Ribosome profiling reveals resemblance between long non-coding RNAs and 5′ leaders of coding RNAs

Abstract

SUMMARYLarge-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5Ј leaders of coding RNAs. Analysis of ribosome profiling data from embryonic stem cells reveals similar properties for mammalian lncRNAs. These results clarify the annotation of developmental lncRNAs and suggest a potential role for translation in lncRNA regulation. In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development.

A long non-coding RNA transcribed from conserved non-coding sequences contributes to the mouse prolyl oligopeptidase gene activation

“…Considering that its full length contained an open reading frame for a peptide of 62 amino acids, lncPrep+96kb might possibly be translated to a peptide. Indeed, recent ribosome profiling analyses indicated that many lncRNAs were bound by ribosomes (42,43). However, other studies argued that a majority of lncRNAs did not encode proteins (44,45), suggesting the function of lncPrep+96kb as an RNA molecule.…”

Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation

“…To further assess the conservation of NED we used ribosome profiling data from different species (human, HEK293 (Liu et al, 2013), mouse (Shalgi et al, 2013), zebrafish (Chew et al, 2013) and C. elegans (Nedialkova and Leidel, 2015)). We classified proteins in these datasets according to the degradation profiles of their human orthologs (in RPE-1 cells).…”

“…The datasets for Human (SRA061778; HEK293 cells no treatment; (Liu et al, 2013)), Zebrafish (GSE46512; 28hours post-fertilization; (Chew et al, 2013) 5) and Shalgi et al 2013(Shalgi et al, 2013 (Fig. 6).…”

Mapping the non-standardized biases of ribosome profiling

“…Eukaryotic cells are lysed on ice by repeated micropipetting or homogenization (Guo et al, 2010;Becker et al, 2013;Chew et al, 2013). Pulverized bacteria or monocellular eukaryotes are homogenized in a mill with liquid nitrogen (Oh et al, 2011;Guydosh and Green, 2014;Woolstenhulme et al, 2015).…”

“…In the majority of ribosome profiling experiments (Ingolia et al, 2009(Ingolia et al, , 2011Guo et al, 2010;Gerashchenko et al, 2012;Li et al, 2012;Chew et al, 2013;Guttman et al, 2013;Aspden et al, 2014;Baudin-Baillieu et al, 2014;Bazzini et al, 2014;Subramaniam et al, 2014), Bowtie (Langmead et al, 2009) is used as a BWT-based mapping program. Bowtie offers two ways of mapping a read to a reference sequence: seed-(parameter n) and mismatchbased approach (parameter v, Table 1).…”