in these three species and computationally predicted its 3D structure and functions. Our study reveals that hundreds of lncRNAs from zebrafish larvae exhibit circadian rhythmicity and should help set the stage for their further functional studies.
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21
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Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021; 9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic development depends on a highly coordinated shift in transcription programs known as the maternal-to-zygotic transition (MZT). It remains unclear how haploid and diploid embryo coordinate their genomic activation and embryonic development during MZT in haplodiploid animals. Here, we applied a single-embryo RNA-seq approach to characterize the embryonic transcriptome dynamics in haploid males vs. diploid females of the haplodiploid insect honeybee (Apis mellifera). We observed typical zygotic genome activation (ZGA) occurred in three major waves specifically in female honeybee embryos; haploid genome activation was much weaker and occurred later. Strikingly, we also observed three waves of transcriptional activation for thousands of long non-coding transcripts (lncRNA), 73% of which are transcribed from intronic regions and 65% were specific to female honeybee embryos. These findings support a model in which introns encode thousands of lncRNAs that are expressed in a diploid-embryo-specific and ZGA-triggered manner that may have potential functions to regulate gene expression during early embryonic development in the haplodiploid insect honeybee.
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Affiliation(s)
- Miao Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Liuwei Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Yu Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Qingsheng Niu
- Department of Scientific Research, Jilin Province Institute of Apicultural Science, Jilin, China
| | - Shuai Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Mishra SK, Liu T, Wang H. Identification of Rhythmically Expressed LncRNAs in the Zebrafish Pineal Gland and Testis. Int J Mol Sci 2021; 22:7810. [PMID: 34360576 PMCID: PMC8346003 DOI: 10.3390/ijms22157810] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
Noncoding RNAs have been known to contribute to a variety of fundamental life processes, such as development, metabolism, and circadian rhythms. However, much remains unrevealed in the huge noncoding RNA datasets, which require further bioinformatic analysis and experimental investigation-and in particular, the coding potential of lncRNAs and the functions of lncRNA-encoded peptides have not been comprehensively studied to date. Through integrating the time-course experimentation with state-of-the-art computational techniques, we studied tens of thousands of zebrafish lncRNAs from our own experiments and from a published study including time-series transcriptome analyses of the testis and the pineal gland. Rhythmicity analysis of these data revealed approximately 700 rhythmically expressed lncRNAs from the pineal gland and the testis, and their GO, COG, and KEGG pathway functions were analyzed. Comparative and conservative analyses determined 14 rhythmically expressed lncRNAs shared between both the pineal gland and the testis, and 15 pineal gland lncRNAs as well as 3 testis lncRNAs conserved among zebrafish, mice, and humans. Further, we computationally analyzed the conserved lncRNA-encoded peptides, and revealed three pineal gland and one testis lncRNA-encoded peptides conserved among these three species, which were further investigated for their three-dimensional (3D) structures and potential functions. Our computational findings provided novel annotations and regulatory mechanisms for hundreds of rhythmically expressed pineal gland and testis lncRNAs in zebrafish, and set the stage for their experimental studies in the near future.
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Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Taole Liu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China; (S.K.M.); (T.L.)
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
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23
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Coon SL, Li T, Iben JR, Mattijssen S, Maraia RJ. Single-molecule polyadenylated tail sequencing (SM-PAT-Seq) to measure polyA tail lengths transcriptome-wide. Methods Enzymol 2021; 655:119-137. [PMID: 34183118 DOI: 10.1016/bs.mie.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Polyadenylation of the 3' end of mRNAs is an important mechanism for regulating their stability and translation. We developed a nucleotide-resolution, transcriptome-wide, single-molecule SM-PAT-Seq method to accurately measure the polyA tail lengths of individual transcripts using long-read sequencing. The method generates cDNA using a double stranded splint adaptor targeting the far 3' end of the polyA tail for first strand synthesis along with random hexamers for second strand synthesis. This straight-forward method yields accurate polyA tail sequence lengths, can identify non-A residues in those tails, and quantitate transcript abundance.
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Affiliation(s)
- Steven L Coon
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Tianwei Li
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sandy Mattijssen
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Richard J Maraia
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States.
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24
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Kandhari N, Kraupner-Taylor CA, Harrison PF, Powell DR, Beilharz TH. The Detection and Bioinformatic Analysis of Alternative 3 ' UTR Isoforms as Potential Cancer Biomarkers. Int J Mol Sci 2021; 22:5322. [PMID: 34070203 PMCID: PMC8158509 DOI: 10.3390/ijms22105322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could advance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.
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Affiliation(s)
- Nitika Kandhari
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
| | - Calvin A. Kraupner-Taylor
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
| | - Paul F. Harrison
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia;
| | - David R. Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia;
| | - Traude H. Beilharz
- Development and Stem Cells Program, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; (N.K.); (C.A.K.-T.); (P.F.H.)
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25
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Slobodin B, Dikstein R. So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes. EMBO Rep 2020; 21:e50799. [PMID: 32803873 PMCID: PMC7507372 DOI: 10.15252/embr.202050799] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Transcription of DNA into mRNA and translation of mRNA into proteins are two major processes underlying gene expression. Due to the distinct molecular mechanisms, timings, and locales of action, these processes are mainly considered to be independent. During the last two decades, however, multiple factors and elements were shown to coordinate transcription and translation, suggesting an intricate level of synchronization. This review discusses the molecular mechanisms that impact both processes in eukaryotic cells of different origins. The emerging global picture suggests evolutionarily conserved regulation and coordination between transcription and mRNA translation, indicating the importance of this phenomenon for the fine-tuning of gene expression and the adjustment to constantly changing conditions.
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Affiliation(s)
- Boris Slobodin
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Rivka Dikstein
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
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