1
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Chabronova A, Holmes TL, Hoang DM, Denning C, James V, Smith JGW, Peffers MJ. SnoRNAs in cardiovascular development, function, and disease. Trends Mol Med 2024; 30:562-578. [PMID: 38523014 DOI: 10.1016/j.molmed.2024.03.004] [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: 12/15/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Small nucleolar RNAs (snoRNAs) are emerging as important regulators of cardiovascular (patho)biology. Several roles of snoRNAs have recently been identified in heart development and congenital heart diseases, as well as their dynamic regulation in hypertrophic and dilated cardiomyopathies, coronary heart disease (CHD), myocardial infarction (MI), cardiac fibrosis, and heart failure. Furthermore, reports of changes in vesicular snoRNA expression and altered levels of circulating snoRNAs in response to cardiac stress suggest that snoRNAs also function in cardiac signaling and intercellular communication. In this review, we summarize and discuss key findings and outline the clinical potential of snoRNAs considering current challenges and gaps in the field of cardiovascular diseases (CVDs).
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Affiliation(s)
- Alzbeta Chabronova
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK.
| | - Terri L Holmes
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Duc M Hoang
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Chris Denning
- Department of Stem Cell Biology, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Victoria James
- School of Veterinary Medicine and Science, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - James G W Smith
- Centre for Metabolic Health, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Mandy J Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
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2
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Liu WW, Zheng SQ, Li T, Fei YF, Wang C, Zhang S, Wang F, Jiang GM, Wang H. RNA modifications in cellular metabolism: implications for metabolism-targeted therapy and immunotherapy. Signal Transduct Target Ther 2024; 9:70. [PMID: 38531882 DOI: 10.1038/s41392-024-01777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/08/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024] Open
Abstract
Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of cells. Relevant studies have been constantly making inroads in our understanding of pathophysiology, and inspiring development of therapeutics. As a crucial component of epigenetics at post-transcription level, RNA modification significantly determines RNA fates, further affecting various biological processes and cellular phenotypes. To be noted, immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological contexts. In this review, we characterize the distribution features, modifying mechanisms and biological functions of 8 RNA modifications, including N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N4-acetylcytosine (ac4C), N7-methylguanosine (m7G), Pseudouridine (Ψ), adenosine-to-inosine (A-to-I) editing, which are relatively the most studied types. Then regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described, categorized as glucose, lipid, amino acid, and mitochondrial metabolism. And we highlight the regulation of RNA modifications on immunometabolism, further influencing immune responses. Above all, we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy, progression of RNA modification-targeted agents, and its potential in RNA-targeted therapeutics. Eventually, we give legitimate perspectives for future researches in this field from methodological requirements, mechanistic insights, to therapeutic applications.
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Affiliation(s)
- Wei-Wei Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Clinical Medicine, Shandong University, Jinan, China
| | - Si-Qing Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Tian Li
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Yun-Fei Fei
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Chen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Shuang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China
| | - Fei Wang
- Neurosurgical Department, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China.
| | - Hao Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Core Unit of National Clinical Research Center for Laboratory Medicine, Hefei, China.
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3
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Wang F, Cao H, Xia Q, Liu Z, Wang M, Gao F, Xu D, Deng B, Diao Y, Kapranov P. Lessons from discovery of true ADAR RNA editing sites in a human cell line. BMC Biol 2023; 21:160. [PMID: 37468903 PMCID: PMC10357658 DOI: 10.1186/s12915-023-01651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Conversion or editing of adenosine (A) into inosine (I) catalyzed by specialized cellular enzymes represents one of the most common post-transcriptional RNA modifications with emerging connection to disease. A-to-I conversions can happen at specific sites and lead to increase in proteome diversity and changes in RNA stability, splicing, and regulation. Such sites can be detected as adenine-to-guanine sequence changes by next-generation RNA sequencing which resulted in millions reported sites from multiple genome-wide surveys. Nonetheless, the lack of extensive independent validation in such endeavors, which is critical considering the relatively high error rate of next-generation sequencing, leads to lingering questions about the validity of the current compendiums of the editing sites and conclusions based on them. RESULTS Strikingly, we found that the current analytical methods suffer from very high false positive rates and that a significant fraction of sites in the public databases cannot be validated. In this work, we present potential solutions to these problems and provide a comprehensive and extensively validated list of A-to-I editing sites in a human cancer cell line. Our findings demonstrate that most of true A-to-I editing sites in a human cancer cell line are located in the non-coding transcripts, the so-called RNA 'dark matter'. On the other hand, many ADAR editing events occurring in exons of human protein-coding mRNAs, including those that can recode the transcriptome, represent false positives and need to be interpreted with caution. Nonetheless, yet undiscovered authentic ADAR sites that increase the diversity of human proteome exist and warrant further identification. CONCLUSIONS Accurate identification of human ADAR sites remains a challenging problem, particularly for the sites in exons of protein-coding mRNAs. As a result, genome-wide surveys of ADAR editome must still be accompanied by extensive Sanger validation efforts. However, given the vast number of unknown human ADAR sites, there is a need for further developments of the analytical techniques, potentially those that are based on deep learning solutions, in order to provide a quick and reliable identification of the editome in any sample.
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Affiliation(s)
- Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
| | - Qiu Xia
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ziheng Liu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ming Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Bolin Deng
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
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4
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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5
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Marty V, Butler JJ, Coutens B, Chargui O, Chagraoui A, Guiard BP, De Deurwaerdère P, Cavaillé J. Deleting Snord115 genes in mice remodels monoaminergic systems activity in the brain toward cortico-subcortical imbalances. Hum Mol Genet 2023; 32:244-261. [PMID: 35951020 DOI: 10.1093/hmg/ddac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/25/2022] [Accepted: 06/09/2022] [Indexed: 01/18/2023] Open
Abstract
The neuronal-specific SNORD115 has gathered interest because its deficiency may contribute to the pathophysiology of Prader-Willi syndrome (PWS), possibly by altering post-transcriptional regulation of the gene encoding the serotonin (HTR2C) receptor. Yet, Snord115-KO mice do not resume the main symptoms of PWS, and only subtle-altered A-to-I RNA editing of Htr2c mRNAs was uncovered. Because HTR2C signaling fine-tunes the activity of monoaminergic neurons, we addressed the hypothesis that lack of Snord115 alters monoaminergic systems. We first showed that Snord115 was expressed in both monoaminergic and non-monoaminergic cells of the ventral tegmental area (VTA) and the dorsal raphe nucleus (DRN) harboring cell bodies of dopaminergic and serotonergic neurons, respectively. Measuring the tissue level of monoamines and metabolites, we found very few differences except that the content of homovanillic acid-a metabolite of dopamine-was decreased in the orbitofrontal and prefrontal cortex of Snord115-KO mice. The latter effects were, however, associated with a few changes in monoamine tissue content connectivity across the 12 sampled brain regions. Using in vivo single-cell extracellular recordings, we reported that the firing rate of VTA dopaminergic neurons and DRN serotonergic neurons was significantly increased in Snord115-KO mice. These neural circuit dysfunctions were not, however, associated with apparent defects in binge eating, conditioned place preference to cocaine, cocaine-induced hyperlocomotion or compulsive behavior. Altogether, our multiscale study shows that the absence of Snord115 impacts central monoaminergic circuits to an extent that does not elicit gross behavioral abnormalities.
