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Martinez ME, Karaczyn A, Wu Z, Bennett CA, Matoin KL, Daigle HM, Hernandez A. Transgenerational epigenetic self-memory of Dio3 dosage is associated with Meg3 methylation and altered growth trajectories and neonatal hormones. Epigenetics 2024; 19:2376948. [PMID: 38991122 PMCID: PMC11244338 DOI: 10.1080/15592294.2024.2376948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
Intergenerational and transgenerational epigenetic effects resulting from conditions in previous generations can contribute to environmental adaptation as well as disease susceptibility. Previous studies in rodent and human models have shown that abnormal developmental exposure to thyroid hormone affects endocrine function and thyroid hormone sensitivity in later generations. Since the imprinted type 3 deiodinase gene (Dio3) regulates sensitivity to thyroid hormones, we hypothesize its epigenetic regulation is altered in descendants of thyroid hormone overexposed individuals. Using DIO3-deficient mice as a model of developmental thyrotoxicosis, we investigated Dio3 total and allelic expression and growth and endocrine phenotypes in descendants. We observed that male and female developmental overexposure to thyroid hormone altered total and allelic Dio3 expression in genetically intact descendants in a tissue-specific manner. This was associated with abnormal growth and neonatal levels of thyroid hormone and leptin. Descendant mice also exhibited molecular abnormalities in the Dlk1-Dio3 imprinted domain, including increased methylation in Meg3 and altered foetal brain expression of other genes of the Dlk1-Dio3 imprinted domain. These molecular abnormalities were also observed in the tissues and germ line of DIO3-deficient ancestors originally overexposed to thyroid hormone in utero. Our results provide a novel paradigm of epigenetic self-memory by which Dio3 gene dosage in a given individual, and its dependent developmental exposure to thyroid hormone, influences its own expression in future generations. This mechanism of epigenetic self-correction of Dio3 expression in each generation may be instrumental in descendants for their adaptive programming of developmental growth and adult endocrine function.
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Affiliation(s)
- M. Elena Martinez
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Aldona Karaczyn
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Zhaofei Wu
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Christian A. Bennett
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Kassey L. Matoin
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Heather M. Daigle
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
| | - Arturo Hernandez
- Center for Molecular Medicine, MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA
- Graduate School for Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Department of Medicine, Tufts University School of Medicine, Boston, MA, USA
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2
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Smal M, Memoli D, Alexandrova E, Di Rosa D, D'Agostino Y, Russo F, Giurato G, Nassa G, Tarallo R, Weisz A, Rizzo F. Small non-coding RNA transcriptomic profiling in adult and fetal human brain. Sci Data 2024; 11:767. [PMID: 38997254 PMCID: PMC11245507 DOI: 10.1038/s41597-024-03604-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024] Open
Abstract
Small non-coding RNAs (sncRNAs) make up ~1% of the transcriptome; nevertheless, they play significant roles in regulating cellular processes. Given the complexity of the central nervous system, sncRNAs likely hold particular importance in the human brain. In this study, we provide sncRNA transcriptomic profiles in a range of adult and prenatal brain regions, with a focus on piRNAs, due to their underexplored expression in somatic cells and tissue-specific nature. Using the WIND workflow, which combines two detection methods, we found 1333 (731 miRNAs, 249 piRNAs, 285 snoRNAs, and 68 other sncRNAs) and 1445 unique sncRNAs (770 miRNAs, 307 piRNAs, 289 snoRNAs, and 79 other sncRNAs) in developing and adult brains, respectively. Significant variations were found upon comparison of fetal and adult brain groups, with 82 miRNAs, 17 piRNAs, and 70 snoRNAs enriched in fetal brains and 22 miRNAs, 11 piRNAs in adult brains. This dataset represents a valuable resource for exploring the sncRNA roles in brain function, their involvement in neurological diseases, and the molecular mechanisms behind brain region interactions.
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Affiliation(s)
- Marharyta Smal
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
| | - Domenico Di Rosa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
| | - Ylenia D'Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
- Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy
| | - Fabio Russo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
- Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
- Genome Research Center for Health - CRGS, Campus of Medicine - University of Salerno, 84081, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
- Genome Research Center for Health - CRGS, Campus of Medicine - University of Salerno, 84081, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy
- Genome Research Center for Health - CRGS, Campus of Medicine - University of Salerno, 84081, Baronissi, SA, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy.
- Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy.
- Genome Research Center for Health - CRGS, Campus of Medicine - University of Salerno, 84081, Baronissi, SA, Italy.
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081, Baronissi, SA, Italy.
- Medical Genomics Program, AOU 'S. Giovanni di Dio e Ruggi d'Aragona', University of Salerno, Salerno, Italy.
- Genome Research Center for Health - CRGS, Campus of Medicine - University of Salerno, 84081, Baronissi, SA, Italy.
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3
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Vihma H, Li K, Welton-Arndt A, Smith AL, Bettadapur KR, Gilmore RB, Gao E, Cotney JL, Huang HC, Collins JL, Chamberlain SJ, Lee HM, Aubé J, Philpot BD. Ube3a unsilencer for the potential treatment of Angelman syndrome. Nat Commun 2024; 15:5558. [PMID: 38977672 PMCID: PMC11231141 DOI: 10.1038/s41467-024-49788-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Deletion of the maternal UBE3A allele causes Angelman syndrome (AS); because paternal UBE3A is epigenetically silenced by a long non-coding antisense (UBE3A-ATS) in neurons, this nearly eliminates UBE3A protein in the brain. Reactivating paternal UBE3A holds promise for treating AS. We previously showed topoisomerase inhibitors can reactivate paternal UBE3A, but their therapeutic challenges prompted our search for small molecule unsilencers with a different mechanism of action. Here, we found that (S)-PHA533533 acts through a novel mechanism to significantly increase paternal Ube3a mRNA and UBE3A protein levels while downregulating Ube3a-ATS in primary neurons derived from AS model mice. Furthermore, peripheral delivery of (S)-PHA533533 in AS model mice induces widespread neuronal UBE3A expression. Finally, we show that (S)-PHA533533 unsilences paternal UBE3A in AS patient-derived neurons, highlighting its translational potential. Our findings provide a lead for developing a small molecule treatment for AS that could be safe, non-invasively delivered, and capable of brain-wide unsilencing of paternal UBE3A.
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Affiliation(s)
- Hanna Vihma
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kelin Li
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anna Welton-Arndt
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Audrey L Smith
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kiran R Bettadapur
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rachel B Gilmore
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Eric Gao
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Hsueh-Cheng Huang
- Deerfield Discovery and Development, Deerfield Management, New York, NY, USA
| | - Jon L Collins
- Office of the Vice Chancellor for Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Hyeong-Min Lee
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Benjamin D Philpot
- Department of Cell Biology and Physiology, Neuroscience Center, and Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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4
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Gómez-Matas J, Duran-Sanchon S, Lozano JJ, Ferrero G, Tarallo S, Pardini B, Naccarati A, Castells A, Gironella M. SnoRNA profiling in colorectal cancer and assessment of non-invasive biomarker capacity by ddPCR in fecal samples. iScience 2024; 27:109283. [PMID: 38450150 PMCID: PMC10915595 DOI: 10.1016/j.isci.2024.109283] [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: 09/18/2023] [Revised: 01/26/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Small nucleolar RNAs (snoRNAs) have been identified dysregulated in several pathologies, and these alterations can be detected in tissues and in circulation. The main aim of this study was to analyze the whole snoRNome in advanced colorectal neoplasms and to identify new potential non-invasive snoRNA-based biomarkers in fecal samples by different analytical approaches. SNORA51, SNORD15B, SNORA54, SNORD12B, SNORD12C, SNORD72, SNORD89, and several members of SNORD115 and SNORD116 clusters were consistently deregulated in both tissue sets. After technical validation, SNORA51 and SNORD15B were detected in FIT+ samples. SNORA51 was significantly upregulated in FIT+ samples from CRC patients compared to healthy controls. This upregulation, together with the fecal hemoglobin concentration, was sufficient to identify, among FIT+ individuals, patients with CRC (AUC = 0.86) and individuals with advanced adenomas (AUC = 0.68). These findings portray snoRNAs as an alternative source of candidates for further studies and SNORA51 appears as a potential non-invasive biomarker for CRC detection.
