1
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McDonald AL, Boddicker AM, Savenkova MI, Brabb IM, Qi X, Moré DD, Cunha CW, Zhao J, Duttke SH. Efficient small fragment sequencing of human, cow, and bison miRNA, small RNA or csRNA-seq libraries using AVITI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596343. [PMID: 38854037 PMCID: PMC11160585 DOI: 10.1101/2024.05.28.596343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Next-Generation Sequencing (NGS) catalyzed breakthroughs across various scientific domains. Illumina's sequencing by synthesis method has long been essential for NGS but emerging technologies like Element Biosciences' sequencing by avidity (AVITI) represent a novel approach. It has been reported that AVITI offers improved signal-to-noise ratios and cost reductions. However, the method relies on rolling circle amplification which can be impacted by polymer size, raising questions about its efficacy sequencing small RNAs (sRNA) molecules including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and others that are crucial regulators of gene expression and involved in various biological processes. In addition, capturing capped small RNAs (csRNA-seq) has emerged as a powerful method to map active or "nascent" RNA polymerase II transcription initiation in tissues and clinical samples. Here, we report a new protocol for seamlessly sequencing short DNA fragments on the AVITI and demonstrate that AVITI and Illumina sequencing technologies equivalently capture human, cattle (Bos taurus) and the bison (Bison bison) sRNA or csRNA sequencing libraries, augmenting the confidence in both approaches. Additionally, analysis of generated nascent transcription start sites (TSSs) data for cattle and bison revealed inaccuracies in their current genome annotations and highlighted the possibility and need to translate small RNA sequencing methodologies to livestock. Our accelerated and optimized protocol therefore bridges the advantages of AVITI sequencing and critical methods that rely on sequencing short DNA fragments.
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Affiliation(s)
- Anna L McDonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | | | - Marina I Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | - Ian M Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
| | | | - Daniela D Moré
- Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA 99164, USA
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | - Cristina W Cunha
- Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA 99164, USA
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164, USA
| | | | - Sascha H Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA
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2
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Meng X, Bai X, Ke A, Li K, Lei Y, Ding S, Dai D. Long Non-Coding RNAs in Drug Resistance of Gastric Cancer: Complex Mechanisms and Potential Clinical Applications. Biomolecules 2024; 14:608. [PMID: 38927012 PMCID: PMC11201466 DOI: 10.3390/biom14060608] [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: 03/10/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Gastric cancer (GC) ranks as the third most prevalent malignancy and a leading cause of cancer-related mortality worldwide. However, the majority of patients with GC are diagnosed at an advanced stage, highlighting the urgent need for effective perioperative and postoperative chemotherapy to prevent relapse and metastasis. The current treatment strategies have limited overall efficacy because of intrinsic or acquired drug resistance. Recent evidence suggests that dysregulated long non-coding RNAs (lncRNAs) play a significant role in mediating drug resistance in GC. Therefore, there is an imperative to explore novel molecular mechanisms underlying drug resistance in order to overcome this challenging issue. With advancements in deep transcriptome sequencing technology, lncRNAs-once considered transcriptional noise-have garnered widespread attention as potential regulators of carcinogenesis, including tumor cell proliferation, metastasis, and sensitivity to chemo- or radiotherapy through multiple regulatory mechanisms. In light of these findings, we aim to review the mechanisms by which lncRNAs contribute to drug therapy resistance in GC with the goal of providing new insights and breakthroughs toward overcoming this formidable obstacle.
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Affiliation(s)
- Xiangyu Meng
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital, Shenyang 110042, China
| | - Xiao Bai
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
| | - Angting Ke
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
| | - Kaiqiang Li
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
| | - Yun Lei
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
| | - Siqi Ding
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
| | - Dongqiu Dai
- Department of Surgical Oncology, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China; (X.M.); (X.B.); (K.L.); (Y.L.); (S.D.)
- Cancer Center, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, China
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3
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Saw PE, Song E. Advancements in clinical RNA therapeutics: Present developments and prospective outlooks. Cell Rep Med 2024; 5:101555. [PMID: 38744276 PMCID: PMC11148805 DOI: 10.1016/j.xcrm.2024.101555] [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: 01/16/2024] [Revised: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
RNA molecules have emerged as promising clinical therapeutics due to their ability to target "undruggable" proteins or molecules with high precision and minimal side effects. Nevertheless, the primary challenge in RNA therapeutics lies in rapid degradation and clearance from systemic circulation, the inability to traverse cell membranes, and the efficient intracellular delivery of bioactive RNA molecules. In this review, we explore the implications of RNAs in diseases and provide a chronological overview of the development of RNA therapeutics. Additionally, we summarize the technological advances in RNA-screening design, encompassing various RNA databases and design platforms. The paper then presents an update on FDA-approved RNA therapeutics and those currently undergoing clinical trials for various diseases, with a specific emphasis on RNA medicine and RNA vaccines.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan 528200, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan 528200, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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4
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Dunn LEM, Baines JD. Herpes simplex virus 1 immediate early transcription initiation, pause-release, elongation, and termination in the presence and absence of ICP4. J Virol 2023; 97:e0096023. [PMID: 37754762 PMCID: PMC10617507 DOI: 10.1128/jvi.00960-23] [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: 06/29/2023] [Accepted: 08/11/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Infection with herpes simplex virus 1 (HSV-1) leads to lifelong infection due to the virus's remarkable ability to control transcription of its own genome, resulting in two transcriptional programs: lytic (highly active) and latent (restricted). The lytic program requires immediate early (IE) proteins to first repress transcription of late viral genes, which then undergo sequential de-repression, leading to a specific sequence of gene expression. Here, we show that the IE ICP4 functions to regulate the cascade by limiting RNA polymerase initiation at immediate early times. However, late viral genes that initiate too early in the absence of ICP4 do not yield mRNA as transcription stalls within gene bodies. It follows that other regulatory steps intercede to prevent elongation of genes at the incorrect time, demonstrating the precise control HSV-1 exerts over its own transcription.
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Affiliation(s)
- Laura E. M. Dunn
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Joel D. Baines
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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5
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Al-Gazally ME, Khan R, Imran M, Ramírez-Coronel AA, Alshahrani SH, Altalbawy FMA, Turki Jalil A, Romero-Parra RM, Zabibah RS, Shahid Iqbal M, Karampoor S, Mirzaei R. The role and mechanism of action of microRNA-122 in cancer: Focusing on the liver. Int Immunopharmacol 2023; 123:110713. [PMID: 37523968 DOI: 10.1016/j.intimp.2023.110713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/08/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
microRNA-122 (miR-122) is a highly conserved microRNA that is predominantly expressed in the liver and plays a critical role in the regulation of liver metabolism. Recent studies have shown that miR-122 is involved in the pathogenesis of various types of cancer, particularly liver cancer. In this sense, The current findings highlighted the potential role of miR-122 in regulating many vital processes in cancer pathophysiology, including apoptosis, signaling pathway, cell metabolism, immune system response, migration, and invasion. These results imply that miR-122, which has been extensively studied for its biological functions and potential therapeutic applications, acts as a tumor suppressor or oncogene in cancer development. We first provide an overview and summary of the physiological function and mode of action of miR-122 in liver cancer. We will examine the various signaling pathways and molecular mechanisms through which miR-122 exerts its effects on cancer cells, including the regulation of oncogenic and tumor suppressor genes, the modulation of cell proliferation and apoptosis, and the regulation of metastasis. Most importantly, we will also discuss the potential diagnostic and therapeutic applications of miR-122 in cancer, including the development of miRNA-based biomarkers for cancer diagnosis and prognosis, and the potential use of miR-122 as a therapeutic target for cancer treatment.
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Affiliation(s)
| | - Ramsha Khan
- MBBS, Nawaz Sharif Medical College, Gujrat, Pakistan
| | - Muhammad Imran
- MBBS, Multan Medical and Dental College, Multan, Pakistan
| | | | | | - Farag M A Altalbawy
- National Institute of Laser Enhanced Sciences (NILES), University of Cairo, Giza 12613, Egypt; Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla 51001, Iraq
| | | | - Rahman S Zabibah
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Muhammad Shahid Iqbal
- Department of Clinical Pharmacy, College of Pharmacy, Prince Sattam bin Abdulaziz University, 11942 Alkharj, Saudi Arabia
| | - Sajad Karampoor
- Gastrointestinal and Liver Diseases Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Rasoul Mirzaei
- Venom and Biotherapeutics Molecules Lab, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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6
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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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7
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 426] [Impact Index Per Article: 426.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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8
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Mukherjee A, Islam S, Kieser RE, Kiss DL, Mukherjee C. Long noncoding RNAs are substrates for cytoplasmic capping enzyme. FEBS Lett 2023; 597:947-961. [PMID: 36856012 PMCID: PMC11119571 DOI: 10.1002/1873-3468.14603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023]
Abstract
Cytoplasmic capping returns a cap to specific mRNAs, thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long noncoding RNAs (lncRNAs) are substrates of the cytoplasmic capping enzyme (cCE). The subcellular localisation of 14 lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5' rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5'-RACE cloned sequences, suggesting that these uncapped lncRNAs are targets of cytoplasmic capping.