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Affiliation(s)
- Virginie Marty
- Molecular, Cellular and Developmental Biology (MCD) unit, Center of Integrative Biology (CBI), CNRS - University of Toulouse; CNRS, UPS, 31 062 Toulouse, France
| | - Jasmine J Butler
- Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (INCIA), CNRS-UMR 5287, 146 rue Léo Saignat, B.P.281, F-33000 Bordeaux Cedex, France
| | - Basile Coutens
- Research Center on Animal Cognition (CRCA), Center of Integrative Biology (CBI), CNRS - University of Toulouse; CNRS, UPS, 31 062 Toulouse, France
| | - Oumaima Chargui
- Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (INCIA), CNRS-UMR 5287, 146 rue Léo Saignat, B.P.281, F-33000 Bordeaux Cedex, France
| | - Abdeslam Chagraoui
- Différenciation et Communication Neuroendocrine, Endocrine et Germinale (NorDic), INSERM U1239, IRIB, CHU Rouen, 76 000 Rouen, France.,Department of Medical Biochemistry, Rouen University Hospital, 76 000 Rouen, France
| | - Bruno P Guiard
- Research Center on Animal Cognition (CRCA), Center of Integrative Biology (CBI), CNRS - University of Toulouse; CNRS, UPS, 31 062 Toulouse, France
| | - Philippe De Deurwaerdère
- Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (INCIA), CNRS-UMR 5287, 146 rue Léo Saignat, B.P.281, F-33000 Bordeaux Cedex, France
| | - Jérôme Cavaillé
- Molecular, Cellular and Developmental Biology (MCD) unit, Center of Integrative Biology (CBI), CNRS - University of Toulouse; CNRS, UPS, 31 062 Toulouse, France
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6
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Nossent AY. The epitranscriptome: RNA modifications in vascular remodelling. Atherosclerosis 2022:S0021-9150(22)01500-3. [DOI: 10.1016/j.atherosclerosis.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/13/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]
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7
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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8
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Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry 2022; 27:3633-3646. [PMID: 35474104 PMCID: PMC9596619 DOI: 10.1038/s41380-022-01570-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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9
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Reference Genes across Nine Brain Areas of Wild Type and Prader-Willi Syndrome Mice: Assessing Differences in Igfbp7, Pcsk1, Nhlh2 and Nlgn3 Expression. Int J Mol Sci 2022; 23:ijms23158729. [PMID: 35955861 PMCID: PMC9369261 DOI: 10.3390/ijms23158729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Prader−Willi syndrome (PWS) is a complex neurodevelopmental disorder caused by the deletion or inactivation of paternally expressed imprinted genes at the chromosomal region 15q11−q13. The PWS-critical region (PWScr) harbors tandemly repeated non-protein coding IPW-A exons hosting the intronic SNORD116 snoRNA gene array that is predominantly expressed in brain. Paternal deletion of PWScr is associated with key PWS symptoms in humans and growth retardation in mice (PWScr model). Dysregulation of the hypothalamic−pituitary axis (HPA) is thought to be causally involved in the PWS phenotype. Here we performed a comprehensive reverse transcription quantitative PCR (RT-qPCR) analysis across nine different brain regions of wild-type (WT) and PWScr mice to identify stably expressed reference genes. Four methods (Delta Ct, BestKeeper, Normfinder and Genorm) were applied to rank 11 selected reference gene candidates according to their expression stability. The resulting panel consists of the top three most stably expressed genes suitable for gene-expression profiling and comparative transcriptome analysis of WT and/or PWScr mouse brain regions. Using these reference genes, we revealed significant differences in the expression patterns of Igfbp7, Nlgn3 and three HPA associated genes: Pcsk1, Pcsk2 and Nhlh2 across investigated brain regions of wild-type and PWScr mice. Our results raise a reasonable doubt on the involvement of the Snord116 in posttranscriptional regulation of Nlgn3 and Nhlh2 genes. We provide a valuable tool for expression analysis of specific genes across different areas of the mouse brain and for comparative investigation of PWScr mouse models to discover and verify different regulatory pathways affecting this complex disorder.
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10
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Woudenberg T, Kruyt ND, Quax PHA, Nossent AY. Change of Heart: the Epitranscriptome of Small Non-coding RNAs in Heart Failure. Curr Heart Fail Rep 2022; 19:255-266. [PMID: 35876969 PMCID: PMC9534797 DOI: 10.1007/s11897-022-00561-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Purpose of Review Small non-coding RNAs regulate gene expression and are highly implicated in heart failure. Recently, an additional level of post-transcriptional regulation has been identified, referred to as the epitranscriptome, which encompasses the body of post-transcriptional modifications that are placed on RNA molecules. In this review, we summarize the current knowledge on the small non-coding RNA epitranscriptome in heart failure. Recent Findings With the rise of new methods to study RNA modifications, epitranscriptome research has begun to take flight. Over the past 3 years, the number of publications on the epitranscriptome in heart failure has significantly increased, and we expect many more highly relevant publications to come out over the next few years. Summary Currently, at least six modifications on small non-coding RNAs have been investigated in heart failure-relevant studies, namely N6-adenosine, N5-cytosine and N7-guanosine methylation, 2’-O-ribose-methylation, adenosine-to-inosine editing, and isomiRs. Their potential role in heart failure is discussed.
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Affiliation(s)
- Tamar Woudenberg
- Department of Surgery, Leiden University Medical Center, D6-P, PO Box 9600, 2300 RC, Leiden, the Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Nyika D Kruyt
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, D6-P, PO Box 9600, 2300 RC, Leiden, the Netherlands.,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, D6-P, PO Box 9600, 2300 RC, Leiden, the Netherlands. .,Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands.
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11
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Deschamps-Francoeur G, Couture S, Abou-Elela S, Scott MS. The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. Nucleic Acids Res 2022; 50:6067-6083. [PMID: 35657102 PMCID: PMC9226514 DOI: 10.1093/nar/gkac475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/13/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2'-O-ribose methylation. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA-RNA interaction datasets detect many snoRNAs binding messenger RNA, but are limited by specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. SnoGloBe is also an excellent tool for discovering viral RNA targets, as shown by its capacity to identify snoRNAs targeting the heavily methylated SARS-CoV-2 RNA. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.
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Affiliation(s)
- Gabrielle Deschamps-Francoeur
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou-Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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12
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Nir R, Hoernes TP, Muramatsu H, Faserl K, Karikó K, Erlacher MD, Sas-Chen A, Schwartz S. A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA. Nucleic Acids Res 2022; 50:4900-4916. [PMID: 35536311 PMCID: PMC9122591 DOI: 10.1093/nar/gkac347] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 04/18/2022] [Accepted: 04/24/2022] [Indexed: 12/25/2022] Open
Abstract
RNA can be extensively modified post-transcriptionally with >170 covalent modifications, expanding its functional and structural repertoire. Pseudouridine (Ψ), the most abundant modified nucleoside in rRNA and tRNA, has recently been found within mRNA molecules. It remains unclear whether pseudouridylation of mRNA can be snoRNA-guided, bearing important implications for understanding the physiological target spectrum of snoRNAs and for their potential therapeutic exploitation in genetic diseases. Here, using a massively parallel reporter based strategy we simultaneously interrogate Ψ levels across hundreds of synthetic constructs with predesigned complementarity against endogenous snoRNAs. Our results demonstrate that snoRNA-mediated pseudouridylation can occur on mRNA targets. However, this is typically achieved at relatively low efficiencies, and is constrained by mRNA localization, snoRNA expression levels and the length of the snoRNA:mRNA complementarity stretches. We exploited these insights for the design of snoRNAs targeting pseudouridylation at premature termination codons, which was previously shown to suppress translational termination. However, in this and follow-up experiments in human cells we observe no evidence for significant levels of readthrough of pseudouridylated stop codons. Our study enhances our understanding of the scope, 'design rules', constraints and consequences of snoRNA-mediated pseudouridylation.
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Affiliation(s)
- Ronit Nir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Thomas Philipp Hoernes
- Institute of Genomics and RNomics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hiromi Muramatsu
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus Faserl
- Institute of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Katalin Karikó
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA.,BioNTech RNA Pharmaceuticals, Mainz, Germany
| | | | - Aldema Sas-Chen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.,The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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14
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Tjahjono E, Revtovich AV, Kirienko NV. Box C/D small nucleolar ribonucleoproteins regulate mitochondrial surveillance and innate immunity. PLoS Genet 2022; 18:e1010103. [PMID: 35275914 PMCID: PMC8942280 DOI: 10.1371/journal.pgen.1010103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/23/2022] [Accepted: 02/14/2022] [Indexed: 12/27/2022] Open
Abstract
Monitoring mitochondrial function is crucial for organismal survival. This task is performed by mitochondrial surveillance or quality control pathways, which are activated by signals originating from mitochondria and relayed to the nucleus (retrograde response) to start transcription of protective genes. In Caenorhabditis elegans, several systems are known to play this role, including the UPRmt, MAPKmt, and the ESRE pathways. These pathways are highly conserved and their loss compromises survival following mitochondrial stress. In this study, we found a novel interaction between the box C/D snoRNA core proteins (snoRNPs) and mitochondrial surveillance and innate immune pathways. We showed that box C/D, but not box H/ACA, snoRNPs are required for the full function of UPRmt and ESRE upon stress. The loss of box C/D snoRNPs reduced mitochondrial mass, mitochondrial membrane potential, and oxygen consumption rate, indicating overall degradation of mitochondrial function. Concomitantly, the loss of C/D snoRNPs increased immune response and reduced host intestinal colonization by infectious bacteria, improving host resistance to pathogenesis. Our data may indicate a model wherein box C/D snoRNP machinery regulates a "switch" of the cell's activity between mitochondrial surveillance and innate immune activation. Understanding this mechanism is likely to be important for understanding multifactorial processes, including responses to infection and aging.
