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Fellah S, Larrue R, Truchi M, Vassaux G, Mari B, Cauffiez C, Pottier N. Pervasive role of the long noncoding RNA DNM3OS in development and diseases. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1736. [PMID: 35491542 DOI: 10.1002/wrna.1736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/04/2022] [Accepted: 04/11/2022] [Indexed: 11/08/2022]
Abstract
Thousands of unique noncoding RNAs (ncRNAs) are expressed in human cells, some are tissue or cell type specific whereas others are considered as house-keeping molecules. Studies over the last decade have modified our perception of ncRNAs from transcriptional noise to functional regulatory transcripts that influence a variety of molecular processes such as chromatin remodeling, transcription, post-transcriptional modifications, or signal transduction. Consequently, aberrant expression of many ncRNAs plays a causative role in the initiation and progression of various diseases. Since the identification of its developmental role, the long ncRNA DNM3OS (Dynamin 3 Opposite Strand) has attracted attention of researchers in distinct fields including oncology, fibroproliferative diseases, or bone disorders. Mechanistic studies have in particular revealed the multifaceted nature of DNM3OS and its important pathogenic role in several human disorders. In this review, we summarize the current knowledge of DNM3OS functions in diseases, with an emphasis on its potential as a novel therapeutic target. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Sandy Fellah
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Romain Larrue
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Georges Vassaux
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Bernard Mari
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France
| | - Christelle Cauffiez
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
| | - Nicolas Pottier
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR-S 1277, Lille, France
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Davis P, Zarowiecki M, Arnaboldi V, Becerra A, Cain S, Chan J, Chen WJ, Cho J, da Veiga Beltrame E, Diamantakis S, Gao S, Grigoriadis D, Grove CA, Harris TW, Kishore R, Le T, Lee RYN, Luypaert M, Müller HM, Nakamura C, Nuin P, Paulini M, Quinton-Tulloch M, Raciti D, Rodgers FH, Russell M, Schindelman G, Singh A, Stickland T, Van Auken K, Wang Q, Williams G, Wright AJ, Yook K, Berriman M, Howe KL, Schedl T, Stein L, Sternberg PW. WormBase in 2022-data, processes, and tools for analyzing Caenorhabditis elegans. Genetics 2022; 220:6521733. [PMID: 35134929 PMCID: PMC8982018 DOI: 10.1093/genetics/iyac003] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/17/2021] [Indexed: 02/06/2023] Open
Abstract
WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.
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Affiliation(s)
- Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Magdalena Zarowiecki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Eduardo da Veiga Beltrame
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sibyl Gao
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Dionysis Grigoriadis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Todd W Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tuan Le
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Raymond Y N Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Hans-Michael Müller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Cecilia Nakamura
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Faye H Rodgers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Archana Singh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tim Stickland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Adam J Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
| | - Matt Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tim Schedl
- Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology, Pasadena, CA 91125, USA
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