Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

Abstract

Recent footprinting studies have made the surprising observation that long noncoding RNAs (lncRNAs) physically interact with ribosomes. However, these findings remain controversial, and the overall proportion of cytoplasmic lncRNAs involved is unknown. Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm. The majority of these (70%) have >50% of their cytoplasmic copies associated with polysomal fractions. These interactions are lost upon disruption of ribosomes by puromycin. Polysomal lncRNAs are distinguished by a number of 5 ′ mRNA-like features, including capping and 5 ′ UTR length. On the other hand, nonpolysomal "free cytoplasmic" lncRNAs have more conserved promoters and a wider range of expression across cell types. Exons of polysomal lncRNAs are depleted of endogenous retroviral insertions, suggesting a role for repetitive elements in lncRNA localization. Finally, we show that blocking of ribosomal elongation results in stabilization of many associated lncRNAs. Together these findings suggest that the ribosome is the default destination for the majority of cytoplasmic long noncoding RNAs and may play a role in their degradation.

Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways

“…This hypothesis is supported by a clear correlation between the number of possible ORFs on these transcripts and the likelihood of being subject to NMD (Fig. 4B) and by the fact that recent ribosome profiling studies and polysome analyses found many noncoding RNAs to be associated with ribosomes (Ingolia et al 2011(Ingolia et al , 2014Carlevaro-Fita et al 2016).…”

“…Given that NMD is a translation-dependent process, it might be surprising at first sight that several genes annotated as "noncoding" are affected. However, many pseudogenes are known to give rise to PTC-containing mRNAs (Mitrovich and Anderson 2005) and recent ribosome profiling studies found many transcripts categorized as lincRNAs to be associated with ribosomes (Ingolia et al 2011;Calviello et al 2015;Carlevaro-Fita et al 2016). In a few cases, the short polypeptides encoded by these lincRNAs were even detected (Ingolia et al 2014) thus revealing them as a misnomer.…”

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

“…In contrast, Carlevaro-Fita et al. [37] have recently shown that ribosomes are the default destination of most cytoplasmic lncRNAs and may play a role in their degradation because blocking ribosomal elongation results in the stabilization of many associated lncRNAs, which may be also the case for the GUT15 lncRNA. In 1995, Taylor and coworkers found that the level of the shorter GUT15 transcript was significantly increased in an actinomycin D (inhibitor of RNAPII transcription)- and cycloheximide (translational inhibitor)-treated tobacco cell line [15].…”

The functions of long noncoding RNAs in development and stem cells

“…This translation is similar to that occurring at 5′ UTRs, and the vast majority of peptides produced by such translation events in lncRNAs and 5′ UTRs are likely to be immediately degraded and nonfunctional [as discussed at length by Housman and Ulitsky (2015)]. The presence of some ribosomeprotected fragments overlapping an lncRNA, or its localization to the polysome fraction (Carlevaro-Fita et al, 2016;van Heesch et al, 2014), do not, therefore, invalidate the noncoding nature of a transcript.…”