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Affiliation(s)
- Avik Mukherjee
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Safirul Islam
- Institute of Health Sciences, Presidency University, Kolkata, India
| | - Rachel E Kieser
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | - Daniel L Kiss
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
- Weill Cornell Medical College, New York, NY, USA
- Houston Methodist Cancer Center, Houston, TX, USA
- Houston Methodist Academic Institute, Houston, TX, USA
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9
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Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24044163. [PMID: 36835575 PMCID: PMC9959880 DOI: 10.3390/ijms24044163] [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: 01/23/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.
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10
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Mattay J. Noncanonical metabolite RNA caps: Classification, quantification, (de)capping, and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1730. [PMID: 35675554 DOI: 10.1002/wrna.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The 5' cap of eukaryotic mRNA is a hallmark for cellular functions from mRNA stability to translation. However, the discovery of novel 5'-terminal RNA caps derived from cellular metabolites has challenged this long-standing singularity in both eukaryotes and prokaryotes. Reminiscent of the 7-methylguanosine (m7G) cap structure, these noncanonical caps originate from abundant coenzymes such as NAD, FAD, or CoA and from metabolites like dinucleoside polyphosphates (NpnN). As of now, the significance of noncanonical RNA caps is elusive: they differ for individual transcripts, occur in distinct types of RNA, and change in response to environmental stimuli. A thorough comparison of their prevalence, quantity, and characteristics is indispensable to define the distinct classes of metabolite-capped RNAs. This is achieved by a structured analysis of all present studies covering functional, quantitative, and sequencing data which help to uncover their biological impact. The biosynthetic strategies of noncanonical RNA capping and the elaborate decapping machinery reveal the regulation and turnover of metabolite-capped RNAs. With noncanonical capping being a universal and ancient phenomenon, organisms have developed diverging strategies to adapt metabolite-derived caps to their metabolic needs, but ultimately to establish noncanonical RNA caps as another intriguing layer of RNA regulation. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Johanna Mattay
- Institute of Biochemistry, University of Münster, Münster, Germany
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11
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Zafar J, Huang J, Xu X, Jin F. Analysis of Long Non-Coding RNA-Mediated Regulatory Networks of Plutella xylostella in Response to Metarhizium anisopliae Infection. INSECTS 2022; 13:916. [PMID: 36292864 PMCID: PMC9604237 DOI: 10.3390/insects13100916] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent a diverse class of RNAs that are structurally similar to messenger RNAs (mRNAs) but do not encode proteins. Growing evidence suggests that in response to biotic and abiotic stresses, the lncRNAs play crucial regulatory roles in plants and animals. However, the potential role of lncRNAs during fungal infection has yet to be characterized in Plutella xylostella, a devastating pest of cruciferous crops. In the current study, we performed a strand-specific RNA sequencing of Metarhizium anisopliae-infected (Px36hT, Px72hT) and uninfected (Px36hCK, Px72hCK) P. xylostella fat body tissues. Comprehensive bioinformatic analysis revealed a total of 5665 and 4941 lncRNAs at 36 and 72-h post-infection (hpi), including 563 (Px36hT), 532 (Px72hT) known and 5102 (Px36hT), 4409 (Px72hT) novel lncRNA transcripts. These lncRNAs shared structural similarities with their counterparts in other species, including shorter exon and intron length, fewer exon numbers, and a lower expression profile than mRNAs. LncRNAs regulate the expression of neighboring protein-coding genes by acting in a cis and trans manner. Functional annotation and pathway analysis of cis-acting lncRNAs revealed their role in several immune-related genes, including Toll, serpin, transferrin, βGRP etc. Furthermore, we identified multiple lncRNAs acting as microRNA (miRNA) precursors. These miRNAs can potentially regulate the expression of mRNAs involved in immunity and development, suggesting a crucial lncRNA-miRNA-mRNA complex. Our findings will provide a genetic resource for future functional studies of lncRNAs involved in P. xylostella immune responses to M. anisopliae infection and shed light on understanding insect host-pathogen interactions.
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Affiliation(s)
| | | | - Xiaoxia Xu
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
| | - Fengliang Jin
- Correspondence: (X.X.); (F.J.); Tel.: +86-135-6047-8369 (F.J.)
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Moody J, Kouno T, Chang JC, Ando Y, Carninci P, Shin JW, Hon CC. SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells. Bioinformatics 2022; 38:5126-5128. [PMID: 36173306 PMCID: PMC9665856 DOI: 10.1093/bioinformatics/btac644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/30/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Cell type-specific activities of cis-regulatory elements (CRE) are central to understanding gene regulation and disease predisposition. Single-cell RNA 5'end sequencing (sc-end5-seq) captures the transcription start sites (TSS) which can be used as a proxy to measure the activity of transcribed CREs (tCREs). However, a substantial fraction of TSS identified from sc-end5-seq data may not be genuine due to various artifacts, hindering the use of sc-end5-seq for de novo discovery of tCREs. RESULTS We developed SCAFE-Single-Cell Analysis of Five-prime Ends-a software suite that processes sc-end5-seq data to de novo identify TSS clusters based on multiple logistic regression. It annotates tCREs based on the identified TSS clusters and generates a tCRE-by-cell count matrix for downstream analyses. The software suite consists of a set of flexible tools that could either be run independently or as pre-configured workflows. AVAILABILITY AND IMPLEMENTATION SCAFE is implemented in Perl and R. The source code and documentation are freely available for download under the MIT License from https://github.com/chung-lab/SCAFE. Docker images are available from https://hub.docker.com/r/cchon/scafe. The submitted software version and test data are archived at https://doi.org/10.5281/zenodo.7023163 and https://doi.org/10.5281/zenodo.7024060, respectively. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Jen-Chien Chang
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan
| | - Yoshinari Ando
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa 230-0045, Japan,Human Technopole, Milan 20157, Italy
| | - Jay W Shin
- To whom correspondence should be addressed. or
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13
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Maslakova AA, Didych DA, Golyshev SA, Katrukha IA, Viushkov VS, Zamalutdinov AV, Potashnikova DM, Rubtsov MA, Smirnova OV, Orlovsky IV. Towards unveiling the nature of short SERPINA1 transcripts: Avoiding the main ORF control to translate alpha1-antitrypsin C-terminal peptides. Int J Biol Macromol 2022; 203:703-717. [PMID: 35090941 DOI: 10.1016/j.ijbiomac.2022.01.131] [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: 10/31/2021] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
Alternative ORFs in-frame with the known genes are challenging to reveal. Yet they may contribute significantly to proteome diversity. Here we focused on the individual expression of the SERPINA1 gene exon 5 leading to direct translation of alpha1-antitrypsin (AAT) C-terminal peptides. The discovery of alternative ways for their production may expand the current understanding of the serpin gene's functioning. We detected short transcripts expressed primarily in hepatocytes. We identified four variants of hepatocyte-specific SERPINA1 short transcripts and individually probed their potential to be translated in living cells. The long mRNA gave the full-length AAT-eGFP fusion, while in case of short transcripts we deduced four active SERPINA1 in-frame alternative ORFs encoding 10, 21, 153 and 169 amino acids AAT C-terminal oligo- and polypeptides. Unlike secretory AAT-eGFP fusion exhibiting classical AAT behavior, truncated AAT-fusions differ by intracellular retention and nuclear enrichment. Immunofluorescence on the endogenous AAT C-terminal epitope showed its accumulation in the cell nucleoli, indicating that short transcripts may be translated in vivo. FANTOM5 CAGE data on SERPINA1 suggest that short transcripts originate from the post-transcriptional cleavage of the spliced mRNA, initiated mainly from the hepatocyte-specific promoter. CONCLUSION: Short SERPINA1 transcripts may represent a source for the direct synthesis of AAT C-terminal peptides with properties uncommon to AAT.
