While nonsense-mediated decay (NMD) pathway, and instead, TINCR-bound
While most early studies of lncRNAs focused on their functions in the chromatin regulation in the nucleus, an expanding body of work implicates roles for lncRNAs in the cytoplasm. Many cytoplasmic lncRNAs can affect cellular function and gene expression by utilizing different mechanisms to regulate mRNA stability, mRNA translation, and protein-protein interactions 77. Interestingly, several lncRNAs with nuclear function also exhibited separate mechanisms in the cytoplasm 77. LincRNA-p21 was initially described as being a downstream repressor of gene targets in the p53 response 78. The nuclear fraction of this transcript can binds and recruits transcriptional repressors and RNA-binding protein HnRNP K to hundreds of loci in trans. In the cytoplasm, LincRNA-p21 can associate with the polysome fraction, directly bind to at least two unique target mRNAs and decrease their translation 79.
Contrarily, lncRNAs can also increase target translation; a lncRNA transcribed antisense to Uchl1 can form a sense-antisense pair with UCHL1 mRNA and can enhance its translation 80. Surprisingly, this ability is dependent on only an overlapping 5′ sequence and an inverted SINEB2 element, and artificial transcripts can be engineered with this feature to enhance the translation of transgenes. Embedded retrotransposon repeats may play key roles in other mRNA-lncRNA pairs. sbsRNAs (STAU1-binding site RNAs) are cytoplasmic lncRNAs that form imperfect duplexes with Alu elements embedded in a subset of target mRNAs 81. This duplex is then bound by STAUFEN-1, which mediates their degradation via the nonsense-mediated-decay pathway. In this way, one lncRNA can regulate a number of target mRNAs 81. The lncRNA TINCR binds and destabilizes target mRNA transcripts through a non-Alu binding motif called the ‘TINCR-box’82. Intriguingly, while TINCR and its targets bind STAUFEN-1, targets are not destroyed via the nonsense-mediated decay (NMD) pathway, and instead, TINCR-bound targets are stabilized by the interaction.
LncRNAs are also been showed to regulate protein-protein interaction. A clear example comes from lnc-DC1. STAT3 transcription factor is sequestered in the cytosol in a dephosphorylated state, and translocates to the nucleus upon phosphorylation. In dendritic cells, the lnc-DC1 non-coding transcript binds STAT3 and effectively prevents its dephosphorylation by phosphatase SHP1 83. Therefore, in addition to posttranscriptional regulation of mRNAs, lncRNAs can block protein-protein interaction in the cytoplasm 83.
There are an increasing number of examples of lncRNAs serving as scaffolds in the cytoplasm for a variety of enzymatic activities. A high-throughput screening assay identified the lncRNA NRON as a cytoplasmic lncRNA that regulates the activation of NFAT 84. Phosphorylated NFAT is cytoplasmic, and upon dephosphorylation, it translocates into the nucleus to act as a transcription factor. Studies demonstrated that NRON exists in a cytoplasmic complex with NFAT, three of its kinases (casein kinase 1, glycogen synthase kinase 3, and dual specificity tyrosine phosphorylation regulated kinase), and the scaffold protein IQGAP1 (IQ motif containing GTPase activating protein) 85. NRON knockdown causes enhanced NFAT dephosphorylation and downstream target activation. HOTAIR can also serve as a molecular scaffold in the cytoplasm; cytoplasmic HOTAIR interacts with E3 ubiquitin ligases and enhances the ubiquitination and subsequent degradation of the target proteins 86. Interestingly, HOTAIR levels and target ubiquitination were increased dramatically in senescent cells, hinting that lncRNA subcellular localization and mechanism of action can be dynamically regulated by external cues.
A final emerging role for lncRNAs in the cytoplasm is serving as ‘sponges’ for microRNAs 87. Linc-RoR was originally discovered as a non-coding RNA that enhances reprogramming of fibroblasts into induced pluripotent stem cells (iPSCs) 88. Linc-RoR shares microRNA binding sites with core pluripotency transcription factors including Nanog, Sox2, and Oct4 88. High expression of this ‘sponge’ lncRNA allows for elevated expression of these factors and maintenance of the pluripotent state. Another example of sponge lncRNA is H19, a cytoplasmic lncRNA expressed from an imprinted locus with key roles in growth and embryonic development 89. A recent study demonstrated that H19 can be processed and serve as a reservoir for miR-675, an anti-growth microRNA 90. H19 additionally harbors binding sites for the let-7 family of microRNAs and can function as a sponge, allowing for the upregulation of let-7 targets 90.