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Affiliation(s)
- Elissa Tjahjono
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Alexey V. Revtovich
- Department of BioSciences, Rice University, Houston, Texas, United States of America
| | - Natalia V. Kirienko
- Department of BioSciences, Rice University, Houston, Texas, United States of America
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15
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Baldini L, Robert A, Charpentier B, Labialle S. Phylogenetic and molecular analyses identify SNORD116 targets involved in the Prader Willi syndrome. Mol Biol Evol 2021; 39:6454102. [PMID: 34893870 PMCID: PMC8789076 DOI: 10.1093/molbev/msab348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The eutherian-specific SNORD116 family of repeated box C/D snoRNA genes is suspected to play a major role in the Prader–Willi syndrome (PWS), yet its molecular function remains poorly understood. Here, we combined phylogenetic and molecular analyses to identify candidate RNA targets. Based on the analysis of several eutherian orthologs, we found evidence of extensive birth-and-death and conversion events during SNORD116 gene history. However, the consequences for phylogenetic conservation were heterogeneous along the gene sequence. The standard snoRNA elements necessary for RNA stability and association with dedicated core proteins were the most conserved, in agreement with the hypothesis that SNORD116 generate genuine snoRNAs. In addition, one of the two antisense elements typically involved in RNA target recognition was largely dominated by a unique sequence present in at least one subset of gene paralogs in most species, likely the result of a selective effect. In agreement with a functional role, this ASE exhibited a hybridization capacity with putative mRNA targets that was strongly conserved in eutherians. Moreover, transient downregulation experiments in human cells showed that Snord116 controls the expression and splicing levels of these mRNAs. The functions of two of them, diacylglycerol kinase kappa and Neuroligin 3, extend the description of the molecular bases of PWS and reveal unexpected molecular links with the Fragile X syndrome and autism spectrum disorders.
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Affiliation(s)
- Laeya Baldini
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Anne Robert
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
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16
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SnoRNA in Cancer Progression, Metastasis and Immunotherapy Response. BIOLOGY 2021; 10:biology10080809. [PMID: 34440039 PMCID: PMC8389557 DOI: 10.3390/biology10080809] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary A much larger number of small nucleolar RNA (snoRNA) have been found encoded within our genomes than we ever expected to see. The activities of the snoRNAs were thought restricted to the nucleolus, where they were first discovered. Now, however, their significant number suggests that their functions are more diverse. Studies in cancers have shown snoRNA levels to associate with different stages of disease progression, including with metastasis. In addition, relationships between snoRNA levels and response to immunotherapies, have been reported. Emerging technologies now allow snoRNA to be targeted directly in cancers, and the therapeutic value of this is being explored. Abstract Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new snoRNA genes have been identified, and multiple studies have shown their functions to be diverse. The consensus now is that many snoRNA are dysregulated in cancers, are differentially expressed between cancer types, stages and metastases, and they can actively modify disease progression. In addition, the regulation of the snoRNA class is dominated by the cancer-supporting mTOR signalling pathway, and they may have particular significance to immune cell function and anti-tumour immune responses. Given the recent advent of therapeutics that can target RNA molecules, snoRNA have robust potential as drug targets, either solely or in the context of immunotherapies.
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17
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Wei P, Wang H, Li Y, Guo R. Nucleolar small molecule RNA SNORA75 promotes endometrial receptivity by regulating the function of miR-146a-3p and ZNF23. Aging (Albany NY) 2021; 13:14924-14939. [PMID: 34030136 PMCID: PMC8221328 DOI: 10.18632/aging.203007] [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: 11/09/2020] [Accepted: 02/09/2021] [Indexed: 11/28/2022]
Abstract
Endometrial receptivity enables the embryo to attach, invade and develop, forming a new individual and species continuity. Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs comprising two classes: C/D box snoRNAs and H/ACA box snoRNAs. Aberrant expression of SNORNAs has been reported in tumorigenesis. However, the role of SNORNAs in maintaining endometrial receptivity has not been reported. First, we detected SNORNA expression in endometrial tissues during proliferative and secretory endometrial periods using RNA sequencing. SNORA75 expression was higher in the secretory endometrium, and its overexpression significantly promoted the proliferation, migration and invasion of endometrial cells. The results of analysis with bioinformatics software and RNA pulldown experiments showed that miR-146a-3p interacted with SNORA75. Western blotting showed that miR-146a-3p regulated the expression of ZNF23, whose overexpression significantly promoted the proliferation, migration and invasion of endometrial cells. SNORA75 modulates endometrial receptivity through the miR-146a/ZNF23 signaling pathway.
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Affiliation(s)
- Peng Wei
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Haitao Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Yuebai Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou 450052, People's Republic of China
| | - Ruixia Guo
- Department of Gynaecology and Obstetrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
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18
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Baldini L, Charpentier B, Labialle S. Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs. Noncoding RNA 2021; 7:ncrna7020030. [PMID: 34066559 PMCID: PMC8162545 DOI: 10.3390/ncrna7020030] [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: 04/12/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.
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Affiliation(s)
| | - Bruno Charpentier
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
| | - Stéphane Labialle
- Correspondence: (B.C.); (S.L.); Tel.: +33-3-72-74-66-27 (B.C.); +33-3-72-74-66-51 (S.L.)
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19
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Wu Y, Zhan S, Xu Y, Gao X. RNA modifications in cardiovascular diseases, the potential therapeutic targets. Life Sci 2021; 278:119565. [PMID: 33965380 DOI: 10.1016/j.lfs.2021.119565] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 02/08/2023]
Abstract
More than one hundred RNA modifications decorate the chemical and topological properties of these ribose nucleotides, thereby executing their biological functions through post-transcriptional regulation. In cardiovascular diseases, a wide range of RNA modifications including m6A (N6-adenosine methylation), m5C (5-methylcytidin), Nm (2'-O-ribose-methylation), Ψ (pseudouridine), m7G (N7-methylguanosine), and m1A (N1-adenosine methylation) have been found in tRNA, rRNA, mRNA and other noncoding RNA, which can function as a novel mechanism in metabolic syndrome, heart failure, coronary heart disease, and hypertension. In this review, we will summarize the current understanding of the regulatory roles and significance of several types of RNA modifications in CVDs (cardiovascular diseases) and the interplay between RNA modifications and noncoding RNA, epigenetics. Finally, we will focus on the potential therapeutic strategies by using RNA modifications.
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Affiliation(s)
- Yirong Wu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China
| | - Siyao Zhan
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China
| | - Yizhou Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China.
| | - Xiangwei Gao
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
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20
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Kummerfeld DM, Raabe CA, Brosius J, Mo D, Skryabin BV, Rozhdestvensky TS. A Comprehensive Review of Genetically Engineered Mouse Models for Prader-Willi Syndrome Research. Int J Mol Sci 2021; 22:3613. [PMID: 33807162 PMCID: PMC8037846 DOI: 10.3390/ijms22073613] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 02/05/2023] Open
Abstract
Prader-Willi syndrome (PWS) is a neurogenetic multifactorial disorder caused by the deletion or inactivation of paternally imprinted genes on human chromosome 15q11-q13. The affected homologous locus is on mouse chromosome 7C. The positional conservation and organization of genes including the imprinting pattern between mice and men implies similar physiological functions of this locus. Therefore, considerable efforts to recreate the pathogenesis of PWS have been accomplished in mouse models. We provide a summary of different mouse models that were generated for the analysis of PWS and discuss their impact on our current understanding of corresponding genes, their putative functions and the pathogenesis of PWS. Murine models of PWS unveiled the contribution of each affected gene to this multi-facetted disease, and also enabled the establishment of the minimal critical genomic region (PWScr) responsible for core symptoms, highlighting the importance of non-protein coding genes in the PWS locus. Although the underlying disease-causing mechanisms of PWS remain widely unresolved and existing mouse models do not fully capture the entire spectrum of the human PWS disorder, continuous improvements of genetically engineered mouse models have proven to be very powerful and valuable tools in PWS research.