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Affiliation(s)
- Javier Gómez-Matas
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Saray Duran-Sanchon
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | | | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Antoni Castells
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
| | - Meritxell Gironella
- Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd)/ Hospital Clínic Barcelona/ Fundació de Recerca Clínic Barcelona – Institut d’investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Catalonia, Spain
- Department of Experimental Pathology, Institute of Biomedical Research of Barcelona-Spanish National Research Council (IIBB-CSIC), Barcelona, Spain
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5
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Berriel Pinho VH, Daher JPL, Kanaan S, Medeiros T. Extracellular vesicles in Alzheimer's disease. ARQUIVOS DE NEURO-PSIQUIATRIA 2024; 82:1-8. [PMID: 38467392 PMCID: PMC10927369 DOI: 10.1055/s-0044-1779296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/01/2023] [Indexed: 03/13/2024]
Abstract
Extracellular vesicles (EVs) are small vesicles released by cells that facilitate cell signaling. They are categorized based on their biogenesis and size. In the context of the central nervous system (CNS), EVs have been extensively studied for their role in both normal physiological functions and diseases like Alzheimer's disease (AD). AD is a neurodegenerative disorder characterized by cognitive decline and neuronal death. EVs have emerged as potential biomarkers for AD due to their involvement in disease progression. Specifically, EVs derived from neurons, astrocytes, and neuron precursor cells exhibit changes in quantity and composition in AD. Neuron-derived EVs have been found to contain key proteins associated with AD pathology, such as amyloid beta (Aß) and tau. Increased levels of Aß in neuron-derived EVs isolated from the plasma have been observed in individuals with AD and mild cognitive impairment, suggesting their potential as early biomarkers. However, the analysis of tau in neuron-derived EVs is still inconclusive. In addition to Aß and tau, neuron-derived EVs also carry other proteins linked to AD, including synaptic proteins. These findings indicate that EVs could serve as biomarkers for AD, particularly for early diagnosis and disease monitoring. However, further research is required to validate their use and explore potential therapeutic applications. To summarize, EVs are small vesicles involved in cell signaling within the CNS. They hold promise as biomarkers for AD, potentially enabling early diagnosis and monitoring of disease progression. Ongoing research aims to refine their use as biomarkers and uncover additional therapeutic applications.
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Affiliation(s)
| | - João Paulo Lima Daher
- Universidade Federal Fluminense, Faculdade de Medicina, Departamento de Patologia, NIterói RJ, Brazil.
| | - Salim Kanaan
- Universidade Federal Fluminense, Faculdade de Medicina, Departamento de Patologia, NIterói RJ, Brazil.
| | - Thalia Medeiros
- Universidade Federal Fluminense, Faculdade de Medicina, Departamento de Patologia, NIterói RJ, Brazil.
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Matveeva A, Vinogradov D, Zhuravlev E, Semenov D, Vlassov V, Stepanov G. Intron Editing Reveals SNORD-Dependent Maturation of the Small Nucleolar RNA Host Gene GAS5 in Human Cells. Int J Mol Sci 2023; 24:17621. [PMID: 38139448 PMCID: PMC10743478 DOI: 10.3390/ijms242417621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
The GAS5 gene encodes a long non-coding RNA (lncRNA) and intron-located small nucleolar RNAs (snoRNAs). Its structure, splice variants, and diverse functions in mammalian cells have been thoroughly investigated. However, there are still no data on a successful knockout of GAS5 in human cells, with most of the loss-of-function experiments utilizing standard techniques to produce knockdowns. By using CRISPR/Cas9 to introduce double-strand breaks in the terminal intronic box C/D snoRNA genes (SNORDs), we created monoclonal cell lines carrying continuous deletions in one of the GAS5 alleles. The levels of GAS5-encoded box C/D snoRNAs and lncRNA GAS5 were assessed, and the formation of the novel splice variants was analyzed. To comprehensively evaluate the influence of specific SNORD mutations, human cell lines with individual mutations in SNORD74 and SNORD81 were obtained. Specific mutations in SNORD74 led to the downregulation of all GAS5-encoded SNORDs and GAS5 lncRNA. Further analysis revealed that SNORD74 contains a specific regulatory element modulating the maturation of the GAS5 precursor transcript. The results demonstrate that the maturation of GAS5 occurs through the m6A-associated pathway in a SNORD-dependent manner, which is a quite intriguing epitranscriptomic mechanism.
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Affiliation(s)
| | | | | | | | | | - Grigory Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (A.M.); (D.V.); (E.Z.); (D.S.)
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Gawade K, Raczynska KD. Imprinted small nucleolar RNAs: Missing link in development and disease? WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1818. [PMID: 37722601 DOI: 10.1002/wrna.1818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/20/2023]
Abstract
The 14q32.2 (DLK1-DIO3) and 15q11-q13 (SNURF-SNRPN) imprinted gene loci harbor the largest known small nucleolar RNA clusters expressed from the respective maternal and paternal alleles. Recent studies have demonstrated significant roles for the 15q11-q13 located SNORD115-SNORD116 C/D box snoRNAs in Prader-Willi syndrome (PWS), a neurodevelopmental disorder. Even though the effect of SNORD116 deletion is apparent in the PWS phenotype, similar effects of a SNORD113-SNORD114 cluster deletion from the 14q32.2 locus in Kagami-Ogata syndrome (KOS14) and upregulation in Temple syndrome (TS14) remain to be explored. Moreover, apart from their probable involvement in neurodevelopmental disorders, snoRNAs from the SNORD113-SNORD114 cluster have been implicated in multiple biological processes, including pluripotency, development, cancers, and RNA modifications. Here we summarize the current understanding of the system to explore the possibility of a link between developmental disorders and C/D box snoRNA expression from the imprinted 14q32.2 locus. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development RNA Processing > Processing of Small RNAs.
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Affiliation(s)
- Kishor Gawade
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Katarzyna D Raczynska
- Laboratory of RNA Processing, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
- Center for Advanced Technology, Adam Mickiewicz University in Poznan, Poznan, Poland
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8
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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9
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de Sena Brandine G, Aston KI, Jenkins TG, Smith AD. Global effects of identity and aging on the human sperm methylome. Clin Epigenetics 2023; 15:127. [PMID: 37550724 PMCID: PMC10408082 DOI: 10.1186/s13148-023-01541-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND As the average age of fatherhood increases worldwide, so too does the need for understanding effects of aging in male germline cells. Molecular change, including epigenomic alterations, may impact offspring. Age-associated change to DNA cytosine methylation in the cytosine-guanine (CpG) context is a hallmark of aging tissues, including sperm. Prior studies have led to accurate models that predict a man's age based on specific methylation features in the DNA of sperm, but the relationship between aging and global DNA methylation in sperm remains opaque. Further clarification requires a more complete survey of the methylome with assessment of variability within and between individuals. RESULTS We collected sperm methylome data in a longitudinal study of ten healthy fertile men. We used whole-genome bisulfite sequencing of samples collected 10 to 18 years apart from each donor. We found that, overall, variability between donors far exceeds age-associated variation. After controlling for donor identity, we see significant age-dependent genome-wide change to the methylome. Notably, trends of change with age depend on genomic location or annotation, with contrasting signatures that correlate with gene density and proximity to centromeres and promoter regions. CONCLUSIONS We uncovered epigenetic signatures that reflect a stable process which begins in early adulthood, progressing steadily through most of the male lifespan, and warrants consideration in any future study of the aging sperm epigenome.
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Affiliation(s)
- Guilherme de Sena Brandine
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA
| | - Kenneth I Aston
- Andrology and IVF Laboratory, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, USA
| | - Timothy G Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, USA
| | - Andrew D Smith
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA.
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10
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Brazane M, Dimitrova DG, Pigeon J, Paolantoni C, Ye T, Marchand V, Da Silva B, Schaefer E, Angelova MT, Stark Z, Delatycki M, Dudding-Byth T, Gecz J, Plaçais PY, Teysset L, Préat T, Piton A, Hassan BA, Roignant JY, Motorin Y, Carré C. The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance. Life Sci Alliance 2023; 6:e202201877. [PMID: 36720500 PMCID: PMC9889914 DOI: 10.26508/lsa.202201877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 02/02/2023] Open
Abstract
FTSJ1 is a conserved human 2'-O-methyltransferase (Nm-MTase) that modifies several tRNAs at position 32 and the wobble position 34 in the anticodon loop. Its loss of function has been linked to X-linked intellectual disability (XLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here, we report a novel FTSJ1 pathogenic variant from an X-linked intellectual disability patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation on all human tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neural progenitor cells into neurons displays long and thin spine neurites compared with control cells. These defects are also observed in Drosophila and are associated with long-term memory deficits. Altogether, our study adds insight into FTSJ1 pathologies in humans and flies by the identification of novel FTSJ1 targets and the defect in neuron morphology.
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Affiliation(s)
- Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Julien Pigeon
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Tao Ye
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, EpiRNASeq Core Facility, UMS2008/US40 IBSLor,Nancy, France
| | - Bruno Da Silva
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Margarita T Angelova
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide; South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Pierre-Yves Plaçais
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Laure Teysset
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
| | - Thomas Préat
- Energy & Memory, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL Research University, Paris, France
| | - Amélie Piton
- Institute of Genetics and Molecular and Cellular Biology, Strasbourg University, CNRS UMR7104, INSERM U1258, Illkirch, France
| | - Bassem A Hassan
- Paris Brain Institute-Institut du Cerveau (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- Université de Lorraine, CNRS, UMR7365 IMoPA, Nancy, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire de Biologie du Développement - Institut de Biologie Paris Seine, Paris, France
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11
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Dindot SV, Christian S, Murphy WJ, Berent A, Panagoulias J, Schlafer A, Ballard J, Radeva K, Robinson R, Myers L, Jepp T, Shaheen H, Hillman P, Konganti K, Hillhouse A, Bredemeyer KR, Black L, Douville J. An ASO therapy for Angelman syndrome that targets an evolutionarily conserved region at the start of the UBE3A-AS transcript. Sci Transl Med 2023; 15:eabf4077. [PMID: 36947593 DOI: 10.1126/scitranslmed.abf4077] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Angelman syndrome is a devastating neurogenetic disorder for which there is currently no effective treatment. It is caused by mutations or epimutations affecting the expression or function of the maternally inherited allele of the ubiquitin-protein ligase E3A (UBE3A) gene. The paternal UBE3A allele is imprinted in neurons of the central nervous system (CNS) by the UBE3A antisense (UBE3A-AS) transcript, which represents the distal end of the small nucleolar host gene 14 (SNHG14) transcription unit. Reactivating the expression of the paternal UBE3A allele in the CNS has long been pursued as a therapeutic option for Angelman syndrome. Here, we described the development of an antisense oligonucleotide (ASO) therapy for Angelman syndrome that targets an evolutionarily conserved region demarcating the start of the UBE3A-AS transcript. We designed and chemically optimized gapmer ASOs targeting specific sequences at the start of the human UBE3A-AS transcript. We showed that ASOs targeting this region precisely and efficiently repress the transcription of UBE3A-AS, reactivating the expression of the paternal UBE3A allele in neurotypical and Angelman syndrome induced pluripotent stem cell-derived neurons. We further showed that human-targeted ASOs administered to the CNS of cynomolgus macaques by lumbar intrathecal injection repress UBE3A-AS and reactivate the expression of the paternal UBE3A allele throughout the CNS. These findings support the advancement of this investigational molecular therapy for Angelman syndrome into clinical development (ClinicalTrials.gov, NCT04259281).
