Widespread localisation of lncRNA to ribosomes: Distinguishing features and evidence for regulatory roles

Abstract

The function of long noncoding RNAs (lncRNAs) depends on their location within the cell. While most studies to date have concentrated on their nuclear roles in transcriptional regulation, evidence is mounting that lncRNA also have cytoplasmic roles. Here we comprehensively map the cytoplasmic and ribosomal lncRNA population in a human cell. Three-quarters (74%) of lncRNAs are detected in the cytoplasm, the majority of which (62%) preferentially cofractionate with polyribosomes. Ribosomal lncRNA are highly expressed across tissues, under purifying evolutionary selection, and have cytoplasmic-to-nuclear ratios comparable to mRNAs and consistent across cell types. LncRNAs may be classified into three groups by their ribosomal interaction: non-ribosomal cytoplasmic lncRNAs, and those associated with either heavy or light polysomes. A number of mRNA-like features destin lncRNA for light polysomes, including capping and 5’UTR length, but not cryptic open reading frames or polyadenylation. Surprisingly, exonic retroviral sequences antagonise recruitment. In contrast, it appears that lncRNAs are recruited to heavy polysomes through basepairing to mRNAs. Finally, we show that the translation machinery actively degrades lncRNA. We propose that light polysomal lncRNAs are translationally engaged, while heavy polysomal lncRNAs are recruited indirectly. These findings point to extensive and reciprocal regulatory interactions between lncRNA and the translation machinery.

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

“…We found that mutating all translated LINC00261 sORFs simultaneously, thereby likely reducing LINC00261's ability to bind ribosomes, did not affect LINC00261 transcript levels in HEK293T cells. This indicates that, in contrast to reports suggesting that translated sORFs can regulate RNA stability by promoting nonsense-mediated RNA decay (Carlevaro-Fita et al, 2016;Tani et al, 2013), the high translation levels and multiple sORFs of LINC00261 are unlikely to be part of a LINC00261 decay pathway. It would have been interesting to determine how concurrent mutation of all sORFs in LINC00261 affects pancreatic cell differentiation.…”

“…To systematically discriminate LINC00261's coding and noncoding roles, we individually mutated its seven most highly translated sORFs independently in hESCs, leaving the lncRNA sequence, and hence any noncoding function coupled to RNA sequence or structure, grossly intact. Each of these hESC lines either carried a homozygous frameshift mutation near the microprotein's N-terminus (for sORFs 1-6) or a full sORF deletion (sORF7; It has been suggested that ribosome association can control lncRNA transcript levels by inducing nonsense-mediated decay (NMD) (Carlevaro-Fita et al, 2016;Tani et al, 2013). Therefore, we determined whether the presence of multiple sORFs could regulate LINC00261 stability.…”

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs

“… Polysomal fractionation: RNA-seq in subcellular fractions of human cells showed that lncRNAs are present in different cellular compartments -nucleus, free cytosolic, and ribosome-associated fractions, with most being enriched in the free cytosolic [62] and in the light polysomal fraction [63]. Ribosome profiling following polysomal fractionation (Poly-Ribo-seq), allows enrichment of transcripts that are translated by only a few ribosomes and therefore likely contain small ORFs (smORFs).…”

Kidney diseases and long non-coding RNAs in the limelight

“…Statistically, lncRNAs are mostly enriched in the cytoplasm, especially in ribosomes. LncRNAs reaching the cytoplasm will come to the default destination ribosome and may be degraded therein (van Heesch et al, 2014;Carlevaro-Fita et al, 2016). LncRNAs participate in forming partial nucleolus networks, regulating ribosome genesis, and modulating the function and structure of the nucleolus.…”