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Affiliation(s)
- A A Maslakova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia.
| | - D A Didych
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya, Moscow 117997, Russia
| | - S A Golyshev
- A.N. Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
| | - I A Katrukha
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; HyTest Ltd., Joukahaisenkatu, Turku 20520, Finland
| | - V S Viushkov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - A V Zamalutdinov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - D M Potashnikova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - M A Rubtsov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; I.M. Sechenov First Moscow State Medical University (Sechenov University), Trubetskaya, Moscow 119991, Russia
| | - O V Smirnova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia
| | - I V Orlovsky
- A.N. Belozersky Research Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia
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14
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Chao H, Hu Y, Zhao L, Xin S, Ni Q, Zhang P, Chen M. Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants. Int J Mol Sci 2022; 23:ijms23073695. [PMID: 35409060 PMCID: PMC8998614 DOI: 10.3390/ijms23073695] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022] Open
Abstract
Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have been classified into two broad categories based on their biogenesis and mechanisms of action, housekeeping ncRNAs and regulatory ncRNAs. With advances in RNA sequencing technology and computational methods, bioinformatics resources continue to emerge and update rapidly, including workflow for in silico ncRNA analysis, up-to-date platforms, databases, and tools dedicated to ncRNA identification and functional annotation. In this review, we aim to describe the biogenesis, biological functions, and interactions with DNA, RNA, protein, and microorganism of five major regulatory ncRNAs (miRNA, siRNA, tsRNA, circRNA, lncRNA) in plants. Then, we systematically summarize tools for analysis and prediction of plant ncRNAs, as well as databases. Furthermore, we discuss the silico analysis process of these ncRNAs and present a protocol for step-by-step computational analysis of ncRNAs. In general, this review will help researchers better understand the world of ncRNAs at multiple levels.
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Affiliation(s)
| | | | | | | | | | - Peijing Zhang
- Correspondence: (P.Z.); (M.C.); Tel./Fax: +86-(0)571-88206612 (M.C.)
| | - Ming Chen
- Correspondence: (P.Z.); (M.C.); Tel./Fax: +86-(0)571-88206612 (M.C.)
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15
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A novel promoter-associated non-coding small RNA paGLI1 recruits FUS/P65 to transactivate GLI1 gene expression and promotes infiltrating glioma progression. Cancer Lett 2022; 530:68-84. [DOI: 10.1016/j.canlet.2022.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/29/2021] [Accepted: 01/13/2022] [Indexed: 11/17/2022]
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16
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Abstract
Long non-coding RNAs (lncRNAs) have important roles in regulating the expression of genes and act as biomarkers in the initial development of different cancers. Increasing research studies have verified that dysregulation of lncRNAs occurs in various pathological processes including tumorigenesis and cancer progression. Among the different lncRNAs, DLX6-AS1 has been reported to act as an oncogene in the development and prognoses of different cancers, by affecting many different signalling pathways. This review summarises and analyses the recent research studies describing the biological functions of DLX6-AS1, its overall effect on signalling pathways and the molecular mechanisms underlying its action on the expression of genes in multiple human cancers. Our critical analysis suggests that different signalling pathways associated to this lncRNA may be used as a biomarker for diagnosis, or targets of treatment in cancers.
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17
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Kugelberg U, Nätt D, Skog S, Kutter C, Öst A. 5´XP sRNA-seq: efficient identification of transcripts with and without 5´ phosphorylation reveals evolutionary conserved small RNA. RNA Biol 2021; 18:1588-1599. [PMID: 33382953 PMCID: PMC8594926 DOI: 10.1080/15476286.2020.1861770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022] Open
Abstract
Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5´ nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5´P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5'-terminal modifications (5´X), with a selective approach for 5-phosphorylated sRNA (5´P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5´ insensitive library strategies with 5´ sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.
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Affiliation(s)
- Unn Kugelberg
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Daniel Nätt
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Signe Skog
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institute, Stockholm
| | - Anita Öst
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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18
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Bhatti GK, Khullar N, Sidhu IS, Navik US, Reddy AP, Reddy PH, Bhatti JS. Emerging role of non-coding RNA in health and disease. Metab Brain Dis 2021; 36:1119-1134. [PMID: 33881724 PMCID: PMC8058498 DOI: 10.1007/s11011-021-00739-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Human diseases have always been a significant turf of concern since the origin of mankind. It is cardinal to know the cause, treatment, and cure for every disease condition. With the advent and advancement in technology, the molecular arena at the microscopic level to study the mechanism, progression, and therapy is more rational and authentic pave than a macroscopic approach. Non-coding RNAs (ncRNAs) have now emerged as indispensable players in the diagnosis, development, and therapeutics of every abnormality concerning physiology, pathology, genetics, epigenetics, oncology, and developmental diseases. This is a comprehensive attempt to collate all the existing and proven strategies, techniques, mechanisms of genetic disorders including Silver Russell Syndrome, Fascio- scapula humeral muscular dystrophy, cardiovascular diseases (atherosclerosis, cardiac fibrosis, hypertension, etc.), neurodegenerative diseases (Spino-cerebral ataxia type 7, Spino-cerebral ataxia type 8, Spinal muscular atrophy, Opitz-Kaveggia syndrome, etc.) cancers (cervix, breast, lung cancer, etc.), and infectious diseases (viral) studied so far. This article encompasses discovery, biogenesis, classification, and evolutionary prospects of the existence of this junk RNA along with the integrated networks involving chromatin remodelling, dosage compensation, genome imprinting, splicing regulation, post-translational regulation and proteomics. In conclusion, all the major human diseases are discussed with a facilitated technology transfer, advancements, loopholes, and tentative future research prospects have also been proposed.
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Affiliation(s)
- Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab India
| | | | - Uma Shanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | | | - P. Hemachandra Reddy
- Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Cell Biology & Biochemistry, Neuroscience & Pharmacology, Neurology, Public Health, School of Health Professions, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430 USA
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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19
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Mohammadnejad A, Baumbach J, Li W, Lund J, Larsen MJ, Li S, Mengel-From J, Michel TM, Christiansen L, Christensen K, Hjelmborg J, Tan Q. Differential lncRNA expression profiling of cognitive function in middle and old aged monozygotic twins using generalized association analysis. J Psychiatr Res 2021; 140:197-204. [PMID: 34118637 DOI: 10.1016/j.jpsychires.2021.05.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 05/18/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022]
Abstract
Cognitive impairment is the most prominent symptom in neurodegenerative disorders affecting quality of life and mortality. However, despite years of research, the molecular mechanism underlying the regulation of cognitive function and its impairment is poorly understood. This study aims to elucidate the role of long non-coding RNAs (lncRNAs) expression and lncRNA-mRNA interaction networks, by analyzing lncRNA expression in whole blood samples of 400 middle and old aged monozygotic twins in association with cognitive function using both linear models and a generalized correlation coefficient (GCC) to capture the diverse patterns of correlation. We detected 13 probes (p < 1e-03) displaying nonlinear and 7 probes (p < 1e-03) showing linear correlations. After combining the results, we identified 20 lncRNA probes with p < 1e-03. The top lncRNA probes were annotated to genes, along with the non-coding MALAT1, that play roles in neurodegenerative diseases. The top lncRNAs were linked to functional clusters including peptidyl-glycine modification, vascular smooth muscle cells, mitotic spindle organization and protein tyrosine phosphatase. In addition, mapping of the top significant lncRNAs to the lncRNA-mRNA interaction network detected significantly enriched biological pathways involving neuroactive ligand-receptor interaction, proteasome and chemokines. We show that GCC served as a complementary approach in detecting lncRNAs missed by the conventional linear models. A combination of GCC and linear models identified lncRNAs of diverse patterns of association enriched for GO biological and molecular functions meaningful in cognitive performance and cognitive decline. The novel lncRNA regulatory network further contributed to detect significant pathways implicated in cognition.
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Affiliation(s)
- Afsaneh Mohammadnejad
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jan Baumbach
- Computational Biomedicine, Department of Mathematics and Computer Science, University of Southern Denmark, Denmark; Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany.
| | - Weilong Li
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jesper Lund
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Martin J Larsen
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark; Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark.
| | - Shuxia Li
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Jonas Mengel-From
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
| | - Tanja Maria Michel
- Department of Psychiatry, Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Psychiatry in the Region of Southern Denmark, Odense University Hospital, Odense, Denmark; Brain Research - Inter-Disciplinary Guided Excellence, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Lene Christiansen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
| | - Jacob Hjelmborg
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark.
| | - Qihua Tan
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Denmark.