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Affiliation(s)
- Delf-Magnus Kummerfeld
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Carsten A. Raabe
- Research Group Regulatory Mechanisms of Inflammation, Institute of Medical Biochemistry (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Juergen Brosius
- Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dingding Mo
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China;
| | - Boris V. Skryabin
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
| | - Timofey S. Rozhdestvensky
- Medical Faculty, Core Facility Transgenic Animal and Genetic Engineering Models (TRAM), University of Muenster, Von-Esmarch-Str. 56, D-48149 Muenster, Germany;
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21
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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22
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Abstract
The brain is one of the organs that are preferentially targeted by adenosine-to-inosine (A-to-I) RNA editing, a posttranscriptional modification. This chemical modification affects neuronal development and functions at multiple levels, leading to normal brain homeostasis by increasing the complexity of the transcriptome. This includes modulation of the properties of ion channel and neurotransmitter receptors by recoding, redirection of miRNA targets by changing sequence complementarity, and suppression of immune response by altering RNA structure. Therefore, from another perspective, it appears that the brain is highly vulnerable to dysregulation of A-to-I RNA editing. Here, we focus on how aberrant A-to-I RNA editing is involved in neurological and neurodegenerative diseases of humans including epilepsy, amyotrophic lateral sclerosis, psychiatric disorders, developmental disorders, brain tumors, and encephalopathy caused by autoimmunity. In addition, we provide information regarding animal models to better understand the mechanisms behind disease phenotype.
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Affiliation(s)
- Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.
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23
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Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action. Biochem Soc Trans 2021; 48:645-656. [PMID: 32267490 PMCID: PMC7200641 DOI: 10.1042/bst20191046] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
Identified five decades ago amongst the most abundant cellular RNAs, small nucleolar RNAs (snoRNAs) were initially described as serving as guides for the methylation and pseudouridylation of ribosomal RNA through direct base pairing. In recent years, however, increasingly powerful high-throughput genomic approaches and strategies have led to the discovery of many new members of the family and surprising diversity in snoRNA functionality and mechanisms of action. SnoRNAs are now known to target RNAs of many biotypes for a wider range of modifications, interact with diverse binding partners, compete with other binders for functional interactions, recruit diverse players to targets and affect protein function and accessibility through direct interaction. This mini-review presents the continuing characterization of the snoRNome through the identification of new snoRNA members and the discovery of their mechanisms of action, revealing a highly versatile noncoding family playing central regulatory roles and connecting the main cellular processes.
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24
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Hebras J, Marty V, Personnaz J, Mercier P, Krogh N, Nielsen H, Aguirrebengoa M, Seitz H, Pradere JP, Guiard BP, Cavaille J. Reassessment of the involvement of Snord115 in the serotonin 2c receptor pathway in a genetically relevant mouse model. eLife 2020; 9:60862. [PMID: 33016258 PMCID: PMC7673782 DOI: 10.7554/elife.60862] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
SNORD115 has been proposed to promote the activity of serotonin (HTR2C) receptor via its ability to base pair with its pre-mRNA and regulate alternative RNA splicing and/or A-to-I RNA editing. Because SNORD115 genes are deleted in most patients with the Prader-Willi syndrome (PWS), diminished HTR2C receptor activity could contribute to the impaired emotional response and/or compulsive overeating characteristic of this disease. In order to test this appealing but never demonstrated hypothesis in vivo, we created a CRISPR/Cas9-mediated Snord115 knockout mouse. Surprisingly, we uncovered only modest region-specific alterations in Htr2c RNA editing profiles, while Htr2c alternative RNA splicing was unchanged. These subtle changes, whose functional relevance remains uncertain, were not accompanied by any discernible defects in anxio-depressive-like phenotypes. Energy balance and eating behavior were also normal, even after exposure to high-fat diet. Our study raises questions concerning the physiological role of SNORD115, notably its involvement in behavioural disturbance associated with PWS.
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Affiliation(s)
- Jade Hebras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Virginie Marty
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Jean Personnaz
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut National de la Santé et de la Recherche Médicale (INSERM), France Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université de Toulouse Université Paul Sabatier, Toulouse, France
| | - Pascale Mercier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Centre National de la Recherche Scientifique UMR5089, Toulouse, France
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marion Aguirrebengoa
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, Toulouse, France
| | - Hervé Seitz
- IGH (CNRS and University of Montpellier), Montpellier, France
| | - Jean-Phillipe Pradere
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut National de la Santé et de la Recherche Médicale (INSERM), France Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université de Toulouse Université Paul Sabatier, Toulouse, France
| | - Bruno P Guiard
- Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Jérôme Cavaille
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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25
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Barbon A, Magri C. RNA Editing and Modifications in Mood Disorders. Genes (Basel) 2020; 11:genes11080872. [PMID: 32752036 PMCID: PMC7464464 DOI: 10.3390/genes11080872] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Major depressive disorder (MDD) is a major health problem with significant limitations in functioning and well-being. The World Health Organization (WHO) evaluates MDD as one of the most disabling disorders in the world and with very high social cost. Great attention has been given to the study of the molecular mechanism underpinning MDD at the genetic, epigenetic and proteomic level. However, the importance of RNA modifications has attracted little attention until now in this field. RNA molecules are extensively and dynamically altered by a variety of mechanisms. Similar to "epigenomic" changes, which modify DNA structure or histones, RNA alterations are now termed "epitranscriptomic" changes and have been predicted to have profound consequences for gene expression and cellular functionality. Two of these modifications, adenosine to inosine (A-to-I) RNA editing and m6A methylations, have fascinated researchers over the last years, showing a new level of complexity in gene expression. In this review, we will summary the studies that focus on the role of RNA editing and m6A methylation in MDD, trying to underline their potential breakthroughs and pitfalls.
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26
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Håkansson KEJ, Goossens EAC, Trompet S, van Ingen E, de Vries MR, van der Kwast RVCT, Ripa RS, Kastrup J, Hohensinner PJ, Kaun C, Wojta J, Böhringer S, Le Cessie S, Jukema JW, Quax PHA, Nossent AY. Genetic associations and regulation of expression indicate an independent role for 14q32 snoRNAs in human cardiovascular disease. Cardiovasc Res 2020; 115:1519-1532. [PMID: 30544252 DOI: 10.1093/cvr/cvy309] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/30/2018] [Accepted: 12/11/2018] [Indexed: 01/12/2023] Open
Abstract
AIMS We have shown that 14q32 microRNAs are highly involved in vascular remodelling and cardiovascular disease. However, the 14q32 locus also encodes 41 'orphan' small nucleolar RNAs (snoRNAs). We aimed to gather evidence for an independent role for 14q32 snoRNAs in human cardiovascular disease. METHODS AND RESULTS We performed a lookup of the 14q32 region within the dataset of a genome wide association scan in 5244 participants of the PROspective Study of Pravastatin in the Elderly at Risk (PROSPER). Single nucleotide polymorphisms (SNPs) in the snoRNA-cluster were significantly associated with heart failure. These snoRNA-cluster SNPs were not linked to SNPs in the microRNA-cluster or in MEG3, indicating that snoRNAs modify the risk of cardiovascular disease independently. We looked at expression of 14q32 snoRNAs throughout the human cardio-vasculature. Expression profiles of the 14q32 snoRNAs appeared highly vessel specific. When we compared expression levels of 14q32 snoRNAs in human vena saphena magna (VSM) with those in failed VSM-coronary bypasses, we found that 14q32 snoRNAs were up-regulated. SNORD113.2, which showed a 17-fold up-regulation in failed bypasses, was also up-regulated two-fold in plasma samples drawn from patients with ST-elevation myocardial infarction directly after hospitalization compared with 30 days after start of treatment. However, fitting with the genomic associations, 14q32 snoRNA expression was highest in failing human hearts. In vitro studies show that the 14q32 snoRNAs bind predominantly to methyl-transferase Fibrillarin, indicating that they act through canonical mechanisms, but on non-canonical RNA targets. The canonical C/D-box snoRNA seed sequences were highly conserved between humans and mice. CONCLUSION 14q32 snoRNAs appear to play an independent role in cardiovascular pathology. 14q32 snoRNAs are specifically regulated throughout the human vasculature and their expression is up-regulated during cardiovascular disease. Our data demonstrate that snoRNAs merit increased effort and attention in future basic and clinical cardiovascular research.
