Long non-coding RNAs: definitions, functions, challenges and recommendations

Mattick, John S, Amaral, Paulo P, Carninci, Piero, Carpenter, Susan, Chang, Howard Y, Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel E, Fitzgerald, Katherine A, Gingeras, Thomas R, Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne B, Lee, Jeannie T, Mendell, Joshua T, Mercer, Timothy R, Moore, Kathryn J, Nakagawa, Shinichi, Rinn, John L, Spector, David L, Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy E, Wu, Mian (January 2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology. ISSN 1471-0072

Abstract

Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.

Item Type:	Paper
Subjects:	bioinformatics > genomics and proteomics > annotation bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes > RNA polymerase bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > enzymes bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > long non-coding RNA organs, tissues, organelles, cell types and functions > organelles, types and functions > nucleus organs, tissues, organelles, cell types and functions > organelles, types and functions organs, tissues, organelles, cell types and functions bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
CSHL Authors:	Gingeras, Thomas R. Spector, David L.
Communities:	CSHL labs > Gingeras lab CSHL labs > Spector lab CSHL Cancer Center Program CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL Cancer Center Program > Gene Regulation and Inheritance Program
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	3 January 2023
Date Deposited:	30 Jan 2023 16:16
Last Modified:	09 Feb 2024 15:30
PMCID:	PMC10213152
URI:	https://repository.cshl.edu/id/eprint/40804

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