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20
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Shamie I, Duttke SH, Karottki KJLC, Han CZ, Hansen AH, Hefzi H, Xiong K, Li S, Roth SJ, Tao J, Lee GM, Glass CK, Kildegaard HF, Benner C, Lewis NE. A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells. NAR Genom Bioinform 2021; 3:lqab061. [PMID: 34268494 PMCID: PMC8276764 DOI: 10.1093/nargab/lqab061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely used for producing biopharmaceuticals, and engineering gene expression in CHO is key to improving drug quality and affordability. However, engineering gene expression or activating silent genes requires accurate annotation of the underlying regulatory elements and transcription start sites (TSSs). Unfortunately, most TSSs in the published Chinese hamster genome sequence were computationally predicted and are frequently inaccurate. Here, we use nascent transcription start site sequencing methods to revise TSS annotations for 15 308 Chinese hamster genes and 3034 non-coding RNAs based on experimental data from CHO-K1 cells and 10 hamster tissues. We further capture tens of thousands of putative transcribed enhancer regions with this method. Our revised TSSs improves upon the RefSeq annotation by revealing core sequence features of gene regulation such as the TATA box and the Initiator and, as exemplified by targeting the glycosyltransferase gene Mgat3, facilitate activating silent genes by CRISPRa. Together, we envision our revised annotation and data will provide a rich resource for the CHO community, improve genome engineering efforts and aid comparative and evolutionary studies.
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Affiliation(s)
- Isaac Shamie
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Sascha H Duttke
- Department of Medicine, University of California, San Diego 92093, USA
| | - Karen J la Cour Karottki
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Claudia Z Han
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Anders H Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Hooman Hefzi
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Kai Xiong
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Shangzhong Li
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
| | - Samuel J Roth
- Department of Medicine, University of California, San Diego 92093, USA
| | - Jenhan Tao
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | - Gyun Min Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Denmark
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego 92093, USA
| | | | | | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at UC San Diego 92093, USA
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21
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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22
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun 2021; 12:3297. [PMID: 34078885 PMCID: PMC8172540 DOI: 10.1038/s41467-021-23143-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.
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23
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Wang H, Huang R, Li L, Zhu J, Li Z, Peng C, Zhuang X, Lin H, Shi S, Huang P. CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini. Cell Discov 2021; 7:25. [PMID: 33867522 PMCID: PMC8053708 DOI: 10.1038/s41421-021-00265-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
High-throughput sequencing reveals the complex landscape of small noncoding RNAs (sRNAs). However, it is limited by requiring 5'-monophosphate and 3'-hydroxyl in RNAs for adapter ligation and hindered by methylated nucleosides that interfere with reverse transcription. Here we develop Cap-Clip acid pyrophosphatase (Cap-Clip), T4 polynucleotide kinase (PNK) and AlkB/AlkB(D135S)-facilitated small ncRNA sequencing (CPA-seq) to detect and quantify sRNAs with terminus multiplicities and nucleoside methylations. CPA-seq identified a large number of previously undetected sRNAs. Comparison of sRNAs with or without AlkB/AlkB(D135S) treatment reveals nucleoside methylations on sRNAs. Using CPA-seq, we profiled the sRNA transcriptomes (sRNomes) of nine mouse tissues and reported the extensive tissue-specific differences of sRNAs. We also observed the transition of sRNomes during hepatic reprogramming. Knockdown of mesenchymal stem cell-enriched U1-5' snsRNA promoted hepatic reprogramming. CPA-seq is a powerful tool with high sensitivity and specificity for profiling sRNAs with methylated nucleosides and diverse termini.
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Affiliation(s)
- Heming Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rong Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ling Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Junjin Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhihong Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Xuran Zhuang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Shuo Shi
- Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, Shanghai, 201210, China.
| | - Pengyu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China. .,Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
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24
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Conserved long-range base pairings are associated with pre-mRNA processing of human genes. Nat Commun 2021; 12:2300. [PMID: 33863890 PMCID: PMC8052449 DOI: 10.1038/s41467-021-22549-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 03/20/2021] [Indexed: 02/07/2023] Open
Abstract
The ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3'-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.
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25
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Goszczynski DE, Halstead MM, Islas-Trejo AD, Zhou H, Ross PJ. Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage. Genome Res 2021; 31:732-744. [PMID: 33722934 PMCID: PMC8015843 DOI: 10.1101/gr.267336.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023]
Abstract
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human and mouse. By using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein-coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE to produce a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-seq. Coexpression networks revealed considerable use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate loci. Furthermore, regions surrounding coexpressed modules were enriched in binding factor motifs representative of each tissue. The comprehensive annotation of promoters in such a large collection of tissues will substantially contribute to our understanding of gene expression in cattle and other mammalian species, shortening the gap between genotypes and phenotypes.
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Affiliation(s)
- Daniel E Goszczynski
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Alma D Islas-Trejo
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, California 95616, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, California 95616, USA
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26
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Jiang L, Cheng C, Ji W, Wang H, Du Q, Dong X, Shao J, Yu W. LINC01116 promotes the proliferation and invasion of glioma by regulating the microRNA‑744‑5p‑MDM2‑p53 axis. Mol Med Rep 2021; 23:366. [PMID: 33760190 PMCID: PMC7986001 DOI: 10.3892/mmr.2021.12005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in the development and progression of tumors. However, the roles and underlying mechanisms of long intergenic non-protein coding RNA 1116 (LINC01116), a member of the lncRNA family, in glioma progression are largely unclear. The expression of LINC01116 and microRNA (miR)-744-5p in glioma tissues and cells was detected by reverse transcription-quantitative PCR. The influences of LINC01116 or miR-744-5p on cell proliferation and invasion were evaluated by Cell Counting Kit-8, colony formation and Transwell assays, and western blotting was used to detect the expression of p53 pathway proteins. A dual-luciferase reporter system was used to locate common binding sites between miR-744-5p and LINC01116 or the 3′ untranslated region of E3 ubiquitin-protein ligase Mdm2 (MDM2). RNA immunoprecipitation was used to determine the interactions between RNAs and proteins. Moreover, a xenograft mouse model was constructed to investigate the effects of LINC01116 in vivo, followed by a TdT-mediated dUTP nick end labeling assay to determine the degree of apoptosis in nude mouse tumors. LINC01116 was found to be highly expressed in glioma tissues, which was associated with a malignant phenotype. LINC01116 promoted the proliferation and invasiveness of glioma cells, and inhibited the p53 pathway by preserving the expression of MDM2 mRNA via miR-744-5p sponging. Furthermore, a low degree of miR-744-5p expression was observed in glioma tissues, which was negatively associated with the expression of LINC01116. Overexpression of miR-744-5p inhibited the proliferation and invasiveness of glioma cells, which was rescued by LINC01116. Finally, LINC01116 knockdown inhibited tumor growth in nude mice. In conclusion, LINC01116 is aberrantly expressed and promotes the progression of glioma by regulating the miR-744-5p-MDM2-p53 pathway. In future, targeting LINC01116 may therefore be a potential therapeutic approach for patients with glioma.
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Affiliation(s)
- Li Jiang
- Department of Neurosurgery, Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Chao Cheng
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Wei Ji
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Hao Wang
- Department of Neurosurgery, Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Quan Du
- Department of Neurosurgery, Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaoqiao Dong
- Department of Neurosurgery, Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Junfei Shao
- Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu 214023, P.R. China
| | - Wenhua Yu
- Department of Neurosurgery, Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
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27
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Chaudhary R. Potential of long non-coding RNAs as a therapeutic target and molecular markers in glioblastoma pathogenesis. Heliyon 2021; 7:e06502. [PMID: 33786397 PMCID: PMC7988331 DOI: 10.1016/j.heliyon.2021.e06502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/20/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GB) is by far the most hostile type of malignant tumor that primarily affects the brain and spine, derived from star-shaped glial cells that are astrocytes and oligodendrocytes. Despite of significant efforts in recent years in glioblastoma research, the clinical efficacy of existing medical intervention is still limited and very few potential diagnostic markers are available. Long non-coding RNAs (lncRNAs) that lacks protein-coding capabilities were previously thought to be "junk sequences" in mammalian genomes are quite indispensible epigenetic regulators that can positively or negatively regulate gene expression and nuclear architecture, with significant roles in the initiation and development of tumors. Nevertheless, the precise mechanism of these distortedly expressed lncRNAs in glioblastoma pathogenesis is not yet fully understood. Since the advent of high-throughput sequencing technologies, more and more research have elucidated that lncRNAs are one of the most promising prognostic biomarkers and therapeutic targets for glioblastoma. In this paper, I briefly outlined the existing findings of lncRNAs. And also summarizes the profiles of different lncRNAs that have been broadly classified in glioblastoma research, with emphasis on both their prognostic and therapeutic values.
