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

• Published in: Nature reviews. Molecular cell biology Vol. 24; no. 6; pp. 430 - 447
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.06.2023; Nature Publishing Group
• Subjects: 631/208/212/2019; 631/337/384/2568; accessible chromatin; Annotations; antisense rna; Biochemistry; Biomedical and Life Sciences; Cancer Research; Cell and Molecular Biology; Cell Biology; Cell differentiation; Cell Nucleus - genetics; Cell- och molekylärbiologi; Chromatin; Chromatin - genetics; Classification; Consensus Statement; Cytoplasm; Developmental Biology; Differentiation (biology); DNA-directed RNA polymerase; dosage compensation; elements; Enhancers; Gene expression; Genes; genome-wide analysis; Genomes; Introns; Isoforms; Life Sciences; messenger-rna; Modular structures; Nomenclatures; Non-coding RNA; Phase separation; regulation; Regulatory Sequences, Nucleic Acid; RNA polymerase; RNA Polymerase II - genetics; RNA, Long Noncoding - genetics; Stem Cells; transcriptional; transposable; xist rna
• ISSN: 1471-0072; 1471-0080; 1471-0080
• DOI: 10.1038/s41580-022-00566-8

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. This Consensus Statement addresses the definition, nomenclature and classification of long non-coding RNAs, and provides a shared viewpoint on their features and functions. The authors also discuss research challenges and provide recommendations to advance our understanding of long non-coding RNAs.