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
- GeneTx Biotherapeutics LLC, Sarasota, FL 34233, USA
- Research Department, Ultragenyx Pharmaceutical, Novato, CA 94949, USA
| | - Sarah Christian
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | | | - Annalise Schlafer
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX 77843, USA
| | - Kamelia Radeva
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Ruth Robinson
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Luke Myers
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Thomas Jepp
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, UK
| | - Hillary Shaheen
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Paul Hillman
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Kranti Konganti
- Texas A&M University Institute for Genome Sciences and Society (TIGSS), Texas A&M University, College Station, TX 77843, USA
| | - Andrew Hillhouse
- Texas A&M University Institute for Genome Sciences and Society (TIGSS), Texas A&M University, College Station, TX 77843, USA
| | - Kevin R Bredemeyer
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | | | - Julie Douville
- Charles River Laboratories, Montreal, Senneville, Quebec H9X 1C1, Canada
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12
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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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13
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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14
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Maggio AG, Shu HT, Laufer BI, Bi C, Lai Y, LaSalle JM, Hu VW. Elevated exposures to persistent endocrine disrupting compounds impact the sperm methylome in regions associated with autism spectrum disorder. Front Genet 2022; 13:929471. [PMID: 36035158 PMCID: PMC9403863 DOI: 10.3389/fgene.2022.929471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Environmental exposures to endocrine disrupting compounds (EDCs) such as the organochlorines have been linked with various diseases including neurodevelopmental disorders. Autism spectrum disorder (ASD) is a highly complex neurodevelopmental disorder that is considered strongly genetic in origin due to its high heritability. However, the rapidly rising prevalence of ASD suggests that environmental factors may also influence risk for ASD. In the present study, whole genome bisulfite sequencing was used to identify genome-wide differentially methylated regions (DMRs) in a total of 52 sperm samples from a cohort of men from the Faroe Islands (Denmark) who were equally divided into high and low exposure groups based on their serum levels of the long-lived organochlorine 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (DDE), a primary breakdown product of the now banned insecticide dichlorodiphenyltrichloroethane (DDT). Aside from being considered a genetic isolate, inhabitants of the Faroe Islands have a native diet that potentially exposes them to a wide range of seafood neurotoxicants in the form of persistent organic pollutants (POPs). The DMRs were mapped to the human genome using Bismark, a 3-letter aligner used for methyl-seq analyses. Gene ontology, functional, and pathway analyses of the DMR-associated genes showed significant enrichment for genes involved in neurological functions and neurodevelopmental processes frequently impacted by ASD. Notably, these genes also significantly overlap with autism risk genes as well as those previously identified in sperm from fathers of children with ASD in comparison to that of fathers of neurotypical children. These results collectively suggest a possible mechanism involving altered methylation of a significant number of neurologically relevant ASD risk genes for introducing epigenetic changes associated with environmental exposures into the sperm methylome. Such changes may provide the potential for transgenerational inheritance of ASD as well as other disorders.
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Affiliation(s)
- Angela G. Maggio
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Henry T. Shu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- The Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Benjamin I. Laufer
- Genome Center, Perinatal Origins of Disparities Center, Environmental Health Sciences Center, Medical Microbiology and Immunology, MIND Institute, UC Davis School of Medicine, Davis, CA, United States
| | - Chongfeng Bi
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Yinglei Lai
- Department of Statistics, The George Washington University, Washington, DC, United States
| | - Janine M. LaSalle
- Genome Center, Perinatal Origins of Disparities Center, Environmental Health Sciences Center, Medical Microbiology and Immunology, MIND Institute, UC Davis School of Medicine, Davis, CA, United States
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
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15
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Splicing inactivation generates hybrid mRNA-snoRNA transcripts targeted by cytoplasmic RNA decay. Proc Natl Acad Sci U S A 2022; 119:e2202473119. [PMID: 35878033 PMCID: PMC9351541 DOI: 10.1073/pnas.2202473119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many small nucleolar RNAs (snoRNA)s are processed from introns of host genes, but the importance of splicing for proper biogenesis and the fate of the snoRNAs is not well understood. Here, we show that inactivation of splicing factors or mutation of splicing signals leads to the accumulation of partially processed hybrid messenger RNA-snoRNA (hmsnoRNA) transcripts. hmsnoRNAs are processed to the mature 3' ends of the snoRNAs by the nuclear exosome and bound by small nucleolar ribonucleoproteins. hmsnoRNAs are unaffected by translation-coupled RNA quality-control pathways, but they are degraded by the major cytoplasmic exonuclease Xrn1p, due to their messenger RNA (mRNA)-like 5' extensions. These results show that completion of splicing is required to promote complete and accurate processing of intron-encoded snoRNAs and that splicing defects lead to degradation of hybrid mRNA-snoRNA species by cytoplasmic decay, underscoring the importance of splicing for the biogenesis of intron-encoded snoRNAs.
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16
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Wu F, Zhang L, Wu P, Wu Y, Zhang T, Zhang D, Tian J. The Potential Role of Small Nucleolar RNAs in Cancers – An Evidence Map. Int J Gen Med 2022; 15:3851-3864. [PMID: 35431571 PMCID: PMC9005336 DOI: 10.2147/ijgm.s352333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
Purpose Cancer seriously endangers human health in every country of the world. New evidence shows that small nucleolar RNAs play important roles in tumorigenesis. Herein, we created this evidence map to systematically assess the impact of dysregulated snoRNAs on cancers. Methods We searched four databases to February 2022 using the keywords, “carcinoma”, “neoplasms”, “tumor”, “cancer”, “snoRNA”, and “small nucleolar rna”. The research data were independently screened by two reviewers. Bubble plot, mind map, heatmap were used to depict the relationship between snoRNAs and cancers. Results In total, 102 studies met the inclusion criteria and were analyzed in this evidence map. In this study, we found that dysregulated snoRNAs were statistically associated with the clinicopathological characteristics of cancer patients, and affected tumor cell phenotypes. Abnormally expressed snoRNAs were associated with poor survival in cancer patients. Current research confirmed that snoRNAs have good diagnostic efficiency for cancers. snoRNAs could modulate biological processes and signaling pathways of different cancer cells by altering rRNA, regulating mRNA, and recruiting protein factors. Conclusion Taken all together, ectopic snoRNAs may serve as new biomarkers for clinical assessment, diagnostic, prognostic prediction of cancer patients, and provide a potential therapeutic strategy for cancer treatment. This article provided a visual analysis of existing evidence on snoRNAs and cancers, which can offer useful information for different researchers interested in snoRNAs.
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Affiliation(s)
- Fanqi Wu
- Department of Respiratory, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Longguo Zhang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Pingfan Wu
- Department of Pathology, The 940th Hospital of the Joint Logistic Support of the People’s Liberation Army, Lanzhou, Gansu Province, People’s Republic of China
| | - Yi Wu
- The Second Clinical Medical School, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
| | - Tao Zhang
- Department of Endocrinology and Metabolism, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
| | - Dekui Zhang
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, Gansu Province, People’s Republic of China
- Correspondence: Dekui Zhang; Jinhui Tian, Tel +86 139 1978 8616; +86 136 1934 2312, Email ;
| | - Jinhui Tian
- Evidence-Based Medicine Center, Lanzhou University, Lanzhou, Gansu Province, People’s Republic of China
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17
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Zaletaev DV, Nemtsova MV, Strelnikov VV. Epigenetic Regulation Disturbances on Gene Expression in Imprinting Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893321050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Cruz J, Lemos B. Post-transcriptional diversity in riboproteins and RNAs in aging and cancer. Semin Cancer Biol 2021; 76:292-300. [PMID: 34474152 PMCID: PMC8627441 DOI: 10.1016/j.semcancer.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/19/2022]
Abstract
Post-transcriptional (PtscM) and post-translational (PtrnM) modifications of nucleotides and amino acids are covalent modifications able to change physio-chemical properties of RNAs and proteins. In the ribosome, the adequate assembly of rRNAs and ribosomal protein subunits in the nucleolus ensures suitable translational activity, with protein synthesis tuned according to intracellular demands of energy production, replication, proliferation, and growth. Disruption in the regulatory control of PtscM and PtrnM can impair ribosome biogenesis and ribosome function. Ribosomal impairment may, in turn, impact the synthesis of proteins engaged in functions as varied as telomere maintenance, apoptosis, and DNA repair, as well as intersect with mitochondria and telomerase activity. These cellular processes often malfunction in carcinogenesis and senescence. Here we discuss regulatory mechanisms of PtscMs and PtrnMs on ribosomal function. We also address chemical modification in rRNAs and their impacts on cellular metabolism, replication control, and senescence. Further, we highlight similarities and differences of PtscMs and PtrnMs in ribosomal intermediates during aging and carcinogenesis. Understanding these regulatory mechanisms may uncover critical steps for the development of more efficient oncologic and anti-aging therapies.