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Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
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28
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De Summa S, Palazzo A, Caputo M, Iacobazzi RM, Pilato B, Porcelli L, Tommasi S, Paradiso AV, Azzariti A. Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: A Feature Selection Approach. Int J Mol Sci 2021; 22:2227. [PMID: 33672425 PMCID: PMC7926489 DOI: 10.3390/ijms22042227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer is one of the most common malignancies in men. It is characterized by a high molecular genomic heterogeneity and, thus, molecular subtypes, that, to date, have not been used in clinical practice. In the present paper, we aimed to better stratify prostate cancer patients through the selection of robust long non-coding RNAs. To fulfill the purpose of the study, a bioinformatic approach focused on feature selection applied to a TCGA dataset was used. In such a way, LINC00668 and long non-coding(lnc)-SAYSD1-1, able to discriminate ERG/not-ERG subtypes, were demonstrated to be positive prognostic biomarkers in ERG-positive patients. Furthermore, we performed a comparison between mutated prostate cancer, identified as "classified", and a group of patients with no peculiar genomic alteration, named "not-classified". Moreover, LINC00920 lncRNA overexpression has been linked to a better outcome of the hormone regimen. Through the feature selection approach, it was found that the overexpression of lnc-ZMAT3-3 is related to low-grade patients, and three lncRNAs: lnc-SNX10-87, lnc-AP1S2-2, and ADPGK-AS1 showed, through a co-expression analysis, significant correlation values with potentially druggable pathways. In conclusion, the data mining of publicly available data and robust bioinformatic analyses are able to explore the unknown biology of malignancies.
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Affiliation(s)
- Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; (M.C.); (B.P.); (S.T.)
| | - Antonio Palazzo
- Laboratory of Nanotechnology, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy;
| | - Mariapia Caputo
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; (M.C.); (B.P.); (S.T.)
| | - Rosa Maria Iacobazzi
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; (R.M.I.); (L.P.); (A.A.)
| | - Brunella Pilato
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; (M.C.); (B.P.); (S.T.)
| | - Letizia Porcelli
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; (R.M.I.); (L.P.); (A.A.)
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; (M.C.); (B.P.); (S.T.)
| | | | - Amalia Azzariti
- Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; (R.M.I.); (L.P.); (A.A.)
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29
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Perdikopanis N, Georgakilas GK, Grigoriadis D, Pierros V, Kavakiotis I, Alexiou P, Hatzigeorgiou A. DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. Nucleic Acids Res 2021; 49:D151-D159. [PMID: 33245765 PMCID: PMC7778932 DOI: 10.1093/nar/gkaa1060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/16/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023] Open
Abstract
Deregulation of microRNA (miRNA) expression plays a critical role in the transition from a physiological to a pathological state. The accurate miRNA promoter identification in multiple cell types is a fundamental endeavor towards understanding and characterizing the underlying mechanisms of both physiological as well as pathological conditions. DIANA-miRGen v4 (www.microrna.gr/mirgenv4) provides cell type specific miRNA transcription start sites (TSSs) for over 1500 miRNAs retrieved from the analysis of >1000 cap analysis of gene expression (CAGE) samples corresponding to 133 tissues, cell lines and primary cells available in FANTOM repository. MiRNA TSS locations were associated with transcription factor binding site (TFBSs) annotation, for >280 TFs, derived from analyzing the majority of ENCODE ChIP-Seq datasets. For the first time, clusters of cell types having common miRNA TSSs are characterized and provided through a user friendly interface with multiple layers of customization. DIANA-miRGen v4 significantly improves our understanding of miRNA biogenesis regulation at the transcriptional level by providing a unique integration of high-quality annotations for hundreds of cell specific miRNA promoters with experimentally derived TFBSs.
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Affiliation(s)
- Nikos Perdikopanis
- Hellenic Pasteur Institute, Athens 11521, Greece.,Department of Electrical and Computer Engineering, University of Thessaly, Volos 38221, Greece.,Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens 15784, Greece
| | - Georgios K Georgakilas
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 62500 Brno, Czech Republic
| | - Dimitris Grigoriadis
- Hellenic Pasteur Institute, Athens 11521, Greece.,Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Vasilis Pierros
- Hellenic Pasteur Institute, Athens 11521, Greece.,Department of Electrical and Computer Engineering, University of Thessaly, Volos 38221, Greece
| | - Ioannis Kavakiotis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
| | - Panagiotis Alexiou
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, 62500 Brno, Czech Republic
| | - Artemis Hatzigeorgiou
- Hellenic Pasteur Institute, Athens 11521, Greece.,Department of Electrical and Computer Engineering, University of Thessaly, Volos 38221, Greece.,Department of Computer Science and Biomedical Informatics, University of Thessaly, Greece
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30
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Dai H, Gu W. Small RNA Plays Important Roles in Virus-Host Interactions. Viruses 2020; 12:E1271. [PMID: 33171824 PMCID: PMC7695165 DOI: 10.3390/v12111271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding small RNAs play important roles in virus-host interactions. For hosts, small RNAs can serve as sensors in antiviral pathways including RNAi and CRISPR; for viruses, small RNAs can be involved in viral transcription and replication. This paper covers several recent discoveries on small RNA mediated virus-host interactions, and focuses on influenza virus cap-snatching and a few important virus sensors including PIR-1, RIG-I like protein DRH-1 and piRNAs. The paper also discusses recent advances in mammalian antiviral RNAi.
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Affiliation(s)
| | - Weifeng Gu
- Department of Molecular, Cell and Systems Biology, University of California, Riverside 900 University Avenue, Riverside, CA 92521, USA;
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31
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Agana BA, Wysocki VH, Schoenberg DR. Cytoplasmic mRNA recapping has limited impact on proteome complexity. Open Biol 2020; 10:200313. [PMID: 33234072 PMCID: PMC7729026 DOI: 10.1098/rsob.200313] [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: 09/29/2020] [Accepted: 10/26/2020] [Indexed: 01/25/2023] Open
Abstract
The m7G cap marks the 5' end of all eukaryotic mRNAs, but there are also capped ends that map downstream within spliced exons. A portion of the mRNA transcriptome undergoes a cyclical process of decapping and recapping, termed cap homeostasis, which impacts the translation and stability of these mRNAs. Blocking cytoplasmic capping results in the appearance of uncapped 5' ends at native cap sites but also near downstream cap sites. If translation initiates at these sites the products would lack the expected N-terminal sequences, raising the possibility of a link between mRNA recapping and proteome complexity. We performed a shotgun proteomics analysis on cells carrying an inducible inhibitor of cytoplasmic capping. A total of 21 875 tryptic peptides corresponding to 3565 proteins were identified in induced and uninduced cells. Of these, only 29 proteins significantly increased, and 28 proteins significantly decreased, when cytoplasmic capping was inhibited, indicating mRNA recapping has little overall impact on protein expression. In addition, overall peptide coverage per protein did not change significantly when cytoplasmic capping was inhibited. Together with previous work, our findings indicate cap homeostasis functions primarily in gating mRNAs between translating and non-translating states, and not as a source of proteome complexity.
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Affiliation(s)
- Bernice A. Agana
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H. Wysocki
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel R. Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
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32
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Cao P, Jin Q, Feng L, Li H, Qin G, Zhou G. Emerging roles and potential clinical applications of noncoding RNAs in hepatocellular carcinoma. Semin Cancer Biol 2020; 75:136-152. [PMID: 32931952 DOI: 10.1016/j.semcancer.2020.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma(HCC) is one of the most common forms of cancer, and accounts for a high proportion of cancer-associated deaths. Growing evidences have demonstrated that non- protein-coding regions of the genome could give rise to transcripts, termed noncoding RNA (ncRNA), that form novel functional layers of the cellular activity. ncRNAs are implicated in different molecular mechanisms and functions at transcriptional, translational and post-translational levels. An increasing number of studies have demonstrated a complex array of molecular and cellular functions of ncRNAs in different stages of the HCC tumorigenesis, either in an oncogenic or tumor-suppressive manner. As a result, several pre-clinical studies have highlighted the great potentials of ncRNAs as novel biomarkers for cancer diagnosis or therapeutics in targeting HCC progression. In this review, we briefly described the characteristics of several representative ncRNAs and summarized the latest findings of their roles and mechanisms in the development of HCC, in order to better understand the cancer biology and their potential clinical applications in this malignancy.
