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

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.

Fig. 1∣. Visible phenotypes of mutations in long non-coding RNA genes in mice.

The following long non-coding RNAs (lncRNAs) are listed in the figure underneath their associated phenotypes: Airn, antisense of IGF2R non-protein-coding RNA^,; Charme, chromatin architect of muscle expression; Chaserr, CHD2 adjacent, suppressive regulatory RNA; Fendrr, FOXF1 adjacent non-coding developmental regulatory RNA^,; Firre, functional intergenic repeating RNA element; Gaplinc gastric adenocarcinoma predictive long intergenic non-coding RNA; H19, clone pH19 (ref. 439); Handsdown, downstream of the protein-coding gene Hand2 (ref. 440) Kcnq1ot1, Kcnq1 overlapping antisense transcript 1 (ref. 441); linc-Brn1b, long intergenic non-coding RNA (lincRNA) downstream of the Bra1 protein-coding gene; linc-Epav, endogenous retrovirus-derived lncRNA positively regulates antiviral responses; lincRNA-Cox2, lincRNA downstream of the inflammation response gene Cox2 (ref. 443); lincRNA-Eps, lincRNA involved in erythroid prosurvival; lnc-Lsm3b, interferon-inducible non-coding splice variant of the U6 small nuclear RNA-associated Sm-like protein lsm3 gene; Maenli, master activator of engrailed1 in the limb; Mdgt, midget; Meg3, maternally expressed gene 3 (also known as Gtl2)^,; Norad, non-coding RNA activated by DNA damage; Peril, perinatal lethal long non-coding RNA; Pnky, pinky (also known as lnc-Pou3f2); Tug1, taurine upregulated gene 1 (refs. 165,166,449) Upperhand, lncRNA upstream of the Hand2 cardiomyocyte transcription factor locus; Xist, X-inactive-specific transcript. Figure courtesy of Daniel Andergassen and John Rinn.

Fig. 2 ∣. Roles of long non-coding RNAs in nuclear organization.

^a, 5’ small nucleolar RNA-capped and 3’-polyadenylated long non-coding (lncRNAs) (SPAs) and small nucleolar RNA-related lncRNAs (sno-lncRNAs) accumulate at their sites of transcription and interact with several splicing factors such as RNA-binding protein FOX-1 homologue 2 (RBFOX2), TAR DNA-binding protein 43 (TDP43) and heterogeneous nuclear ribonucleoprotein M (hnRNPM) to form a microscopically visible nuclear body that is involved in the regulation of alternative splicing. b, The lncRNA functional intergenic repeating RNA element (Firre) is transcribed from the mouse X chromosome and interacts with the nuclear matrix factor hnRNPU to tether chromosome X (chrX), chr2, chr9, chr15 and chr17 into a nuclear domain^,. c, The lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) is essential for the formation of paraspeckles. NEAT1 sequesters numerous paraspeckle proteins to form a highly organized core–shell (dark and light purple, respectively) spheroidal nuclear body. The middle region of NEAT1 is localized in the centre of paraspeckles, and the 3’-end and 5’-end regions are localized in the periphery. Different paraspeckle proteins are embedded by NEAT1 into the spheroidal structure in the core region (non-POU domain-containing octamer-binding protein (NONO), fused in sarcoma (FUS) and splicing factor, proline- and glutamine-rich (SFPQ)) or in the shell region (RNA-binding motif protein 14 (RBM14)). d, The lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is localized at the periphery of nuclear speckles^, and is involved in the regulation of pre-mRNA splicing^,. MALAT1 interacts with the U1 small nuclear RNA (U1 snRNA), whereas proteins such as SON DNA- and RNA-binding protein and splicing component 35 kDa (SC35) are localized at the centre of nuclear speckles. e, The lncRNA CHD2 adjacent, suppressive regulatory RNA (Chaserr) forms a compartment within a region of the mouse chromosome corresponding to a topologically associating domain that includes its own gene as well as the Chd2 gene (encoding chromodomain DNA helicase protein 2 (CHD2)). Chaserr limits in cis the expression of Chd2, which is important for proper regulation of many genes (not shown). f, The perinucleolar compartment contains the lncRNA pyrimidine-rich non-coding transcript (PNCTR), which sequesters pyrimidine tract-binding protein 1 (PTBP1) and thus suppresses PTPBP1-mediated pre-mRNA splicing elsewhere in the nucleoplasm. The size of nuclear bodies is indicated where relevant. Figure adapted from ref. , Springer Nature. Part e courtesy of Inna-Marie Strazhnik and Mitch Guttman.

Fig. 3 ∣. Modular structures of long non-coding RNAs.

a, Targeted RNA sequencing has revealed that human chromosome 21 (chr21) is pervasively transcribed into long non-coding RNAs (lncRNAs) and that lncRNA exons are almost universally (but not randomly) alternatively spliced to form diverse and complex isoforms. The circle indicates the fraction of non-coding exons across all chr21 transcripts that are alternatively or constitutively spliced. b, Modular structural domains in lncRNAs that fulfil a range of functions^-, including targeting DNA, such as in the case of auxin-regulated promoter loop (APOLO); binding other RNAs – for example, terminal differentiation-induced non-coding RNA (TINCR), potentially involving RNA-binding proteins such as Staufen 1; and recruitment of proteins – for example, pyrimidine-rich non-coding transcript (PNCTR) recruiting of pyrimidine tract-binding protein 1 (PTBP1) through special RNA motifs and X-inactive-specific transcript (XIST) recruiting split ends homologue (SPEN) and Polycomb repressive complex 2 (PRC2), perhaps in concert, which is the subject of active exploration and debate^,,,,,. Modular functional domains can be repeated within a lncRNA or in multiple different lncRNAs^,,,,,,-. Figure courtesy of Tim R. Mercer.