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Affiliation(s)
- Jurandir Cruz
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP 01246, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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19
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Keshavarz M, Savriama Y, Refki P, Reeves RG, Tautz D. Natural copy number variation of tandemly repeated regulatory SNORD RNAs leads to individual phenotypic differences in mice. Mol Ecol 2021; 30:4708-4722. [PMID: 34252239 DOI: 10.1111/mec.16076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/05/2021] [Indexed: 12/01/2022]
Abstract
Genic copy number differences can have phenotypic consequences, but so far this has not been studied in detail in natural populations. Here, we analysed the natural variation of two families of tandemly repeated regulatory small nucleolar RNAs (SNORD115 and SNORD116) in the house mouse (Mus musculus). They are encoded within the Prader-Willi Syndrome gene region, known to be involved in behavioural, metabolic, and osteogenic functions in mammals. We determined that the copy numbers of these SNORD RNAs show substantial natural variation, both in wild-derived mice as well as in an inbred mouse strain (C57BL/6J). We show that copy number differences are subject to change across generations, making them highly variable and resulting in individual differences. In transcriptome data from brain samples, we found SNORD copy-number correlated regulation of possible target genes, including Htr2c, a predicted target gene of SNORD115, as well as Ankrd11, a predicted target gene of SNORD116. Ankrd11 is a chromatin regulator, which has previously been implicated in regulating the development of the skull. Based on morphometric shape analysis of the skulls of individual mice of the inbred strain, we show that shape measures correlate with SNORD116 copy numbers in the respective individuals. Our results suggest that the variable dosage of regulatory RNAs can lead to phenotypic variation between individuals that would typically have been ascribed to environmentally induced variation, while it is actually encoded in individual differences of copy numbers of regulatory molecules.
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Affiliation(s)
| | - Yoland Savriama
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Peter Refki
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - R Guy Reeves
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
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20
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Langouët M, Gorka D, Orniacki C, Dupont-Thibert CM, Chung MS, Glatt-Deeley HR, Germain N, Crandall LJ, Cotney JL, Stoddard CE, Lalande M, Chamberlain SJ. Specific ZNF274 binding interference at SNORD116 activates the maternal transcripts in Prader-Willi syndrome neurons. Hum Mol Genet 2021; 29:3285-3295. [PMID: 32977341 DOI: 10.1093/hmg/ddaa210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/15/2020] [Accepted: 08/26/2020] [Indexed: 12/27/2022] Open
Abstract
Prader-Willi syndrome (PWS) is characterized by neonatal hypotonia, developmental delay and hyperphagia/obesity. This disorder is caused by the absence of paternally expressed gene products from chromosome 15q11-q13. We previously demonstrated that knocking out ZNF274, a Kruppel-associated box-A-domain zinc finger protein capable of recruiting epigenetic machinery to deposit the H3K9me3 repressive histone modification, can activate expression from the normally silent maternal allele of SNORD116 in neurons derived from PWS induced pluripotent stem cells (iPSCs). However, ZNF274 has many other targets in the genome in addition to SNORD116. Depleting ZNF274 will surely affect the expression of other important genes and disrupt other pathways. Here, we used CRISPR/Cas9 to delete ZNF274 binding sites at the SNORD116 locus to determine whether activation of the maternal copy of SNORD116 could be achieved without altering ZNF274 protein levels. We obtained similar activation of gene expression from the normally silenced maternal allele in neurons derived from PWS iPSCs, compared with ZNF274 knockout, demonstrating that ZNF274 is directly involved in the repression of SNORD116. These results suggest that interfering with ZNF274 binding at the maternal SNORD116 locus is a potential therapeutic strategy for PWS.
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Affiliation(s)
- Maéva Langouët
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Dea Gorka
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clarisse Orniacki
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Clémence M Dupont-Thibert
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Michael S Chung
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Heather R Glatt-Deeley
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Noelle Germain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Leann J Crandall
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Christopher E Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA
| | - Marc Lalande
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Stormy J Chamberlain
- Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
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21
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Fafard-Couture É, Bergeron D, Couture S, Abou-Elela S, Scott MS. Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships. Genome Biol 2021; 22:172. [PMID: 34088344 PMCID: PMC8176728 DOI: 10.1186/s13059-021-02391-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. RESULTS We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver, and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level, and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. Fifty-nine percent of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. CONCLUSIONS Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.
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Affiliation(s)
- Étienne Fafard-Couture
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4 K8, Canada
| | - Danny Bergeron
- Département de biochimie et de génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4 K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1E 4 K8, 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 4 K8, 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 4 K8, Canada.
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22
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Epple R, Krüger D, Berulava T, Brehm G, Ninov M, Islam R, Köster S, Fischer A. The Coding and Small Non-coding Hippocampal Synaptic RNAome. Mol Neurobiol 2021; 58:2940-2953. [PMID: 33569760 PMCID: PMC8128755 DOI: 10.1007/s12035-021-02296-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022]
Abstract
Neurons are highly compartmentalized cells that depend on local protein synthesis. Messenger RNAs (mRNAs) have thus been detected in neuronal dendrites, and more recently in the pre- and postsynaptic compartments as well. Other RNA species such as microRNAs have also been described at synapses where they are believed to control mRNA availability for local translation. A combined dataset analyzing the synaptic coding and non-coding RNAome via next-generation sequencing approaches is, however, still lacking. Here, we isolate synaptosomes from the hippocampus of young wild-type mice and provide the coding and non-coding synaptic RNAome. These data are complemented by a novel approach for analyzing the synaptic RNAome from primary hippocampal neurons grown in microfluidic chambers. Our data show that synaptic microRNAs control almost the entire synaptic mRNAome, and we identified several hub microRNAs. By combining the in vivo synaptosomal data with our novel microfluidic chamber system, our findings also support the hypothesis that part of the synaptic microRNAome may be supplied to neurons via astrocytes. Moreover, the microfluidic system is suitable for studying the dynamics of the synaptic RNAome in response to stimulation. In conclusion, our data provide a valuable resource and point to several important targets for further research.
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Affiliation(s)
- Robert Epple
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Dennis Krüger
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
- Bioinformatics Unit, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Tea Berulava
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Gerrit Brehm
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Momchil Ninov
- Department of Neurobiology, Max-Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Rezaul Islam
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Goettingen, Goettingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Andre Fischer
- Department of Systems Medicine and Epigenetics, German Center for Neurodegenerative Diseases (DZNE), Von Siebold Str. 3a, 37075, Goettingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany.
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany.
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23
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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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24
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Tauber M, Hoybye C. Endocrine disorders in Prader-Willi syndrome: a model to understand and treat hypothalamic dysfunction. Lancet Diabetes Endocrinol 2021; 9:235-246. [PMID: 33647242 DOI: 10.1016/s2213-8587(21)00002-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022]
Abstract
Prader-Willi syndrome is a rare genetic neurodevelopmental disorder resulting from the loss of expression of maternally imprinted genes located in the paternal chromosomal region, 15q11-13. Impaired hypothalamic development and function is the cause of most of the phenotypes comprising the developmental trajectory of Prader-Willi syndrome: from anorexia at birth to excessive weight gain preceding hyperphagia, and early severe obesity with hormonal deficiencies, behavioural problems, and dysautonomia. Growth hormone deficiency, hypogonadism, hypothyroidism, premature adrenarche, corticotropin deficiency, precocious puberty, and glucose metabolism disorders are the main endocrine dysfunctions observed. Additionally, as a result of hypothalamic dysfunction, oxytocin and ghrelin systems are impaired in most patients. Standard pituitary and gonadal hormone replacement therapies are required. In this Review, we discuss Prader-Willi syndrome as a model of hypothalamic dysfunction, and provide a comprehensive description of the accumulated knowledge on genetics, pathophysiology, and treatment approaches of this rare disorder.