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Affiliation(s)
- Kjell E J Håkansson
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Reginald V C T van der Kwast
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Rasmus S Ripa
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | - Jens Kastrup
- Department of Cardiology, Rigshospitalet University of Copenhagen, Copenhagen, Denmark
| | | | - Christoph Kaun
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Johann Wojta
- Department of Internal Medicine II, Medical University of Vienna, Vienna, Austria
| | - Stefan Böhringer
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia Le Cessie
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, K6-R, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Ludwig Boltzmann Cluster for Cardiovascular Research, Vienna, Austria
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27
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Liu S, Li B, Liang Q, Liu A, Qu L, Yang J. Classification and function of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1601. [PMID: 32488992 DOI: 10.1002/wrna.1601] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Almost all RNAs need to interact with proteins to fully exert their functions, and proteins also bind to RNAs to act as regulators. It has now become clear that RNA-protein interactions play important roles in many biological processes among organisms. Despite the great progress that has been made in the field, there is still no precise classification system for RNA-protein interactions, which makes it challenging to further decipher the functions and mechanisms of these interactions. In this review, we propose four different categories of RNA-protein interactions according to their basic characteristics: RNA motif-dependent RNA-protein interactions, RNA structure-dependent RNA-protein interactions, RNA modification-dependent RNA-protein interactions, and RNA guide-based RNA-protein interactions. Moreover, the integration of different types of RNA-protein interactions and the regulatory factors implicated in these interactions are discussed. Furthermore, we emphasize the functional diversity of these four types of interactions in biological processes and disease development and assess emerging trends in this exciting research field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiaoxia Liang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anrui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
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28
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Najafi H, Naseri M, Zahiri J, Totonchi M, Sadeghizadeh M. Identification of the Molecular Events Involved in the Development of Prefrontal Cortex Through the Analysis of RNA-Seq Data From BrainSpan. ASN Neuro 2020; 11:1759091419854627. [PMID: 31213068 PMCID: PMC6582306 DOI: 10.1177/1759091419854627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human brain development is a complex process that follows sequential
orchestration of gene expression, begins at conceptual stages, and continues
into adulthood. Altered profile of gene expression drives many cellular and
molecular events required for development. Here, the molecular events during
development of human prefrontal cortex (PFC) (as an important executive part of
the brain) were investigated. First, the RNA-sequencing data of BrainSpan were
used to obtain differentially expressed genes between each two developmental
stages and then, the relevant biological processes and signaling pathways were
deduced by gene set enrichment analysis. In addition, the changes in
transcriptome landscape of PFC during development were analyzed and the
potential biological processes underlie the changes were found. Comparison of
the four regions of PFC based on their biological processes showed that
additional to common biological processes and signaling pathways, each PFC
region had its own molecular characteristics, conforming their previously
reported functional roles in brain physiology. The most heterogeneity in
transcriptome between the PFC regions was observed at the time of birth which
was concurrent with the activity of some region-specific regulatory systems such
as DNA methylation, transcription regulation, RNA splicing, and presence of
different transcription factors and microRNAs. In conclusion, this study used
bioinformatics to present a comprehensive molecular overview on PFC development
which may explain the etiology of brain neuropsychiatric disorders originated
from malfunctioning of PFC.
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Affiliation(s)
- Hadi Najafi
- 1 Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohadeseh Naseri
- 2 Department of Biophysics, Bioinformatics and Computational Omics Lab (BioCOOL), Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- 2 Department of Biophysics, Bioinformatics and Computational Omics Lab (BioCOOL), Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Totonchi
- 3 Department of Genetics and Stem Cell, Royan Institute, Tehran, Iran
| | - Majid Sadeghizadeh
- 1 Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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29
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Davies JR, Wilkinson LS, Isles AR, Humby T. Prader-Willi syndrome imprinting centre deletion mice have impaired baseline and 5-HT2CR-mediated response inhibition. Hum Mol Genet 2020; 28:3013-3023. [PMID: 31087031 PMCID: PMC6737253 DOI: 10.1093/hmg/ddz100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022] Open
Abstract
Prader–Willi syndrome (PWS) is a neurodevelopmental disorder caused by deletion or inactivation of paternally expressed imprinted genes on human chromosome 15q11–q13. In addition to endocrine and developmental issues, PWS presents with behavioural problems including stereotyped behaviour, impulsiveness and cognitive deficits. The PWS genetic interval contains several brain-expressed small nucleolar (sno) RNA species that are subject to genomic imprinting, including snord115 that negatively regulates post-transcriptional modification of the serotonin 2C receptor (5-HT2CR) pre-mRNA potentially leading to a reduction in 5-HT2CR function. Using the imprinting centre deletion mouse model for PWS (PWSICdel) we have previously shown impairments in a number of behaviours, some of which are abnormally sensitive to 5-HT2CR-selective drugs. In the stop-signal reaction time task test of impulsivity, PWSICdel mice showed increased impulsivity relative to wild-type (WT) littermates. Challenge with the selective 5-HT2CR agonist WAY163909 reduced impulsivity in PWSICdel mice but had no effect on WT behaviour. This behavioural dissociation in was also reflected in differential patterns of immunoreactivity of the immediate early gene c-Fos, with a blunted response to the drug in the orbitofrontal cortex of PWSICdel mice, but no difference in c-Fos activation in the nucleus accumbens. These findings suggest specific facets of response inhibition are impaired in PWSICdel mice and that abnormal 5-HT2CR function may mediate this dissociation. These data have implications for our understanding of the aetiology of PWS-related behavioural traits and translational relevance for individuals with PWS who may seek to control appetite with the new obesity treatment 5-HT2CR agonist lorcaserin.
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Affiliation(s)
- Jennifer R Davies
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Schools of Medicine
| | - Lawrence S Wilkinson
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Schools of Medicine.,Psychology, Cardiff University, Cardiff, UK
| | - Anthony R Isles
- Behavioural Genetics Group, MRC Centre for Neuropsychiatric Genetics and Genomics, Neuroscience and Mental Health Research Institute, Schools of Medicine
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30
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van der Kwast RV, Quax PH, Nossent AY. An Emerging Role for isomiRs and the microRNA Epitranscriptome in Neovascularization. Cells 2019; 9:cells9010061. [PMID: 31881725 PMCID: PMC7017316 DOI: 10.3390/cells9010061] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/19/2019] [Accepted: 12/21/2019] [Indexed: 02/06/2023] Open
Abstract
Therapeutic neovascularization can facilitate blood flow recovery in patients with ischemic cardiovascular disease, the leading cause of death worldwide. Neovascularization encompasses both angiogenesis, the sprouting of new capillaries from existing vessels, and arteriogenesis, the maturation of preexisting collateral arterioles into fully functional arteries. Both angiogenesis and arteriogenesis are highly multifactorial processes that require a multifactorial regulator to be stimulated simultaneously. MicroRNAs can regulate both angiogenesis and arteriogenesis due to their ability to modulate expression of many genes simultaneously. Recent studies have revealed that many microRNAs have variants with altered terminal sequences, known as isomiRs. Additionally, endogenous microRNAs have been identified that carry biochemically modified nucleotides, revealing a dynamic microRNA epitranscriptome. Both types of microRNA alterations were shown to be dynamically regulated in response to ischemia and are able to influence neovascularization by affecting the microRNA’s biogenesis, or even its silencing activity. Therefore, these novel regulatory layers influence microRNA functioning and could provide new opportunities to stimulate neovascularization. In this review we will highlight the formation and function of isomiRs and various forms of microRNA modifications, and discuss recent findings that demonstrate that both isomiRs and microRNA modifications directly affect neovascularization and vascular remodeling.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Paul H.A. Quax
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - A. Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Laboratory Medicine and Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
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31
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Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression. Sci Rep 2019; 9:18397. [PMID: 31804585 PMCID: PMC6895083 DOI: 10.1038/s41598-019-54924-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/18/2019] [Indexed: 01/15/2023] Open
Abstract
In recent years, a number of small RNA molecules derived from snoRNAs have been observed. Findings concerning the functions of snoRNA-derived small RNAs (sdRNAs) in cells are limited primarily to their involvement in microRNA pathways. However, similar molecules have been observed in Saccharomyces cerevisiae, which is an organism lacking miRNA machinery. Here we examined the subcellular localization of sdRNAs in yeast. Our findings reveal that both sdRNAs and their precursors, snoRNAs, are present in the cytoplasm at levels dependent upon stress conditions. Moreover, both sdRNAs and snoRNAs may interact with translating ribosomes in a stress-dependent manner. Likely consequential to their ribosome association and protein synthesis suppression features, yeast sdRNAs may exert inhibitory activity on translation. Observed levels of sdRNAs and snoRNAs in the cytoplasm and their apparent presence in the ribosomal fractions suggest independent regulation of these molecules by yet unknown factors.
