Quantitative profiling of peptides from RNAs classified as noncoding

Abstract

Only a small fraction of the mammalian genome codes for messenger RNAs destined to be translated into proteins, and it is generally assumed that a large portion of transcribed sequences - including introns and several classes of non-coding RNAs (ncRNAs) do not give rise to peptide products. A systematic examination of translation and physiological regulation of ncRNAs has not been conducted. Here, we use computational methods to identify the products of non-canonical translation in mouse neurons by analyzing unannotated transcripts in combination with proteomic data. This study supports the existence of non-canonical translation products from both intragenic and extragenic genomic regions, including peptides derived from anti-sense transcripts and introns. Moreover, the studied novel translation products exhibit temporal regulation similar to that of proteins known to be involved in neuronal activity processes. These observations highlight a potentially large and complex set of biologically regulated translational events from transcripts formerly thought to lack coding potential.

The Landscape of long noncoding RNA classification

“…Peptide sequencing data revealed presence of 250 novel mouse peptides encoded by presumed lncRNAs [113]. The full extent of the novel mammalian proteome encoded by lncRNAs is not yet clear however.…”

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

“… Prabakaran et al [78] reported 250 novel peptides coming from unannotated regions, but only 25 of those mapped to regions outside the boundaries of protein-coding genes, and only three of those had support from Ribo-seq data. When we mapped the 250 peptides from this study against a collection of lncRNAs defined by PLAR [14] and passing stringent filters, we found only two matches, and both mapped to probable pseudogenes.…”

“…Accordingly, recent studies have proposed improved MS methods, including a peptidomics approach [47,75], combined fractional diagonal chromatography (COFRADIC) [72,74,76,77], and other improvements [67,73]; constructed potential peptide databases using RNA-seq or Ribo-seq-based transcriptome reconstructions [47,67,72,78]; and combined multiple MS experiments to increase proteome coverage depth [23,68].…”

The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions

“…The most direct evidence for the presence of peptides in planta can be obtained from mass spectrometry analyses. The latter allowed successful detection of several sPEPs in other higher eukaryotes, but many of these were noncanonical sPEPs (Slavoff et al, 2013;Prabakaran et al, 2014). Moreover, since sPEPs often occur at low abundance (Hanada et al, 2013;Andrews and Rothnagel, 2014) and classical proteomic analyses involving data-dependent acquisition mass spectrometry have a bias for highly abundant peptides, they have limited potential to detect sPEPs.…”