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Affiliation(s)
- Maithé Tauber
- Centre de Référence du Syndrome de Prader-Willi, Hôpital des Enfants, Toulouse, France; Axe Pédiatrique du CIC 9302/INSERM, Hôpital des Enfants, Toulouse, France; Institut Toulousain des Maladies Infectieuses et Inflammatoires, INSERM UMR1291, CNRS UMR5051, Université Toulouse III, Toulouse, France, France; International Prader-Willi Syndrome Organisation, Cambridge, UK.
| | - Charlotte Hoybye
- International Prader-Willi Syndrome Organisation, Cambridge, UK; Department of Endocrinology, Karolinska University Hospital and Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
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25
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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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26
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Salles J, Lacassagne E, Eddiry S, Franchitto N, Salles JP, Tauber M. What can we learn from PWS and SNORD116 genes about the pathophysiology of addictive disorders? Mol Psychiatry 2021; 26:51-59. [PMID: 33082508 DOI: 10.1038/s41380-020-00917-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/16/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
Addictive disorders have been much investigated and many studies have underlined the role of environmental factors such as social interaction in the vulnerability to and maintenance of addictive behaviors. Research on addiction pathophysiology now suggests that certain behavioral disorders are addictive, one example being food addiction. Yet, despite the growing body of knowledge on addiction, it is still unknown why only some of the individuals exposed to a drug become addicted to it. This observation has prompted the consideration of genetic heritage, neurodevelopmental trajectories, and gene-environment interactions in addiction vulnerability. Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder in which children become addicted to food and show early social impairment. PWS is caused by the deficiency of imprinted genes located on the 15q11-q13 chromosome. Among them, the SNORD116 gene was identified as the minimal gene responsible for the PWS phenotype. Several studies have also indicated the role of the Snord116 gene in animal and cellular models to explain PWS pathophysiology and phenotype (including social impairment and food addiction). We thus present here the evidence suggesting the potential involvement of the SNORD116 gene in addictive disorders.
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Affiliation(s)
- Juliette Salles
- Université de Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Service de psychiatrie et psychologie, psychiatrie Toulouse, F-31000, Toulouse, France.,Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Institut des Handicaps Neurologiques, Psychiatriques et Sensoriels, F-31000, Toulouse, France
| | - Emmanuelle Lacassagne
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Sanaa Eddiry
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Nicolas Franchitto
- Université de Toulouse III, F-31000, Toulouse, France.,CHU de Toulouse, Service d'addictologie clinique, urgences réanimation médecine, F-31000, Toulouse, France
| | - Jean-Pierre Salles
- Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France
| | - Maithé Tauber
- Université de Toulouse III, F-31000, Toulouse, France. .,Inserm Unité 1043, CNRS 5828, Université Paul Sabatier, Toulouse III, F-31000, Toulouse, France. .,CHU de Toulouse, Institut des Handicaps Neurologiques, Psychiatriques et Sensoriels, F-31000, Toulouse, France. .,CHU de Toulouse, Centre de référence du Syndrome de Prader-Willi et autres syndromes avec troubles du comportement alimentaire, Unité d'endocrinologie, obésités, maladies osseuses, génétique et gynécologie médicale, F-31000, Toulouse, France.
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27
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Zhu Y, Wang S, Xi X, Zhang M, Liu X, Tang W, Cai P, Xing S, Bao P, Jin Y, Zhao W, Chen Y, Zhao H, Jia X, Lu S, Lu Y, Chen L, Yin J, Lu ZJ. Integrative analysis of long extracellular RNAs reveals a detection panel of noncoding RNAs for liver cancer. Theranostics 2021; 11:181-193. [PMID: 33391469 PMCID: PMC7681086 DOI: 10.7150/thno.48206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/06/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Long extracellular RNAs (exRNAs) in plasma can be profiled by new sequencing technologies, even with low abundance. However, cancer-related exRNAs and their variations remain understudied. Methods: We investigated different variations (i.e. differential expression, alternative splicing, alternative polyadenylation, and differential editing) in diverse long exRNA species (e.g. long noncoding RNAs and circular RNAs) using 79 plasma exosomal RNA-seq (exoRNA-seq) datasets of multiple cancer types. We then integrated 53 exoRNA-seq datasets and 65 self-profiled cell-free RNA-seq (cfRNA-seq) datasets to identify recurrent variations in liver cancer patients. We further combined TCGA tissue RNA-seq datasets and validated biomarker candidates by RT-qPCR in an individual cohort of more than 100 plasma samples. Finally, we used machine learning models to identify a signature of 3 noncoding RNAs for the detection of liver cancer. Results: We found that different types of RNA variations identified from exoRNA-seq data were enriched in pathways related to tumorigenesis and metastasis, immune, and metabolism, suggesting that cancer signals can be detected from long exRNAs. Subsequently, we identified more than 100 recurrent variations in plasma from liver cancer patients by integrating exoRNA-seq and cfRNA-seq datasets. From these datasets, 5 significantly up-regulated long exRNAs were confirmed by TCGA data and validated by RT-qPCR in an independent cohort. When using machine learning models to combine two of these validated circular and structured RNAs (SNORD3B-1, circ-0080695) with a miRNA (miR-122) as a panel to classify liver cancer patients from healthy donors, the average AUROC of the cross-validation was 89.4%. The selected 3-RNA panel successfully detected 79.2% AFP-negative samples and 77.1% early-stage liver cancer samples in the testing and validation sets. Conclusions: Our study revealed that different types of RNA variations related to cancer can be detected in plasma and identified a 3-RNA detection panel for liver cancer, especially for AFP-negative and early-stage patients.
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Affiliation(s)
- Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Department of Maternal, Child and Adolescent Health, School of Public Health, Anhui Medical University, MOE Key Laboratory of Population Health Across Life Cycle, NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Provincial Key Laboratory of Population Health and Aristogenics, No 81 Meishan Road, Hefei 230032, Anhui, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaochen Xi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Minfeng Zhang
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai 200433, China
| | - Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weina Tang
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Peng Cai
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yunfan Jin
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihao Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinghui Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Huanan Zhao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Shanshan Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Yinying Lu
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
| | - Lei Chen
- International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military medical University, Shanghai 200438, China
- National Center for Liver Cancer, Shanghai 201805, China
| | - Jianhua Yin
- Department of Epidemiology, Faculty of Navy Medicine, Navy Medical University, Shanghai 200433, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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28
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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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29
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Qian X, Xu C, Wu B, Tang H, Zhao P, Qi Z. SNORD126 Promotes Hepatitis C Virus Infection by Upregulating Claudin-1 via Activation of PI3K-AKT Signaling Pathway. Front Microbiol 2020; 11:565590. [PMID: 33042070 PMCID: PMC7522514 DOI: 10.3389/fmicb.2020.565590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) infection involves a variety of viral and host factors, some of which promote the infection process. A small nucleolar RNA, C/D box 126 (SNORD126), was previously shown to be associated with hepatocellular carcinoma (HCC). However, the role of SNORD126 in HCV infection, which is one of the primary reasons for HCC development, has not been elucidated. In the present study, using small nucleolar RNA profiling, we observed that SNORD126 was significantly downregulated during HCV infection in both Huh7 and Huh7.5.1 cells. In addition, overexpression of SNORD126 enhanced HCV entry into host cells, whereas SNORD126 knockdown showed the opposite effect, suggesting that SNORD126 promotes HCV infection, especially through viral entry. Further functional analysis revealed that SNORD126 could enhance the expression level of claudin-1 (CLDN1), a key HCV entry factor, by increasing the levels of phosphorylated AKT. Additionally, the function of SNORD126 in HCV infection was associated with ribonucleoprotein (RNP) complexes. In summary, our findings demonstrate that oncogenic SNORD126 levels are decreased during HCV infection probably due to the host defense reaction, and SNORD126 may be important to promote viral entry by increasing CLDN1 expression through activation of the PI3K-AKT pathway, the mechanism of which is partly associated with SNORD126-mediated snoRNA RNP (snoRNP) function. Our work here provides initial evidence that endogenous snoRNA takes part in HCV infection and shows potential as a diagnostic or antiviral agent.
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Affiliation(s)
- Xijing Qian
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Chen Xu
- Spine Center, Department of Orthopedics, Changzheng Hospital Affiliated to Second Military Medical University, Shanghai, China
| | - Bingan Wu
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Hailin Tang
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai, China
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30
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The RDoC approach for translational psychiatry: Could a genetic disorder with psychiatric symptoms help fill the matrix? the example of Prader-Willi syndrome. Transl Psychiatry 2020; 10:274. [PMID: 32772048 PMCID: PMC7415132 DOI: 10.1038/s41398-020-00964-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022] Open
Abstract
The Research Domain Criteria project (RDoc) proposes a new classification system based on information from several fields in order to encourage translational perspectives. Nevertheless, integrating genetic markers into this classification has remained difficult because of the lack of powerful associations between targeted genes and RDoC domains. We hypothesized that genetic diseases with psychiatric manifestations would be good models for RDoC gene investigations and would thereby extend the translational approach to involve targeted gene pathways. To explore this possibility, we reviewed the current knowledge on Prader-Willi syndrome, a genetic disorder caused by the absence of expression of some of the genes of the chromosome 15q11-13 region inherited from the father. Indeed, we found that the associations between genes of the PW locus and the modification identified in the relevant behavioral, physiological, and brain imaging studies followed the structure of the RDoC matrix and its six domains (positive valence, negative valence, social processing, cognitive systems, arousal/regulatory systems, and sensorimotor systems).