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32
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Jain M, Jantsch MF, Licht K. The Editor's I on Disease Development. Trends Genet 2019; 35:903-913. [PMID: 31648814 DOI: 10.1016/j.tig.2019.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventing autoimmune disorders. Interestingly, A-to-I editing can be used not only to correct genomic mutations at the RNA level but also to modulate tumor antigenicity with large therapeutic potential. We highlight recent developments in the field, focusing on cancer and other human diseases.
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Affiliation(s)
- Mamta Jain
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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33
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Filippova JA, Matveeva AM, Zhuravlev ES, Balakhonova EA, Prokhorova DV, Malanin SJ, Shah Mahmud R, Grigoryeva TV, Anufrieva KS, Semenov DV, Vlassov VV, Stepanov GA. Are Small Nucleolar RNAs "CRISPRable"? A Report on Box C/D Small Nucleolar RNA Editing in Human Cells. Front Pharmacol 2019; 10:1246. [PMID: 31780925 PMCID: PMC6856654 DOI: 10.3389/fphar.2019.01246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/27/2019] [Indexed: 01/20/2023] Open
Abstract
CRISPR technologies are nowadays widely used for targeted knockout of numerous protein-coding genes and for the study of various processes and metabolic pathways in human cells. Most attention in the genome editing field is now focused on the cleavage of protein-coding genes or genes encoding long non-coding RNAs (lncRNAs), while the studies on targeted knockout of intron-encoded regulatory RNAs are sparse. Small nucleolar RNAs (snoRNAs) present a class of non-coding RNAs encoded within the introns of various host genes and involved in post-transcriptional maturation of ribosomal RNAs (rRNAs) in eukaryotic cells. Box C/D snoRNAs direct 2'-O-methylation of rRNA nucleotides. These short RNAs have specific elements in their structure, namely, boxes C and D, and a target-recognizing region. Here, we present the study devoted to CRISPR/Cas9-mediated editing of box C/D snoRNA genes in Gas5. We obtained monoclonal cell lines carrying mutations in snoRNA genes and analyzed the levels of the mutant box C/D snoRNA as well as the 2'-O-methylation status of the target rRNA nucleotide in the obtained cells. Mutations in SNORD75 in the obtained monoclonal cell line were shown to result in aberrant splicing of Gas5 with exclusion of exons 3 to 5, which was confirmed by RT-PCR and RNA-Seq. The obtained results suggest that SNORD75 contains an element for binding of some factors regulating maturation of Gas5 pre-lncRNA. We suggest that METTL3/METTL14 is among such factors, and m6A-methylation pathways are involved in regulation of Gas5 splicing. Our results shell light on the role of SNORDs in regulating splicing of the host gene.
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Affiliation(s)
- Julia A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anastasiya M Matveeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Evgenia A Balakhonova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Sergey J Malanin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Raihan Shah Mahmud
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Tatiana V Grigoryeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ksenia S Anufrieva
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Moscow, Russia.,Laboratory of Cell Biology, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry V Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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34
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Sperling R. Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194406. [PMID: 31323432 DOI: 10.1016/j.bbagrm.2019.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Splicing and alternative splicing (AS), which occur in the endogenous spliceosome, play major roles in regulating gene expression, and defects in them are involved in numerous human diseases including cancer. Although the mechanism of the splicing reaction is well understood, the regulation of AS remains to be elucidated. A group of essential regulatory factors in gene expression are small non-coding RNAs (sncRNA): e.g. microRNA, mainly known for their inhibitory role in translation in the cytoplasm; and small nucleolar RNA, known for their role in methylating non-coding RNA in the nucleolus. Here I highlight a new aspect of sncRNAs found within the endogenous spliceosome. Assembled in non-canonical complexes and through different base pairing than their canonical ones, spliceosomal sncRNAs can potentially target different RNAs. Examples of spliceosomal sncRNAs regulating AS, regulating gene expression, and acting in a quality control of AS are reviewed, suggesting novel functions for spliceosomal sncRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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35
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Liang J, Wen J, Huang Z, Chen XP, Zhang BX, Chu L. Small Nucleolar RNAs: Insight Into Their Function in Cancer. Front Oncol 2019; 9:587. [PMID: 31338327 PMCID: PMC6629867 DOI: 10.3389/fonc.2019.00587] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 06/17/2019] [Indexed: 02/04/2023] Open
Abstract
Small nucleolar RNAs (SnoRNAs) are a class of non-coding RNAs divided into two classes: C/D box snoRNAs and H/ACA box snoRNAs. The canonical function of C/D box and H/ACA box snoRNAs are 2'-O-ribose methylation and pseudouridylation of ribosomal RNAs (rRNAs), respectively. Emerging evidence has demonstrated that snoRNAs are involved in various physiological and pathological cellular processes. Mutations and aberrant expression of snoRNAs have been reported in cell transformation, tumorigenesis, and metastasis, indicating that snoRNAs may serve as biomarkers and/or therapeutic targets of cancer. Hence, further study of the functions and underlying mechanism of snoRNAs is valuable. In this review, we summarize the biogenesis and functions of snoRNAs, as well as the association of snoRNAs in different types of cancers and their potential roles in cancer diagnosis and therapy.
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Affiliation(s)
- Junnan Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingyuan Wen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Huang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Ping Chen
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bi-Xiang Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liang Chu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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36
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Ectopic expression of Snord115 in choroid plexus interferes with editing but not splicing of 5-Ht2c receptor pre-mRNA in mice. Sci Rep 2019; 9:4300. [PMID: 30862860 PMCID: PMC6414643 DOI: 10.1038/s41598-019-39940-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Serotonin 5-HT2C receptor is a G-protein coupled excitatory receptor that regulates several biochemical pathways and has been implicated in obesity, mental state, sleep cycles, autism, neuropsychiatric disorders and neurodegenerative diseases. The activity of 5-HT2CR is regulated via alternative splicing and A to I editing of exon Vb of its pre-mRNA. Snord115 is a small nucleolar RNA that is expressed in mouse neurons and displays an 18-nucleotide base complementary to exon Vb of 5-HT2CR pre-mRNA. For almost two decades this putative guide element of Snord115 has wandered like a ghost through the literature in attempts to elucidate the biological significance of this complementarity. In mice, Snord115 is expressed in neurons and absent in the choroid plexus where, in contrast, 5-Ht2cr mRNA is highly abundant. Here we report the analysis of 5-Ht2cr pre-mRNA posttranscriptional processing via RNA deep sequencing in a mouse model that ectopically expresses Snord115 in the choroid plexus. In contrast to previous reports, our analysis demonstrated that Snord115 does not control alternative splicing of 5-Ht2cr pre-mRNA in vivo. We identified a modest, yet statistically significant reduction of 5-Ht2cr pre-mRNA A to I editing at the major A, B, C and D sites. We suggest that Snord115 and exon Vb of 5Ht2cr pre-mRNA form a double-stranded structure that is subject to ADAR-mediated A to I editing. To the best of our knowledge, this is the first comprehensive Snord115 gain-of-function analysis based on in vivo mouse models.
