What is a Long Non-Coding RNA?
Long non-coding (lnc) RNAs are defined as non-protein coding RNAs distinct from housekeeping RNAs such as tRNAs, rRNAs, and snRNAs, and independent from small RNAs with specific molecular processing machinery such as micro- or piwi-RNAs1.
The co-occurrence of massively parallel sequencing technology applied to RNA and the recognition that non-coding, functional RNA species may not be restricted to X-chromosome inactivation2 or to protein synthesis machinery, have revealed an RNA universe of remarkable diversity in plant and animal cells. Non-coding (nc) RNAs, those RNA molecules that are not templates for protein synthesis, make up a large portion of the total RNA in the cell suggesting a profound functional importance3. Genomes are extensively transcribed and give rise to thousands of long non-coding RNAs (lncRNAs), which are defined as RNAs longer than 200 nucleotides that are not translated into functional proteins. This broad definition encompasses a large and highly heterogeneous collection of transcripts that differ in their biogenesis and genomic origin4,5.
It is well documented that a growing number of lncRNAs have important cellular functions. The expression of a considerable number of lncRNAs is regulated and some have roles in different mechanisms of gene regulation. Several lncRNAs control the expression of nearby genes by affecting their transcription, and also affect other facets of chromatin biology, such as DNA replication or the response to DNA damage and repair. Other lncRNAs function away from their loci; their functions can be of a structural and/or regulatory nature and involve different stages of mRNA life, including splicing, turnover and translation, as well as signaling pathways. Consequently, lncRNAs affect several cellular functions that are of great physiological relevance, and alteration of their expression is inherent to numerous diseases. The specific expression patterns of these functional lncRNAs have the potential of being used as optimal disease biomarkers, and strategies are under development for their therapeutic targeting6.

Biogenesis and Cellular Fates of Long Non-Coding RNAs
Most lncRNA species are transcribed by Pol II. As such, many have 5′-end m7G caps and 3′-end poly(A) tails and are presumed to be transcribed and processed similarly to mRNAs. Importantly, distinct transcription, processing, export, and turnover of lncRNAs, which are closely linked with their cellular fates and functions.
Compared with mRNAs, a greater proportion of lncRNAs are localized in the nucleus8–10. Dissection of the global features of lncRNAs and mRNAs suggests that lncRNA genes are less evolutionarily conserved, contain fewer exons, and are less abundantly expressed. Early studies indicated that lncRNA genes likely contain fewer exons than mRNAs10–12. The recently developed RNA capture long seq enabled better annotation of the full length of lncRNAs, including their 5′ ends13,14, revealing little length difference with mRNAs, although lncRNAs contain fewer and longer exons. Single-cell sequencing found that some lncRNAs can be abundantly expressed in the human neocortex15.

Like proteins, the function of lncRNAs depends on their subcellular localization/fates. Many lncRNAs are recognized as important modulators for nuclear functions2,16, and exhibit distinct nuclear localization patterns (Fig. 3a-d). Others must be exported to the cytoplasm to carry out their regulatory roles (Fig. 3e). In this review, several well-characterized lncRNAs are classified into three groups depending on their subcellular localization to illustrate the association of lncRNA localization and function: those that are absolutely nuclear localized in cis (Fig. 3a-b), those that are mainly nuclear localized and function in trans (Fig. 3c-d), and those that largely localize and function in the cytoplasm (Fig. 3e). It is worth noting that a recent large-scale evaluation of the subcellular fates of lncRNAs in human cell lines using single-molecule RNA fluorescence in situ hybridization revealed that lncRNAs exhibited a wide range of subcellular localization patterns, including not only distinct patterns of nuclear localization but also nonspecific location in both the nucleus and cytoplasm17.

Overall, lncRNAs are spliced less efficiently than mRNAs10,14,19. They have weaker internal splicing signals and longer distances between the 3′ splice site and the branch point14,20, which correlate with augmented nuclear retention10,14,19 (Fig. 2d). Other factors, such as differential expression of certain splicing regulators, also contribute to the accumulation of lncRNAs in the nucleus. For example, in mouse embryonic stem cells (mESCs), the highly expressed splicing inhibitor peptidylprolyl isomerase E suppresses the splicing of a subset of lncRNAs, leading to significant nuclear accumulation of many lncRNAs in mESCs10 (Fig. 2e). Alternative polyadenylation signals within lncRNAs may also modulate their subcellular localization. For example, the CCAT1 lncRNA gene produces two isoforms: the long isoform (CCAT1-L) is nuclear and contains an internal polyadenylation site corresponding with the 3′ ends of the short isoform (CCAT1-S), which is cytoplasmic21. Additionally, to these general features of lncRNA transcription and processing, lncRNAs often contain embedded sequence motifs that can recruit certain nuclear factors, which promote the nuclear localization and function of the lncRNA (Fig. 2e). For example, the lncRNA maternally expressed gene 3 (MEG3) contains a 356-nucleotide nuclear retention element that associates with U1 snRNP, which in turn retains MEG3 in the nucleus22.
Simply put, lncRNAs are a large and diverse class of transcripts that affect gene regulation through a variety of mechanisms. Depending on their genomic origin, subcellular localization, or functional pathways, lncRNAs can be classified into different groups. Like proteins, lncRNAs must localize to specific subcellular compartments to execute their functions. The nuclear localization and fate of lncRNAs are coordinately regulated at multiple layers, from transcription and processing to nuclear export through multiple sequence motifs in cis and factors in trans. However, how the specific localization of lncRNAs is achieved and regulated and what rules lncRNAs follow to make them so remarkably different from mRNAs remain largely unknown. In addition, the nucleocytoplasmic export of cytoplasmic lncRNAs and their life cycle in the cytoplasm also require a thorough investigation. Nevertheless, understanding these features of lncRNAs will greatly expand our current knowledge of lncRNA biology and shed new light into the study of their cellular roles in depth18.
References
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- Xiang, J.-F. et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res 24, 513–531 (2014).
- Azam, S. et al. Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus. RNA Biology 16, 1001–1009 (2019).
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