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Velázquez-Flores MÁ, Rodríguez-Corona JM, López-Aguilar JE, Siordia-Reyes G, Ramírez-Reyes G, Sánchez-Rodríguez G, Ruiz Esparza-Garrido R. Noncoding RNAs as potential biomarkers for DIPG diagnosis and prognosis: XIST and XIST-210 involvement. Clin Transl Oncol 2020; 23:501-513. [PMID: 32661825 DOI: 10.1007/s12094-020-02443-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/23/2020] [Indexed: 01/22/2023]
Abstract
PURPOSE Diffuse intrinsic pontine gliomas (DIPGs) are the most fatal primary brainstem tumors in pediatric patients. The identification of new molecular features, mediating their formation and progression, as non-coding RNAs (ncRNAs), would be of great importance for the development of effective treatments. METHODS We analyzed the DIPGs transcriptome with the HTA2.0 array and it was compared with pediatric non-brainstem astrocytoma expression profiles (GSE72269). RESULTS More than 50% of the differentially expressed transcripts were ncRNAs and based on this, we proposed a DIPGs ncRNA signature. LncRNAs XIST and XIST-210, and the HBII-52 and HBII-85 snoRNA clusters were markedly downregulated in DIPGs. qPCR assays demonstrated XIST downregulation in all non-brainstem astrocytomas, in a gender, age, and brain location-independent manner, as well as in DIPGs affecting boys; however, DIPGs affecting girls showed both downregulation and upregulation of XIST. Girls' with longer survival positively correlated with XIST expression. CONCLUSIONS The involvement of ncRNAs in DIPGs is imminent and their expression profile is useful to differentiate them from non-neoplastic tissues and non-brain stem astrocytomas, which suggests their potential use as DIPG biomarkers. In fact, XIST and XIST-210 are potential DIPG prognostic biomarkers.
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Affiliation(s)
- M Á Velázquez-Flores
- Non-coding RNAs Laboratory, Medical Research Unit in Human Genetics, Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS), 06720, Mexico City, CDMX, Mexico
| | - J M Rodríguez-Corona
- Technological Institute of Ciudad Victoria, National Technological Institute of Mexico, 87010, Ciudad Victoria, Tamaulipas, Mexico
| | - J E López-Aguilar
- Medical Chief of the Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS), 06720, Mexico City, CDMX, Mexico
| | - G Siordia-Reyes
- Pathology Department, Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS), 06720, Mexico City, CDMX, Mexico
| | - G Ramírez-Reyes
- Neurosurgery Department, Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS), 06720, Mexico City, CDMX, Mexico
| | - G Sánchez-Rodríguez
- Neurosurgery Department, Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS), 06720, Mexico City, CDMX, Mexico
| | - R Ruiz Esparza-Garrido
- Catedrática CONACyT, Non-coding RNAs Laboratory, Medical Research Unit in Human Genetics, Children's Hospital "Dr. Silvestre Frenk Freund", National Medical Center XXI Century, Mexican Institute of Social Security (Instituto Mexicano del Seguro Social, IMSS) 06720 Mexico City CDMX Mexico, Av. Cuauhtémoc 330, Doctores, 06720, Mexico City, CDMX, Mexico.
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Bouchard-Bourelle P, Desjardins-Henri C, Mathurin-St-Pierre D, Deschamps-Francoeur G, Fafard-Couture É, Garant JM, Elela SA, Scott MS. snoDB: an interactive database of human snoRNA sequences, abundance and interactions. Nucleic Acids Res 2020; 48:D220-D225. [PMID: 31598696 PMCID: PMC6943035 DOI: 10.1093/nar/gkz884] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are an abundant type of non-coding RNA with conserved functions in all known eukaryotes. Classified into two main families, the box C/D and H/ACA snoRNAs, they enact their most well characterized role of guiding site specific modifications in ribosomal RNA, through the formation of specific ribonucleoprotein complexes, with fundamental implications in ribosome biogenesis. However, it is becoming increasingly clear that the landscape of snoRNA cellular functionality is much broader than it once seemed with novel members, non-uniform expression patterns, new and diverse targets as well as several emerging non-canonical functions ranging from the modulation of alternative splicing to the regulation of chromatin architecture. In order to facilitate the further characterization of human snoRNAs in a holistic manner, we introduce an online interactive database tool: snoDB. Its purpose is to consolidate information on human snoRNAs from different sources such as sequence databases, target information, both canonical and non-canonical from the literature and from high-throughput RNA-RNA interaction datasets, as well as high-throughput sequencing data that can be visualized interactively.
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Affiliation(s)
- Philia Bouchard-Bourelle
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Clément Desjardins-Henri
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Darren Mathurin-St-Pierre
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Gabrielle Deschamps-Francoeur
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Étienne Fafard-Couture
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Jean-Michel Garant
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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34
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He JY, Liu X, Qi ZH, Wang Q, Lu WQ, Zhang QT, He SY, Wang ZD. Small Nucleolar RNA, C/D Box 16 (SNORD16) Acts as a Potential Prognostic Biomarker in Colon Cancer. Dose Response 2020; 18:1559325820917829. [PMID: 32704240 PMCID: PMC7359415 DOI: 10.1177/1559325820917829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/07/2020] [Indexed: 12/15/2022] Open
Abstract
Colon cancer (CC) is considered one of the most common and lethal malignancies occurring both in male and female. Its widespread prevalence demonstrates the need for novel diagnostic and prognostic biomarkers for CC. Emerging evidence has shown that small nucleolar RNAs play critical roles in tumor development. In this study, we investigated the expression profile and functions of SNORD16 in CC. Our data showed that SNORD16, rather than its host gene (RPL4), was upregulated in CC cell lines. Compared to matched adjacent normal tissues, CC tissues showed higher SNORD16 expression levels, and no correlation was found between SNORD16 and RPL4. Patients with high SNORD16 expression levels had a worse prognosis, and multivariate analysis showed the high SNORD16 expression was an independent prognostic factor for CC. In vitro gain- and loss-of-function studies revealed that SNORD16 can promote cell growth, proliferation, migration, and invasion of CC cells by inhibiting apoptosis. These results suggested that SNORD16 has an oncogenic role in CC and might be a novel diagnostic and prognostic biomarker for CC.
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Affiliation(s)
- Jun-Yan He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, China.,Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xin Liu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Zhen-Hua Qi
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qi Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Wen-Qing Lu
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Qing-Tong Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Shu-Ya He
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, China
| | - Zhi-Dong Wang
- Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China.,School of Public Health, University of South China, Hengyang, China
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35
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Bratkovič T, Božič J, Rogelj B. Functional diversity of small nucleolar RNAs. Nucleic Acids Res 2020; 48:1627-1651. [PMID: 31828325 PMCID: PMC7038934 DOI: 10.1093/nar/gkz1140] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/17/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) are short non-protein-coding RNAs with a long-recognized role in tuning ribosomal and spliceosomal function by guiding ribose methylation and pseudouridylation at targeted nucleotide residues of ribosomal and small nuclear RNAs, respectively. SnoRNAs are increasingly being implicated in regulation of new types of post-transcriptional processes, for example rRNA acetylation, modulation of splicing patterns, control of mRNA abundance and translational efficiency, or they themselves are processed to shorter stable RNA species that seem to be the principal or alternative bioactive isoform. Intriguingly, some display unusual cellular localization under exogenous stimuli, or tissue-specific distribution. Here, we discuss the new and unforeseen roles attributed to snoRNAs, focusing on the presumed mechanisms of action. Furthermore, we review the experimental approaches to study snoRNA function, including high resolution RNA:protein and RNA:RNA interaction mapping, techniques for analyzing modifications on targeted RNAs, and cellular and animal models used in snoRNA biology research.
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Affiliation(s)
- Tomaž Bratkovič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia
| | - Janja Božič
- Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia
| | - Boris Rogelj
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva cesta 7, SI1000 Ljubljana, Slovenia.,Jozef Stefan Institute, Department of Biotechnology, Jamova cesta 39, SI1000 Ljubljana, Slovenia.,Biomedical Research Institute BRIS, Puhova ulica 10, SI1000 Ljubljana, Slovenia.,University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, SI1000 Ljubljana, Slovenia
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Salminen I, Read S, Hurd P, Crespi B. Does SNORD116 mediate aspects of psychosis in Prader-Willi syndrome? Evidence from a non-clinical population. Psychiatry Res 2020; 286:112858. [PMID: 32065983 DOI: 10.1016/j.psychres.2020.112858] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022]
Abstract
The paternally expressed gene SNORD116 encodes a set of short nucleolar RNAs that affect the expression of hundreds of other genes via epigenetic interactions. Lack of expression for SNORD116 has been implicated in major phenotypes of Prader-Willi Syndrome (PWS). Rates of psychosis and autism spectrum disorders are greatly increased in PWS, but the genetic and epigenetic causes of these increases remain unknown. We genotyped a large population of typical individuals for five SNPs within SNORD116 and phenotyped them for variation in schizotypal and autism spectrum traits. SNORD116 SNP and haplotype variation mediated variation exclusively in the Schizotypal Personality Questionnaire - Ideas of Reference subscale, which reflects variation in aspects of paranoia. The effect was restricted to females. SNORD116 represents, in addition to UBE3A and NDN-MAGEL2, a third, independent locus in the 15q11-q13 imprinted region that preferentially or exclusively affects levels of paranoia. This convergent pattern may reflect a common neural pathway affected by multiple genes, or an effect of interactions between the imprinted loci.