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Affiliation(s)
- Pengbo Cao
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qian Jin
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Lan Feng
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China
| | - Haibei Li
- Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin Institute of Environmental & Operational Medicine, Tianjin City, China
| | - Geng Qin
- State Key Laboratory of Rare Earth Resources Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun City, China
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, National Center for Protein Sciences at Beijing, Beijing Institute of Radiation Medicine, Beijing, China; Collaborative Innovation Center for Personalized Cancer Medicine, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing City, China; Medical College, Guizhou University, Guiyang City, China.
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33
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Li L, Dai H, Nguyen AP, Hai R, Gu W. Influenza A virus utilizes noncanonical cap-snatching to diversify its mRNA/ncRNA. RNA (NEW YORK, N.Y.) 2020; 26:1170-1183. [PMID: 32444459 PMCID: PMC7430677 DOI: 10.1261/rna.073866.119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
Influenza A virus (IAV) utilizes cap-snatching to obtain host capped small RNAs for priming viral mRNA synthesis, generating capped hybrid mRNAs for translation. Previous studies have been focusing on canonical cap-snatching, which occurs at the very 5' end of viral mRNAs. Here we discovered noncanonical cap-snatching, which generates capped hybrid mRNAs/noncoding RNAs mapped to the region ∼300 nucleotides (nt) upstream of each mRNA 3' end, and to the 5' region, primarily starting at the second nt, of each virion RNAs (vRNA). Like canonical cap-snatching, noncanonical cap-snatching utilizes a base-pairing between the last nt G of host capped RNAs and a nt C of template RNAs to prime RNA synthesis. However, the nt upstream of this template C is usually A/U rather than just U; prime-realignment occurs less frequently. We also demonstrate that IAV can snatch capped IAV RNAs in addition to host RNAs. Noncanonical cap-snatching likely generates novel mRNAs with start AUG encoded in viral or host RNAs. These findings expand our understanding of cap-snatching mechanisms and suggest that IAV may utilize noncanonical cap-snatching to diversify its mRNAs/ncRNAs.
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Affiliation(s)
- Lichao Li
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Hui Dai
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - An-Phong Nguyen
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Rong Hai
- Department of Microbiology and Plant Pathology, University of California, Riverside, California 92521, USA
| | - Weifeng Gu
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
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34
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Dai H, Gu W. Strategies and Best Practice in Cloning Small RNAs. GENE TECHNOLOGY 2020; 9:151. [PMID: 32953938 PMCID: PMC7500658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High-throughput sequencing has become a standard and powerful tool for analyzing nucleic acids primarily due to its sensitivity and convenience. Small RNAs play important roles in regulating cellular and viral genes. The conventional methods for small RNA analyses are tedious and often lack accuracy, specificity and sensitivity for many small RNA species. Therefore, high-throughput sequencing becomes an indispensable tool for analyzing small RNAs. However, it is challenging to generate a reliable and representative small RNA library for high-throughput sequencing since small RNAs are usually expressed at extremely low levels and often contain modifications which affect library construction, usually causing biased readouts. This review compares various strategies for generating small RNA libraries of high quality and reliability, and provides recommendations on best practice in preparing high-throughput sequencing RNA libraries.
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35
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Chen Q, Meng X, Liao Q, Chen M. Versatile interactions and bioinformatics analysis of noncoding RNAs. Brief Bioinform 2020; 20:1781-1794. [PMID: 29939215 DOI: 10.1093/bib/bby050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/02/2018] [Indexed: 02/07/2023] Open
Abstract
Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.
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Affiliation(s)
- Qi Chen
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Xianwen Meng
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Qi Liao
- Department of Bioinformatics, The State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, P. R. China
| | - Ming Chen
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathological and Physiological Technology, Medical School of Ningbo University, Ningbo, Zhejiang, P. R. China
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36
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Del Valle Morales D, Trotman JB, Bundschuh R, Schoenberg DR. Inhibition of cytoplasmic cap methylation identifies 5' TOP mRNAs as recapping targets and reveals recapping sites downstream of native 5' ends. Nucleic Acids Res 2020; 48:3806-3815. [PMID: 31996904 PMCID: PMC7144985 DOI: 10.1093/nar/gkaa046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/30/2019] [Accepted: 01/23/2020] [Indexed: 12/20/2022] Open
Abstract
Cap homeostasis is the cyclical process of decapping and recapping that maintains the translation and stability of a subset of the transcriptome. Previous work showed levels of some recapping targets decline following transient expression of an inactive form of RNMT (ΔN-RNMT), likely due to degradation of mRNAs with improperly methylated caps. The current study examined transcriptome-wide changes following inhibition of cytoplasmic cap methylation. This identified mRNAs with 5′-terminal oligopyrimidine (TOP) sequences as the largest single class of recapping targets. Cap end mapping of several TOP mRNAs identified recapping events at native 5′ ends and downstream of the TOP sequence of EIF3K and EIF3D. This provides the first direct evidence for downstream recapping. Inhibition of cytoplasmic cap methylation was also associated with mRNA abundance increases for a number of transcription, splicing, and 3′ processing factors. Previous work suggested a role for alternative polyadenylation in target selection, but this proved not to be the case. However, inhibition of cytoplasmic cap methylation resulted in a shift of upstream polyadenylation sites to annotated 3′ ends. Together, these results solidify cap homeostasis as a fundamental process of gene expression control and show cytoplasmic recapping can impact regulatory elements present at the ends of mRNA molecules.
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Affiliation(s)
- Daniel Del Valle Morales
- Center for RNA Biology, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA.,Molecular, Cellular and Developmental Biology Program, Columbus, OH 43210, USA
| | - Jackson B Trotman
- Center for RNA Biology, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, Columbus, OH 43210, USA.,Department of Physics, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, Columbus, OH 43210, USA.,Division of Hematology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, Columbus, OH 43210, USA
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37
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Le NT, Harukawa Y, Miura S, Boer D, Kawabe A, Saze H. Epigenetic regulation of spurious transcription initiation in Arabidopsis. Nat Commun 2020; 11:3224. [PMID: 32591528 PMCID: PMC7319988 DOI: 10.1038/s41467-020-16951-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs. Epigenetic regulation can silence transposons and maintain gene expression. Here the authors survey Arabidopsis mutants defective in epigenetic regulation and show ectopic activation of thousands of cryptic TSSs and altered expression of nearby genes demonstrating the importance of suppressing spurious transcription.
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Affiliation(s)
- Ngoc Tu Le
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Damian Boer
- Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, Netherlands
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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38
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Thieffry A, Vigh ML, Bornholdt J, Ivanov M, Brodersen P, Sandelin A. Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways. THE PLANT CELL 2020; 32:1845-1867. [PMID: 32213639 PMCID: PMC7268790 DOI: 10.1105/tpc.19.00815] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/03/2020] [Accepted: 03/20/2020] [Indexed: 05/20/2023]
Abstract
In animals, RNA polymerase II initiates transcription bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are degraded by the nuclear exosome. Previous studies based on nascent RNA approaches concluded that Arabidopsis (Arabidopsis thaliana) does not produce PROMPTs. Here, we used steady-state RNA sequencing in mutants defective in nuclear RNA decay including the exosome to reassess the existence of Arabidopsis PROMPTs. While they are rare, we identified ∼100 cases of exosome-sensitive PROMPTs in Arabidopsis. Such PROMPTs are sources of small interfering RNAs in exosome-deficient mutants, perhaps explaining why plants have evolved mechanisms to suppress PROMPTs. In addition, we found ∼200 long, unspliced and exosome-sensitive antisense RNAs that arise from transcription start sites within parts of the genome encoding 3'-untranslated regions on the sense strand. The previously characterized noncoding RNA that regulates expression of the key seed dormancy regulator, DELAY OF GERMINATION1, is a typical representative of this class of RNAs. Transcription factor genes are overrepresented among loci with exosome-sensitive antisense RNAs, suggesting a potential for widespread control of gene expression via this class of noncoding RNAs. Lastly, we assess the use of alternative promoters in Arabidopsis and compare the accuracy of existing TSS annotations.