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Sinigaglia K, Wiatrek D, Khan A, Michalik D, Sambrani N, Sedmík J, Vukić D, O'Connell MA, Keegan LP. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:356-369. [DOI: 10.1016/j.bbagrm.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/12/2018] [Accepted: 10/27/2018] [Indexed: 01/24/2023]
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Rubio K, Dobersch S, Barreto G. Functional interactions between scaffold proteins, noncoding RNAs, and genome loci induce liquid-liquid phase separation as organizing principle for 3-dimensional nuclear architecture: implications in cancer. FASEB J 2019; 33:5814-5822. [PMID: 30742773 DOI: 10.1096/fj.201802715r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The eukaryotic cell nucleus consists of functionally specialized subcompartments. These nuclear subcompartments are biomolecular aggregates built of proteins, transcripts, and specific genome loci. The structure and function of each nuclear subcompartment are defined by the composition and dynamic interaction between these 3 components. The spatio-temporal localization of biochemical reactions into membraneless nuclear subcompartments can be achieved through liquid-liquid phase separation. Based on this organizing principle, nuclear subcompartments are droplet-like structures that adopt spherical shapes, flow, and fuse like liquids or gels. In the present review, we bring into the spotlight seminal works elucidating the functional interactions between scaffold proteins, noncoding RNAs, and genomic loci, thereby inducing liquid-liquid phase separation as an organizing principle for 3-dimensional nuclear architecture. We also discuss the implications in different cancer types as well as the potential use of this knowledge to develop novel therapeutic strategies against cancer.-Rubio, K., Dobersch, S., Barreto, G. Functional interactions between scaffold proteins, noncoding RNAs, and genome loci induce liquid-liquid phase separation as organizing principle for 3-dimensional nuclear architecture: implications in cancer.
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Affiliation(s)
- Karla Rubio
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stephanie Dobersch
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetic, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Laboratoire Croissance, Réparation, et Régénération Tissulaires (CRRET), Centre National de la Recherche Scientifique (CNRS) Équipe de Recherche Labellisée (ERL) 9215, Université Paris Est Créteil, Créteil, France.,Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russian Federation.,Excellence Cluster Cardio Pulmonary System (ECCPS), Universities of Giessen-Marburg Lung Center (UGMLC), Giessen, Germany.,German Center of Lung Research, Giessen, Germany
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39
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Dimitrova DG, Teysset L, Carré C. RNA 2'-O-Methylation (Nm) Modification in Human Diseases. Genes (Basel) 2019; 10:E117. [PMID: 30764532 PMCID: PMC6409641 DOI: 10.3390/genes10020117] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/24/2022] Open
Abstract
Nm (2'-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects.
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Affiliation(s)
- Dilyana G Dimitrova
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Laure Teysset
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Clément Carré
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
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Eukaryotic Translation Elongation is Modulated by Single Natural Nucleotide Derivatives in the Coding Sequences of mRNAs. Genes (Basel) 2019; 10:genes10020084. [PMID: 30691071 PMCID: PMC6409545 DOI: 10.3390/genes10020084] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/14/2019] [Accepted: 01/23/2019] [Indexed: 12/16/2022] Open
Abstract
RNA modifications are crucial factors for efficient protein synthesis. All classes of RNAs that are involved in translation are modified to different extents. Recently, mRNA modifications and their impact on gene regulation became a focus of interest because they can exert a variety of effects on the fate of mRNAs. mRNA modifications within coding sequences can either directly or indirectly interfere with protein synthesis. In order to investigate the roles of various natural occurring modified nucleotides, we site-specifically introduced them into the coding sequence of reporter mRNAs and subsequently translated them in HEK293T cells. The analysis of the respective protein products revealed a strong position-dependent impact of RNA modifications on translation efficiency and accuracy. Whereas a single 5-methylcytosine (m5C) or pseudouridine (Ψ) did not reduce product yields, N1-methyladenosine (m1A) generally impeded the translation of the respective modified mRNA. An inhibitory effect of 2′O-methlyated nucleotides (Nm) and N6-methyladenosine (m6A) was strongly dependent on their position within the codon. Finally, we could not attribute any miscoding potential to the set of mRNA modifications tested in HEK293T cells.
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Quinones-Valdez G, Tran SS, Jun HI, Bahn JH, Yang EW, Zhan L, Brümmer A, Wei X, Van Nostrand EL, Pratt GA, Yeo GW, Graveley BR, Xiao X. Regulation of RNA editing by RNA-binding proteins in human cells. Commun Biol 2019; 2:19. [PMID: 30652130 PMCID: PMC6331435 DOI: 10.1038/s42003-018-0271-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/13/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) editing, mediated by the ADAR enzymes, diversifies the transcriptome by altering RNA sequences. Recent studies reported global changes in RNA editing in disease and development. Such widespread editing variations necessitate an improved understanding of the regulatory mechanisms of RNA editing. Here, we study the roles of >200 RNA-binding proteins (RBPs) in mediating RNA editing in two human cell lines. Using RNA-sequencing and global protein-RNA binding data, we identify a number of RBPs as key regulators of A-to-I editing. These RBPs, such as TDP-43, DROSHA, NF45/90 and Ro60, mediate editing through various mechanisms including regulation of ADAR1 expression, interaction with ADAR1, and binding to Alu elements. We highlight that editing regulation by Ro60 is consistent with the global up-regulation of RNA editing in systemic lupus erythematosus. Additionally, most key editing regulators act in a cell type-specific manner. Together, our work provides insights for the regulatory mechanisms of RNA editing.
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Affiliation(s)
| | - Stephen S. Tran
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Hyun-Ik Jun
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Jae Hoon Bahn
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Ei-Wen Yang
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Anneke Brümmer
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Eric L. Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Gabriel A. Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093 USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030 USA
| | - Xinshu Xiao
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA 90095 USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095 USA
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 USA
- Institute for Quantitative and Computational Biology, University of California Los Angeles, Los Angeles, CA 90095 USA
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Kung CP, Maggi LB, Weber JD. The Role of RNA Editing in Cancer Development and Metabolic Disorders. Front Endocrinol (Lausanne) 2018; 9:762. [PMID: 30619092 PMCID: PMC6305585 DOI: 10.3389/fendo.2018.00762] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/03/2018] [Indexed: 12/26/2022] Open
Abstract
Numerous human diseases arise from alterations of genetic information, most notably DNA mutations. Thought to be merely the intermediate between DNA and protein, changes in RNA sequence were an afterthought until the discovery of RNA editing 30 years ago. RNA editing alters RNA sequence without altering the sequence or integrity of genomic DNA. The most common RNA editing events are A-to-I changes mediated by adenosine deaminase acting on RNA (ADAR), and C-to-U editing mediated by apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (APOBEC1). Both A-to-I and C-to-U editing were first identified in the context of embryonic development and physiological homeostasis. The role of RNA editing in human disease has only recently started to be understood. In this review, the impact of RNA editing on the development of cancer and metabolic disorders will be examined. Distinctive functions of each RNA editase that regulate either A-to-I or C-to-U editing will be highlighted in addition to pointing out important regulatory mechanisms governing these processes. The potential of developing novel therapeutic approaches through intervention of RNA editing will be explored. As the role of RNA editing in human disease is elucidated, the clinical utility of RNA editing targeted therapies will be needed. This review aims to serve as a bridge of information between past findings and future directions of RNA editing in the context of cancer and metabolic disease.
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Affiliation(s)
- Che-Pei Kung
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Leonard B. Maggi
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Jason D. Weber
- ICCE Institute, Washington University School of Medicine, Saint Louis, MO, United States
- Division of Molecular Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
- Siteman Cancer Center, Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, United States
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44
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The Role of the Prader-Willi Syndrome Critical Interval for Epigenetic Regulation, Transcription and Phenotype. EPIGENOMES 2018. [DOI: 10.3390/epigenomes2040018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Prader-Willi Syndrome (PWS) is a neurodevelopmental disorder caused by loss of expression of the paternally inherited genes on chromosome 15q11.2-q13. However, the core features of PWS have been attributed to a critical interval (PWS-cr) within the 15q11.2-q13 imprinted gene cluster, containing the small nucleolar RNA (snoRNA) SNORD116 and non-coding RNA IPW (Imprinted in Prader-Willi) exons. SNORD116 affects the transcription profile of hundreds of genes, possibly via DNA methylation or post-transcriptional modification, although the exact mechanism is not completely clear. IPW on the other hand has been shown to specifically modulate histone methylation of a separate imprinted locus, the DLK1-DIO3 cluster, which itself is associated with several neurodevelopmental disorders with similarities to PWS. Here we review what is currently known of the molecular targets of SNORD116 and IPW and begin to disentangle their roles in contributing to the Prader-Willi Syndrome phenotype.
