Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

Abstract

BackgroundLong noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensive understanding of the extent to which lncRNAs bind ribosomes, we performed systematic RNA sequencing on ribosome-associated RNA pools obtained through ribosomal fractionation and compared the RNA content with nuclear and (non-ribosome bound) cytosolic RNA pools.ResultsThe RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1.ConclusionsMost studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes.

Epigenetic regulation in human melanoma: past and future

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“…4G). 67 Some lncRNAs influence the stability of protein complexes by interacting with RNA-binding domains of components of those complexes (Fig. 4I).…”

The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function

“…Perhaps a significant fraction of mRNA-like long intervening non-protein-coding RNAs are mRNAs after all, encoding peptides and short proteins. The question on how many of the non-protein-coding RNAs are associated with polysomes for productive translation is currently under debate (Ingolia et al 2011;Guttman et al 2013;Ingolia et al 2013;Ulitsky and Bartel 2013;van Heesch et al 2014). …”

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

“…Thousands of lncRNAs have been annotated in eukaryotic genomes (Derrien et al 2012;Ulitsky and Bartel 2013), many of which are preferentially located in the cytoplasm (van Heesch et al 2014), where they can engage in miRNA-mediated interactions with other transcripts. Both computational and experimental evidence support the extensive targeting of lncRNAs by miRNAs (Paraskevopoulou et al 2013).…”