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Affiliation(s)
- Axel Thieffry
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Maria Louisa Vigh
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Jette Bornholdt
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Maxim Ivanov
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Albin Sandelin
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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39
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Zytnicki M, Gaspin C. mmannot: How to improve small-RNA annotation? PLoS One 2020; 15:e0231738. [PMID: 32463818 PMCID: PMC7255610 DOI: 10.1371/journal.pone.0231738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 03/30/2020] [Indexed: 12/04/2022] Open
Abstract
High-throughput sequencing makes it possible to provide the genome-wide distribution of small non coding RNAs in a single experiment, and contributed greatly to the identification and understanding of these RNAs in the last decade. Small non coding RNAs gather a wide collection of classes, such as microRNAs, tRNA-derived fragments, small nucleolar RNAs and small nuclear RNAs, to name a few. As usual in RNA-seq studies, the sequencing step is followed by a feature quantification step: when a genome is available, the reads are aligned to the genome, their genomic positions are compared to the already available annotations, and the corresponding features are quantified. However, problem arises when many reads map at several positions and while different strategies exist to circumvent this problem, all of them are biased. In this article, we present a new strategy that compares all the reads that map at several positions, and their annotations when available. In many cases, all the hits co-localize with the same feature annotation (a duplicated miRNA or a duplicated gene, for instance). When different annotations exist for a given read, we propose to merge existing features and provide the counts for the merged features. This new strategy has been implemented in a tool, mmannot, freely available at https://github.com/mzytnicki/mmannot.
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Affiliation(s)
- Matthias Zytnicki
- Unité de Mathématiques et Informatique Appliquées, Toulouse INRA, Castanet Tolosan, France
- * E-mail:
| | - Christine Gaspin
- Unité de Mathématiques et Informatique Appliquées, Toulouse INRA, Castanet Tolosan, France
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40
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Borbolis F, Rallis J, Kanatouris G, Kokla N, Karamalegkos A, Vasileiou C, Vakaloglou KM, Diallinas G, Stravopodis DJ, Zervas CG, Syntichaki P. mRNA decapping is an evolutionarily conserved modulator of neuroendocrine signaling that controls development and ageing. eLife 2020; 9:e53757. [PMID: 32366357 PMCID: PMC7200159 DOI: 10.7554/elife.53757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/22/2020] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic 5'-3' mRNA decay plays important roles during development and in response to stress, regulating gene expression post-transcriptionally. In Caenorhabditis elegans, deficiency of DCAP-1/DCP1, the essential co-factor of the major cytoplasmic mRNA decapping enzyme, impacts normal development, stress survival and ageing. Here, we show that overexpression of dcap-1 in neurons of worms is sufficient to increase lifespan through the function of the insulin/IGF-like signaling and its effector DAF-16/FOXO transcription factor. Neuronal DCAP-1 affects basal levels of INS-7, an ageing-related insulin-like peptide, which acts in the intestine to determine lifespan. Short-lived dcap-1 mutants exhibit a neurosecretion-dependent upregulation of intestinal ins-7 transcription, and diminished nuclear localization of DAF-16/FOXO. Moreover, neuronal overexpression of DCP1 in Drosophila melanogaster confers longevity in adults, while neuronal DCP1 deficiency shortens lifespan and affects wing morphogenesis, cell non-autonomously. Our genetic analysis in two model-organisms suggests a critical and conserved function of DCAP-1/DCP1 in developmental events and lifespan modulation.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - John Rallis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - George Kanatouris
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - Nikolitsa Kokla
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - Antonis Karamalegkos
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - Christina Vasileiou
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
- Department of Molecular Biology and Genetics, Democritus University of ThraceAlex/polisGreece
| | - Katerina M Vakaloglou
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
| | - George Diallinas
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - Dimitrios J Stravopodis
- Department of Biology, School of Science, National and Kapodistrian University of AthensAthensGreece
| | - Christos G Zervas
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic ResearchAthensGreece
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41
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Li L, Dai H, Nguyen AP, Gu W. A convenient strategy to clone small RNA and mRNA for high-throughput sequencing. RNA (NEW YORK, N.Y.) 2020; 26:218-227. [PMID: 31754076 PMCID: PMC6961543 DOI: 10.1261/rna.071605.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
High-throughput sequencing has become a standard tool for analyzing RNA and DNA. This method usually needs a cDNA/DNA library ligated with specific 5' and 3' linkers. Unlike mRNA, small RNA often contains modifications including 5' cap or triphosphate and 2'-O-methyl, requiring additional processing steps before linker additions during cloning processes; due to low expression levels, it is difficult to clone small RNA with a small amount of total RNA. Here we present a new strategy to clone 5' modified or unmodified small RNA in an all-liquid-based reaction carried out in a single PCR tube with as little as 20 ng total RNA. The 7-h cloning process only needs ∼1 h of labor. Moreover, this method can also clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA; the barcoded PCR primers are also compatible with non-cDNA cloning applications, including the preparation of genomic libraries. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, versatile, and cost-effective. Moreover, the all-liquid-based reaction can be performed in an automated manner.
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Affiliation(s)
- Lichao Li
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Hui Dai
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - An-Phong Nguyen
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
| | - Weifeng Gu
- Department of Molecular, Cell, and Systems Biology, University of California, Riverside, California 92521, USA
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42
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Georgakilas GK, Perdikopanis N, Hatzigeorgiou A. Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE data. Sci Rep 2020; 10:877. [PMID: 31965016 PMCID: PMC6972925 DOI: 10.1038/s41598-020-57811-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
Cap Analysis of Gene Expression (CAGE) has emerged as a powerful experimental technique for assisting in the identification of transcription start sites (TSSs). There is strong evidence that CAGE also identifies capping sites along various other locations of transcribed loci such as splicing byproducts, alternative isoforms and capped molecules overlapping introns and exons. We present ADAPT-CAGE, a Machine Learning framework which is trained to distinguish between CAGE signal derived from TSSs and transcriptional noise. ADAPT-CAGE provides highly accurate experimentally derived TSSs on a genome-wide scale. It has been specifically designed for flexibility and ease-of-use by only requiring aligned CAGE data and the underlying genomic sequence. When compared to existing algorithms, ADAPT-CAGE exhibits improved performance on every benchmark that we designed based on both annotation- and experimentally-driven strategies. This performance boost brings ADAPT-CAGE in the spotlight as a computational framework that is able to assist in the refinement of gene regulatory networks, the incorporation of accurate information of gene expression regulators and alternative promoter usage in both physiological and pathological conditions.
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Affiliation(s)
- Georgios K Georgakilas
- Hellenic Pasteur Institute, Athens, 11521, Greece. .,Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece. .,Central European Institute of Technology, Masaryk University, Kamenice 735/5, 62500, Brno, Czech Republic.
| | - Nikos Perdikopanis
- Hellenic Pasteur Institute, Athens, 11521, Greece.,Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece.,Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Athens, Greece
| | - Artemis Hatzigeorgiou
- Hellenic Pasteur Institute, Athens, 11521, Greece. .,Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece.
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43
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Morioka MS, Kawaji H, Nishiyori-Sueki H, Murata M, Kojima-Ishiyama M, Carninci P, Itoh M. Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites. Methods Mol Biol 2020; 2120:277-301. [PMID: 32124327 DOI: 10.1007/978-1-0716-0327-7_20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cap analysis of gene expression (CAGE) is an approach to identify and monitor the activity (transcription initiation frequency) of transcription start sites (TSSs) at single base-pair resolution across the genome. It has been effectively used to identify active promoter and enhancer regions in cancer cells, with potential utility to identify key factors to immunotherapy. Here, we overview a series of CAGE protocols and describe detailed experimental steps of the latest protocol based on the Illumina sequencing platform; both experimental steps (see Subheadings 3.1-3.11) and computational processing steps (see Subheadings 3.12-3.20) are described.
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Affiliation(s)
- Masaki Suimye Morioka
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Hideya Kawaji
- Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiromi Nishiyori-Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Mitsuyoshi Murata
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Miki Kojima-Ishiyama
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.
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44
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Jiang YH, Li X, Niu W, Wang D, Wu B, Yang CH. β-Sitosterol regulated microRNAs in endothelial cells against an oxidized low-density lipoprotein. Food Funct 2020; 11:1881-1890. [PMID: 32068754 DOI: 10.1039/c9fo01976f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
β-sitosterol is shown to demonstrate endothelial protective effects, which inhibited apoptosis, increased cell migration, and improved mitochondrial function of human aortic endothelial cells.