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Leighton LJ, Bredy TW. Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain. Noncoding RNA 2018; 4:E15. [PMID: 29880782 PMCID: PMC6027130 DOI: 10.3390/ncrna4020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 12/11/2022] Open
Abstract
Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.
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Affiliation(s)
- Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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46
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Tiku V, Antebi A. Nucleolar Function in Lifespan Regulation. Trends Cell Biol 2018; 28:662-672. [PMID: 29779866 DOI: 10.1016/j.tcb.2018.03.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 12/12/2022]
Abstract
The nucleolus is a prominent membraneless organelle residing within the nucleus. The nucleolus has been regarded as a housekeeping structure mainly known for its role in ribosomal RNA (rRNA) production and ribosome assembly. However, accumulating evidence has revealed its functions in numerous cellular processes that control organismal physiology, thereby taking the nucleolus much beyond its conventional role in ribosome biogenesis. Perturbations in nucleolar functions have been associated with severe diseases such as cancer and progeria. Recent studies have also uncovered the role of the nucleolus in development and aging. In this review we discuss major nucleolar functions that impact organismal aging.
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Affiliation(s)
- Varnesh Tiku
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany; Present Address: Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Strasse 9b, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany.
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47
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Angelova MT, Dimitrova DG, Dinges N, Lence T, Worpenberg L, Carré C, Roignant JY. The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. Front Bioeng Biotechnol 2018; 6:46. [PMID: 29707539 PMCID: PMC5908907 DOI: 10.3389/fbioe.2018.00046] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.
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Affiliation(s)
- Margarita T Angelova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Nadja Dinges
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Tina Lence
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Lina Worpenberg
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Jean-Yves Roignant
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
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Bratkovič T, Modic M, Camargo Ortega G, Drukker M, Rogelj B. Neuronal differentiation induces SNORD115 expression and is accompanied by post-transcriptional changes of serotonin receptor 2c mRNA. Sci Rep 2018; 8:5101. [PMID: 29572515 PMCID: PMC5865145 DOI: 10.1038/s41598-018-23293-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
The serotonin neurotransmitter system is widespread in the brain and implicated in modulation of neuronal responses to other neurotransmitters. Among 14 serotonin receptor subtypes, 5-HT2cR plays a pivotal role in controlling neuronal network excitability. Serotonergic activity conveyed through receptor 5-HT2cR is regulated post-transcriptionally via two mechanisms, alternative splicing and A-to-I RNA editing. Brain-specific small nucleolar RNA SNORD115 harbours a phylogenetically conserved 18-nucleotide antisense element with perfect complementarity to the region of 5ht2c primary transcript that undergoes post-transcriptional changes. Previous 5ht2c minigene studies have implicated SNORD115 in fine-tuning of both post-transcriptional events. We monitored post-transcriptional changes of endogenous 5ht2c transcripts during neuronal differentiation. Both SNORD115 and 5ht2c were upregulated upon neuronal commitment. We detected increased 5ht2c alternative exon Vb inclusion already at the stage of neuronal progenitors, and more extensive A-to-I editing of non-targeted sites A and B compared to adjacent adenosines at sites E, C and D throughout differentiation. As the extent of editing is known to positively correlate with exon Vb usage while it reduces receptor functionality, our data support the model where SNORD115 directly promotes alternative exon inclusion without the requirement for conversion of key adenosines to inosines, thereby favouring production of full-length receptor isoforms with higher potency.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Biology, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Miha Modic
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Germán Camargo Ortega
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilian University Munich, Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research and the Induced Pluripotent Stem Cell Core Facility, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology, Jamova 39, 1000, Ljubljana, Slovenia. .,Biomedical Research Institute BRIS, Puhova 10, 1000, Ljubljana, Slovenia. .,University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, 1000, Ljubljana, Slovenia.
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Hoernes TP, Erlacher MD. Methylated mRNA Nucleotides as Regulators for Ribosomal Translation. Methods Mol Biol 2018; 1562:283-294. [PMID: 28349468 DOI: 10.1007/978-1-4939-6807-7_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Methylated RNA nucleotides were recently discovered to be highly abundant in RNAs. The effects of these methylations were mainly attributed to altered mRNA stabilities, protein-binding affinities, or RNA structures. The direct impact of RNA modifications on the performance of the ribosome has not been investigated so far. In this chapter, we describe an approach that allows introducing RNA modifications site-specifically into coding sequences of mRNAs and determining their effect on the translation machinery in a well-defined bacterial in vitro system.
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Affiliation(s)
- Thomas P Hoernes
- Division of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, Innsbruck, 6020, Austria
| | - Matthias D Erlacher
- Division of Genomics and RNomics, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80/82, Innsbruck, 6020, Austria.
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50
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van der Kwast RV, van Ingen E, Parma L, Peters HA, Quax PH, Nossent AY. Adenosine-to-Inosine Editing of MicroRNA-487b Alters Target Gene Selection After Ischemia and Promotes Neovascularization. Circ Res 2018; 122:444-456. [DOI: 10.1161/circresaha.117.312345] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/19/2017] [Accepted: 12/27/2017] [Indexed: 12/20/2022]
Abstract
Rationale:
Adenosine-to-inosine editing of microRNAs has the potential to cause a shift in target site selection. 2′-O-ribose-methylation of adenosine residues, however, has been shown to inhibit adenosine-to-inosine editing.
Objective:
To investigate whether angiomiR miR487b is subject to adenosine-to-inosine editing or 2′-O-ribose-methylation during neovascularization.
Methods and Results:
Complementary DNA was prepared from C57BL/6-mice subjected to hindlimb ischemia. Using Sanger sequencing and endonuclease digestion, we identified and validated adenosine-to-inosine editing of the miR487b seed sequence. In the gastrocnemius muscle, pri-miR487b editing increased from 6.7±0.4% before to 11.7±1.6% (
P
=0.02) 1 day after ischemia. Edited pri-miR487b is processed into a novel microRNA, edited miR487b, which is also upregulated after ischemia. We confirmed editing of miR487b in multiple human primary vascular cell types. Short interfering RNA–mediated knockdown demonstrated that editing is adenosine deaminase acting on RNA 1 and 2 dependent. Using reverse-transcription at low dNTP concentrations followed by quantitative-PCR, we found that the same adenosine residue is methylated in mice and human primary cells. In the murine gastrocnemius, the estimated methylation fraction increased from 32.8±14% before to 53.6±12% 1 day after ischemia. Short interfering RNA knockdown confirmed that methylation is fibrillarin dependent. Although we could not confirm that methylation directly inhibits editing, we do show that adenosine deaminase acting on RNA 1 and 2 and fibrillarin negatively influence each other’s expression. Using multiple luciferase reporter gene assays, we could demonstrate that editing results in a complete switch of target site selection. In human primary cells, we confirmed the shift in miR487b targeting after editing, resulting in a edited miR487b targetome that is enriched for multiple proangiogenic pathways. Furthermore, overexpression of edited miR487b, but not wild-type miR487b, stimulates angiogenesis in both in vitro and ex vivo assays.
Conclusions:
MiR487b is edited in the seed sequence in mice and humans, resulting in a novel, proangiogenic microRNA with a unique targetome. The rate of miR487b editing, as well as 2′-O-ribose-methylation, is increased in murine muscle tissue during postischemic neovascularization. Our findings suggest miR487b editing plays an intricate role in postischemic neovascularization.
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Affiliation(s)
- Reginald V.C.T. van der Kwast
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Eva van Ingen
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Laura Parma
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Hendrika A.B. Peters
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - Paul H.A. Quax
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
| | - A. Yaël Nossent
- From the Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, The Netherlands
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