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Affiliation(s)
- Iiro Salminen
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Silven Read
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pete Hurd
- Department of Psychology and Centre for Neuroscience, University of Alberta, Edmonton, Canada
| | - Bernard Crespi
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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Shuwen H, Xi Y, Quan Q, Yin J, Miao D. Can small nucleolar RNA be a novel molecular target for hepatocellular carcinoma? Gene 2020; 733:144384. [PMID: 31978508 DOI: 10.1016/j.gene.2020.144384] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Globally, hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death. Recently, many studies have demonstrated that small nucleolar RNA (snoRNA) was closely related to HCC. OBJECTIVE To explore whether snoRNA can be used as a molecular target for HCC. METHODS The PubMed, Embase, and Cochrane databases were searched for the published literatures related to snoRNA and HCC until August 12, 2019. After identification, screening, and verification, this study finally included 26 studies correlating small nucleolar RNA host gene (SNHG) and HCC, and 8 studies correlating snoRNA and HCC. Based on the collation of the relevant literature, the correlation network diagram between snoRNAs and HCC was constructed. RESULTS The SNHGs, such as SNHG1, SNHG6, SNHG16, and SNHG20 can play varied roles in HCC through different regulatory mechanisms. These SNHGs can promote and inhibit tumorigenesis. SNORD76 can promote the proliferation of tumor tissues and cells in vitro through different pathways. SnoU2_19 and SNORD76 can function through the same pathway. SNHG3, SNHG20, SNHG6, SNORD76, and snoRA47 can modulate epithelial-mesenchymal transition (EMT) to regulate the development of HCC cell or tissue. SNHG16, SNORD76, and SnoU2_19 can regulate the development of HCC through Wnt/β-catenin signaling pathway. CONCLUSION snoRNA can regulate the occurrence of HCC by modulating multiple molecular signaling pathways. Hence, snoRNA can be a potential molecular target for HCC.
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Affiliation(s)
- Han Shuwen
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops HuZhou University, 198 Hongqi Rd, Huzhou, Zhejiang, PR China
| | - Yang Xi
- Department of Intervention and Radiotherapy, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Qi Quan
- Department of Oncology, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Jin Yin
- Department of Clinical Laboratory, Huzhou Central Hospital, No. 198 Hongqi Road, Huzhou, Zhejiang Province 313000, PR China
| | - Da Miao
- Department of Nursing, Huzhou Third Municipal Hospital, Huzhou, Zhejiang Province, PR China.
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Yoshino Y, Dwivedi Y. Non-Coding RNAs in Psychiatric Disorders and Suicidal Behavior. Front Psychiatry 2020; 11:543893. [PMID: 33101077 PMCID: PMC7522197 DOI: 10.3389/fpsyt.2020.543893] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/14/2020] [Indexed: 12/18/2022] Open
Abstract
It is well known that only a small proportion of the human genome code for proteins; the rest belong to the family of RNAs that do not code for protein and are known as non-coding RNAs (ncRNAs). ncRNAs are further divided into two subclasses based on size: 1) long non-coding RNAs (lncRNAs; >200 nucleotides) and 2) small RNAs (<200 nucleotides). Small RNAs contain various family members that include microRNAs (miRNAs), small interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and small nuclear RNAs (snRNAs). The roles of ncRNAs, especially lncRNAs and miRNAs, are well documented in brain development, homeostasis, stress responses, and neural plasticity. It has also been reported that ncRNAs can influence the development of psychiatric disorders including schizophrenia, major depressive disorder, and bipolar disorder. More recently, their roles are being investigated in suicidal behavior. In this article, we have comprehensively reviewed the findings of lncRNA and miRNA expression changes and their functions in various psychiatric disorders including suicidal behavior. We primarily focused on studies that have been done in postmortem human brain. In addition, we have briefly reviewed the role of other small RNAs (e.g. piwiRNA, siRNA, snRNA, and snoRNAs) and their expression changes in psychiatric illnesses.
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Affiliation(s)
- Yuta Yoshino
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, United States
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39
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Lefterov I, Wolfe CM, Fitz NF, Nam KN, Letronne F, Biedrzycki RJ, Kofler J, Han X, Wang J, Schug J, Koldamova R. APOE2 orchestrated differences in transcriptomic and lipidomic profiles of postmortem AD brain. Alzheimers Res Ther 2019; 11:113. [PMID: 31888770 PMCID: PMC6937981 DOI: 10.1186/s13195-019-0558-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The application of advanced sequencing technologies and improved mass-spectrometry platforms revealed significant changes in gene expression and lipids in Alzheimer's disease (AD) brain. The results so far have prompted further research using "multi-omics" approaches. These approaches become particularly relevant, considering the inheritance of APOEε4 allele as a major genetic risk factor of AD, disease protective effect of APOEε2 allele, and a major role of APOE in brain lipid metabolism. METHODS Postmortem brain samples from inferior parietal lobule genotyped as APOEε2/c (APOEε2/carriers), APOEε3/3, and APOEε4/c (APOEε4/carriers), age- and gender-matched, were used to reveal APOE allele-associated changes in transcriptomes and lipidomes. Differential gene expression and co-expression network analyses were applied to identify up- and downregulated Gene Ontology (GO) terms and pathways for correlation to lipidomics data. RESULTS Significantly affected GO terms and pathways were determined based on the comparisons of APOEε2/c datasets to those of APOEε3/3 and APOEε4/c brain samples. The analysis of lists of genes in highly correlated network modules and of those differentially expressed demonstrated significant enrichment in GO terms associated with genes involved in intracellular proteasomal and lysosomal degradation of proteins, protein aggregates and organelles, ER stress, and response to unfolded protein, as well as mitochondrial function, electron transport, and ATP synthesis. Small nucleolar RNA coding units important for posttranscriptional modification of mRNA and therefore translation and protein synthesis were upregulated in APOEε2/c brain samples compared to both APOEε3/3 and APOEε4/c. The analysis of lipidomics datasets revealed significant changes in ten major lipid classes (exclusively a decrease in APOEε4/c samples), most notably non-bilayer-forming phosphatidylethanolamine and phosphatidic acid, as well as mitochondrial membrane-forming lipids. CONCLUSIONS The results of this study, despite the advanced stage of AD, point to the significant differences in postmortem brain transcriptomes and lipidomes, suggesting APOE allele associated differences in pathogenic mechanisms. Correlations within and between lipidomes and transcriptomes indicate coordinated effects of changes in the proteasomal system and autophagy-canonical and selective, facilitating intracellular degradation, protein entry into ER, response to ER stress, nucleolar modifications of mRNA, and likely myelination in APOEε2/c brains. Additional research and a better knowledge of the molecular mechanisms of proteostasis in the early stages of AD are required to develop more effective diagnostic approaches and eventually efficient therapeutic strategies.
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Affiliation(s)
- Iliya Lefterov
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
| | - Cody M Wolfe
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Nicholas F Fitz
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Kyong Nyon Nam
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Florent Letronne
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Richard J Biedrzycki
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA
| | - Julia Kofler
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Xianlin Han
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jianing Wang
- Department of Medicine & Biochemistry, Barshop Institute for Longevity and Aging Studies, UT Health-San Antonio, San Antonio, TX, 78229, USA
| | - Jonathan Schug
- Department of Genetics, Functional Genomics Core, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Radosveta Koldamova
- Department of Environmental and Occupational Health, University of Pittsburgh, 130 De Soto Str., Pittsburgh, PA, 15261, USA.
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40
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Hebras J, Krogh N, Marty V, Nielsen H, Cavaillé J. Developmental changes of rRNA ribose methylations in the mouse. RNA Biol 2019; 17:150-164. [PMID: 31566069 DOI: 10.1080/15476286.2019.1670598] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns in mouse adult tissues and during development. In contrast to previous reports based on studies of human cancer cell lines, almost all methylation sites were close to fully methylated in adult tissues. A subset of sites was differentially modified in developing tissues compared to their adult counterparts and showed clear developmental dynamics. This provides the first evidence for ribosome heterogeneity at the level of rRNA modifications during mouse development. In a prominent example, the expression levels of SNORD78 during development appeared to be regulated by alternative splicing of the Gas5 host-gene and to correlate with the methylation level of its target site at LSU-G4593. The results are discussed in the context of the specialized ribosome hypothesis.
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Affiliation(s)
- Jade Hebras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Virginie Marty
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jérôme Cavaillé
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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Viaene AN, Zhang B, Martinez-Lage M, Xiang C, Tosi U, Thawani JP, Gungor B, Zhu Y, Roccograndi L, Zhang L, Bailey RL, Storm PB, O’Rourke DM, Resnick AC, Grady MS, Dahmane N. Transcriptome signatures associated with meningioma progression. Acta Neuropathol Commun 2019; 7:67. [PMID: 31039818 PMCID: PMC6489307 DOI: 10.1186/s40478-019-0690-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022] Open
Abstract
Meningiomas are the most common primary brain tumor of adults. The majority are benign (WHO grade I), with a mostly indolent course; 20% of them (WHO grade II and III) are, however, considered aggressive and require a more complex management. WHO grade II and III tumors are heterogeneous and, in some cases, can develop from a prior lower grade meningioma, although most arise de novo. Mechanisms leading to progression or implicated in de novo grade II and III tumorigenesis are poorly understood. RNA-seq was used to profile the transcriptome of grade I, II, and III meningiomas and to identify genes that may be involved in progression. Bioinformatic analyses showed that grade I meningiomas that progress to a higher grade are molecularly different from those that do not. As such, we identify GREM2, a regulator of the BMP pathway, and the snoRNAs SNORA46 and SNORA48, as being significantly reduced in meningioma progression. Additionally, our study has identified several novel fusion transcripts that are differentially present in meningiomas, with grade I tumors that did not progress presenting more fusion transcripts than all other tumors. Interestingly, our study also points to a difference in the tumor immune microenvironment that correlates with histopathological grade.