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Affiliation(s)
- Yue-Hua Jiang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
- First Clinical Medical College
- Shandong University of Traditional Chinese Medicine
| | - Xiao Li
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
| | - Weipin Niu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
| | - DongLi Wang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
| | - Bo Wu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
| | - Chuan-Hua Yang
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine
- Jinan 250014
- China
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45
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Miyazato P, Matsuo M, Tan BJY, Tokunaga M, Katsuya H, Islam S, Ito J, Murakawa Y, Satou Y. HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP. Retrovirology 2019; 16:38. [PMID: 31842935 PMCID: PMC6915898 DOI: 10.1186/s12977-019-0500-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022] Open
Abstract
Background Human T cell leukaemia virus type 1 (HTLV-1) is a retrovirus associated with human diseases such as adult T-cell leukaemia/lymphoma and HTLV-1 associated myelopathy/tropical spastic paraparesis. In contrast to another human retrovirus, human immunodeficiency virus type 1 (HIV-1), HTLV-1 persists in the host not via vigorous virus production but mainly via proliferation and/or long-term survival in the form of silent proviruses in infected host cells. As a result, HTLV-1-infected cells rarely produce virus particles in vivo even without anti-retroviral treatment. That should be an advantage for the virus to escape from the host immune surveillance by minimizing the expression of viral antigens in host cells. However, why HIV-1 and HTLV-1 behave so differently during natural infection is not fully understood. Results We performed cap analysis of gene expression (CAGE) using total RNAs and nascent, chromatin-associated, RNAs in the nucleus and found that HTLV-1 RNAs were processed post-transcriptionally in infected cells. RNA processing was evident for the sense viral transcripts but not the anti-sense ones. We also found a higher proportion of CG di-nucleotides in proviral sequences of HTLV-1-infected cells, when compared to the HIV-1 genomic sequence. It has been reported recently that CG dinucleotide content of viral sequence is associated with susceptibility to the antiviral ZC3HAV1 (ZAP), suggesting the involvement of this protein in the regulation of HTLV-1 transcripts. To analyse the effect of ZAP on HTLV-1 transcripts, we over-expressed it in HTLV-1-infected cells. We found there was a dose-dependent reduction in virus production with ZAP expression. We further knocked down endogenous ZAP with two independent targeting siRNAs and observed a significant increase in virus production in the culture supernatant. Other delta-type retroviruses such as simian T-cell leukaemia virus and bovine leukaemia virus, also contain high CG-dinucleotide contents in their viral genomes, suggesting that ZAP-mediated suppression of viral transcripts might be a common feature of delta-type retroviruses, which cause minimal viremia in their natural hosts. Conclusions The post-transcriptional regulatory mechanism involving ZAP might allow HTLV-1 to maintain a delicate balance required for prolonged survival in infected individuals.
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Affiliation(s)
- Paola Miyazato
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Misaki Matsuo
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Benjy J Y Tan
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Michiyo Tokunaga
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Hiroo Katsuya
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.,Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Saiful Islam
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yasuhiro Murakawa
- RIKEN-IFOM Joint Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0811, Japan. .,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
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46
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Sudmant PH, Lee H, Dominguez D, Heiman M, Burge CB. Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Cell Rep 2019; 25:2447-2456.e4. [PMID: 30485811 DOI: 10.1016/j.celrep.2018.10.094] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/24/2018] [Accepted: 10/25/2018] [Indexed: 12/21/2022] Open
Abstract
Particular brain regions and cell populations exhibit increased susceptibility to aging-related stresses. Here, we describe the age-specific and brain-region-specific accumulation of ribosome-associated 3' UTR RNAs that lack the 5' UTR and open reading frame. Our study reveals that this phenomenon impacts hundreds of genes in aged D1 spiny projection neurons of the mouse striatum and also occurs in the aging human brain. Isolated 3' UTR accumulation is tightly correlated with mitochondrial gene expression and oxidative stress, with full-length mRNA expression that is reduced but not eliminated, and with production of short 3' UTR-encoded peptides. Depletion of the oxidation-sensitive Fe-S cluster ribosome recycling factor ABCE1 induces the accumulation of 3' UTRs, consistent with a model in which ribosome stalling and mRNA cleavage by No-Go decay yields isolated 3' UTR RNAs protected by ribosomes. Isolated 3' UTR accumulation is a hallmark of brain aging, likely reflecting regional differences in metabolism and oxidative stress.
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Affiliation(s)
- Peter H Sudmant
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Hyeseung Lee
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Myriam Heiman
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
| | - Christopher B Burge
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA.
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47
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Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, Scavelli A, Gingeras TR, Wold BJ, Myers RM, Guigó R, Mortazavi A. Dynamics of microRNA expression during mouse prenatal development. Genome Res 2019; 29:1900-1909. [PMID: 31645363 PMCID: PMC6836743 DOI: 10.1101/gr.248997.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) play a critical role as posttranscriptional regulators of gene expression. The ENCODE Project profiled the expression of miRNAs in an extensive set of organs during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct organ-specific and developmental stage-specific miRNA expression clusters, with an overall pattern of increasing organ-specific expression as embryonic development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by organ type rather than by species. An analysis of messenger RNA expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the organ in which these miRNAs are expressed during embryonic development. Our results provide the most comprehensive time-course of miRNA expression as part of an integrated ENCODE reference data set for mouse embryonic development.
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Affiliation(s)
- Sorena Rahmanian
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA
| | - Rabi Murad
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA
| | - Alessandra Breschi
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Catalonia, Spain
| | - Weihua Zeng
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Brian Williams
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Carrie A Davis
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sarah Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Dianna Moore
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Diane Trout
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Chris Zaleski
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Alex Dobin
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Lei-Hoon Sei
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jorg Drenkow
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Alex Scavelli
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Thomas R Gingeras
- Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Barbara J Wold
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Roderic Guigó
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG) and UPF, Barcelona 08003, Catalonia, Spain
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, Irvine, California 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA
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48
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Duttke SH, Chang MW, Heinz S, Benner C. Identification and dynamic quantification of regulatory elements using total RNA. Genome Res 2019; 29:1836-1846. [PMID: 31649059 PMCID: PMC6836739 DOI: 10.1101/gr.253492.119] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.
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Affiliation(s)
- Sascha H Duttke
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Max W Chang
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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49
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Zhang P, Wu W, Chen Q, Chen M. Non-Coding RNAs and their Integrated Networks. J Integr Bioinform 2019; 16:/j/jib.2019.16.issue-3/jib-2019-0027/jib-2019-0027.xml. [PMID: 31301674 PMCID: PMC6798851 DOI: 10.1515/jib-2019-0027] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/02/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.
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Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenyi Wu
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qi Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
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50
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Zhang Y, Zhang D, Lv J, Wang S, Zhang Q. LncRNA SNHG15 acts as an oncogene in prostate cancer by regulating miR-338-3p/FKBP1A axis. Gene 2019; 705:44-50. [PMID: 30981837 DOI: 10.1016/j.gene.2019.04.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 12/26/2022]
Abstract
Long non-coding RNAs (lncRNAs) are crucial regulators in the progression of various diseases. Although the role of lncRNAs in prostate cancer (PCa) has been studied in recent years, there are still numerous lncRNAs need to be elucidated. This study aims to detect the role of lncRNA small nucleolar RNA host gene 15 (SNHG15) in human prostate cancer. Using qRT-PCR analysis, we identified the upregulation of SNHG15 in PCa cell lines. Loss-of function assays were conducted to determine the regulatory effect of SNHG15 on PCa cell proliferation, migration and epithelial-mesenchymal transition (EMT). According to the results of functional assays, we found that knockdown of SNHG15 impaired cell viability, suppressed cell proliferation, inhibited cell migration and invasion, reversed EMT progress. All these findings revealed the oncogenic function of SNHG15 in PCa. Mechanism investigation revealed that SNHG15 was located in the cytoplasm of PCa cells and acted as a molecular sponge of microRNA-338-3p (miR-338-3p). Moreover, FKBP prolyl isomerase 1A (FKBP1A) was a target of miR-338-3p. This investigation demonstrated that SNHG15 may serve as a competing endogenous RNA (ceRNA) to regulate miR-338-3p and FKBP1A. Finally, the involvement of miR-338-3p and FKBP1A in SNHG15-mediated biological function was demonstrated by performing rescue assays. In summary, our study revealed the function of a novel pathway in PCa.
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Affiliation(s)
- Yuelong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Dahong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Jia Lv
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Shuai Wang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Qi Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
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