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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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Stamm S, Lodmell JS. C/D box snoRNAs in viral infections: RNA viruses use old dogs for new tricks. Noncoding RNA Res 2019; 4:46-53. [PMID: 31193534 PMCID: PMC6533054 DOI: 10.1016/j.ncrna.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/27/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022] Open
Abstract
C/D box snoRNAs (SNORDs) are a highly expressed class of non-coding RNAs. Besides their well-established role in rRNA modification, C/D box snoRNAs form protein complexes devoid of fibrillarin and regulate pre-mRNA splicing and polyadenylation of numerous genes. There is an emerging body of evidence for functional interactions between RNA viruses and C/D box snoRNAs. The infectivity of some RNA viruses depends on enzymatically active fibrillarin, and many RNA viral proteins associate with nucleolin or nucleophosmin, suggesting that viruses benefit from their cytosolic accumulation. These interactions are likely reflected by morphological changes in the nucleolus, often leading to relocalization of nucleolar proteins and ncRNAs to the cytosol that are a characteristic feature of viral infections. Knock-down studies have also shown that RNA viruses need specific C/D box snoRNAs for optimal replication, suggesting that RNA viruses benefit from gene expression programs regulated by SNORDs, or that viruses have evolved “new” uses for these humble ncRNAs to advance their prospects during infection.
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Affiliation(s)
- Stefan Stamm
- University of Kentucky, Molecular and Cellular Biochemistry, 741 South Limestone, Lexington, KY 40536, USA
| | - J Stephen Lodmell
- Division of Biological Sciences and Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, MT, USA
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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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46
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Costa RA, Ferreira IR, Cintra HA, Gomes LHF, Guida LDC. Genotype-Phenotype Relationships and Endocrine Findings in Prader-Willi Syndrome. Front Endocrinol (Lausanne) 2019; 10:864. [PMID: 31920975 PMCID: PMC6923197 DOI: 10.3389/fendo.2019.00864] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Prader-Willi syndrome (PWS) is a complex imprinting disorder related to genomic errors that inactivate paternally-inherited genes on chromosome 15q11-q13 with severe implications on endocrine, cognitive and neurologic systems, metabolism, and behavior. The absence of expression of one or more genes at the PWS critical region contributes to different phenotypes. There are three molecular mechanisms of occurrence: paternal deletion of the 15q11-q13 region; maternal uniparental disomy 15; or imprinting defects. Although there is a clinical diagnostic consensus criteria, DNA methylation status must be confirmed through genetic testing. The endocrine system can be the most affected in PWS, and growth hormone replacement therapy provides improvement in growth, body composition, and behavioral and physical attributes. A key feature of the syndrome is the hypothalamic dysfunction that may be the basis of several endocrine symptoms. Clinical and molecular complexity in PWS enhances the importance of genetic diagnosis in therapeutic definition and genetic counseling. So far, no single gene mutation has been described to contribute to this genetic disorder or related to any exclusive symptoms. Here we proposed to review individually disrupted genes within the PWS critical region and their reported clinical phenotypes related to the syndrome. While genes such as MKRN3, MAGEL2, NDN, or SNORD115 do not address the full spectrum of PWS symptoms and are less likely to have causal implications in PWS major clinical signs, SNORD116 has emerged as a critical, and possibly, a determinant candidate in PWS, in the recent years. Besides that, the understanding of the biology of the PWS SNORD genes is fairly low at the present. These non-coding RNAs exhibit all the hallmarks of RNA methylation guides and can be incorporated into ribonucleoprotein complexes with possible hypothalamic and endocrine functions. Also, DNA conservation between SNORD sequences across placental mammals strongly suggests that they have a functional role as RNA entities on an evolutionary basis. The broad clinical spectrum observed in PWS and the absence of a clear genotype-phenotype specific correlation imply that the numerous genes involved in the syndrome have an additive deleterious effect on different phenotypes when deficiently expressed.
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Krogh N, Nielsen H. Sequencing-based methods for detection and quantitation of ribose methylations in RNA. Methods 2018; 156:5-15. [PMID: 30503826 DOI: 10.1016/j.ymeth.2018.11.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022] Open
Abstract
Ribose methylation is one of the most abundant RNA modifications and is found in all domains of life and all major classes of RNA (rRNA, tRNA, and mRNA). Ribose methylations are introduced by stand-alone enzymes or by generic enzymes guided to the target by small RNA guides. Recent years have seen the development of several sequencing-based methods for RNA modifications relying on different principles. In this review, we compare mapping and quantitation studies of ribose methylations from yeast and human culture cells. The emphasis is on ribosomal RNA for which the results can be compared to results from RNA fingerprinting and mass spectrometry. One sequencing approach is consistent with these methods and paints a conservative picture of rRNA modifications. Other approaches detect many more sites. Similar discrepancies are found in measurements of modification stoichiometry. The results are discussed in relation to the more challenging task of mapping ribose methylations in mRNA.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark.
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Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ. Autism spectrum disorder: insights into convergent mechanisms from transcriptomics. Nat Rev Genet 2018; 20:51-63. [DOI: 10.1038/s41576-018-0066-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Mertsch S, Schlicht K, Melkonyan H, Schlatt S, Thanos S. snRPN controls the ability of neurons to regenerate axons. Restor Neurol Neurosci 2018; 36:31-43. [PMID: 29439367 DOI: 10.3233/rnn-170780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Retinal ganglion cells (RGCs) of mammals lose the ability to regenerate injured axons during postnatal maturation, but little is known about the underlying molecular mechanisms. OBJECTIVE It remains of particular importance to understand the mechanisms of axonal regeneration to develop new therapeutic approaches for nerve injuries. METHODS Retinas from newborn to adult monkeys (Callithrix jacchus)1 were obtained immediately after death and cultured in vitro. Growths of axons were monitored using microscopy and time-lapse video cinematography. Immunohistochemistry, Western blotting, qRT-PCR, and genomics were performed to characterize molecules associated with axonal regeneration and growth. A genomic screen was performed by using retinal explants versus native and non-regenerative explants obtained from eye cadavers on the day of birth, and hybridizing the mRNA with cross-reacting cDNA on conventional human microarrays. Followed the genomic screen, siRNA experiments were conducted to identify the functional involvement of identified candidates. RESULTS Neuron-specific human ribonucleoprotein N (snRPN) was found to be a potential regulator of impaired axonal regeneration during neuronal maturation in these animals. In particular, up-regulation of snRPN was observed during retinal maturation, coinciding with a decline in regenerative ability. Axon regeneration was reactivated in snRPN-knockout retinal ex vivo explants of adult monkey. CONCLUSION These results suggest that coordinated snRPN-driven activities within the neuron-specific ribonucleoprotein complex regulate the regenerative ability of RGCs in primates, thereby highlighting a potential new role for snRPN within neurons and the possibility of novel postinjury therapies.
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Affiliation(s)
- Sonja Mertsch
- Institute of Experimental Ophthalmology and DFG-Excellence Center, Cells in Motion (CiM, area C.4), School of Medicine, University of Münster, Münster, Germany.,Department of Ophthalmology, Laboratory of Experimental Ophthalmology, University Clinic Duesseldorf, Duesseldorf, Germany
| | - Katrin Schlicht
- Institute of Experimental Ophthalmology and DFG-Excellence Center, Cells in Motion (CiM, area C.4), School of Medicine, University of Münster, Münster, Germany
| | - Harutyun Melkonyan
- Institute of Experimental Ophthalmology and DFG-Excellence Center, Cells in Motion (CiM, area C.4), School of Medicine, University of Münster, Münster, Germany
| | - Stefan Schlatt
- Institute of Regenerative Medicine (CeRA) and DFG-Excellence Center, Cells in Motion (CiM, area A.2), School of Medicine, University of Münster, Münster, Germany
| | - Solon Thanos
- Institute of Experimental Ophthalmology and DFG-Excellence Center, Cells in Motion (CiM, area C.4), School of Medicine, University of Münster, Münster, Germany
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Abstract
Small nucleolar RNAs (snoRNAs) are a family of conserved nuclear RNAs that function in the modification of small nuclear RNAs (snRNAs) or ribosomal RNAs (rRNAs), or participate in the processing of rRNAs during ribosome subunit maturation. Eukaryotic DNA transcription and RNA processing produce many long noncoding RNA (lncRNA) species. Although most lncRNAs are processed like typical mRNAs to be 5' capped and 3' polyadenylated, other types of lncRNAs are stabilized from primary Pol II transcripts by alternative mechanisms. One way to generate stable lncRNAs is to co-operate with snoRNA processing to produce snoRNA-ended lncRNAs (sno-lncRNAs) and 5' snoRNA-ended and 3'-polyadenylated lncRNAs (SPAs). Rather than silently accumulating in the nucleus, some sno-lncRNAs and SPAs are involved in the regulation of pre-rRNA transcription and alternative splicing of pre-mRNAs. Here we provide a mini-review to discuss the biogenesis and functions of these unusually processed lncRNAs.
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Affiliation(s)
- Yu-Hang Xing
- a State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai , China
| | - Ling-Ling Chen
- a State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai , China.,b School of Life Science and Technology , ShanghaiTech University , Shanghai , China
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