Abstract
Small non-coding RNAs (sncRNAs) represent an important class of regulatory RNAs involved in the regulation of transcription, RNA splicing or translation. Among these sncRNAs, small nucleolar RNAs (snoRNAs) mostly originate from intron splicing in humans and are central to posttranscriptional regulation of gene expression. However, the characterization of the complete repertoire of sncRNAs in a given cellular context and the functional annotation of the human transcriptome are far from complete. Here, we report the large-scale identification of sncRNAs in the size range of 50 to 200 nucleotides without a priori on their biogenesis, structure and genomic origin in the context of normal human muscle cells. We provided a complete set of experimental validation of novel candidate snoRNAs by evaluating the prerequisites for their biogenesis and functionality, leading to their validation as genuine snoRNAs. Interestingly, we also found intergenic snoRNAs, which we showed are in fact integrated into candidate introns of unannotated transcripts or degraded by the Nonsense Mediated Decay pathway. Hence, intergenic snoRNAs represent a new type of landmark for the identification of new transcripts that have gone undetected because of low abundance or degradation after the release of the snoRNA.
Highlights
The continuous progress in the annotation of mammalian genomes first led to the striking conclusion that they are mostly non-coding, with only 2% having information to encode proteins [1]
To systematically identify small non-coding RNAs (ncRNAs) candidates without a priori on their genomic location, secondary structure and biogenesis and independently of their host transcript, we isolated ribo- and poly(A)-depleted RNAs extracted from human myoblasts (MBs) and their differentiated myotube (MT) counterparts
We focused on clusters of at least 20 reads mapping to intergenic or intronic regions, which could represent new small ncRNA candidates
Summary
The continuous progress in the annotation of mammalian genomes first led to the striking conclusion that they are mostly non-coding, with only 2% having information to encode proteins [1]. SIDs include some non-canonical miRNAs such as mirtrons, simtrons and agotrons, and all snoRNAs, which represent the largest group of SIDs in humans [17,18,19,20] These ncRNAs, 50–300 nt in length, mainly operate as guides to mediate posttranscriptional modifications on other ncRNAs such as ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs) [21,22]. This work provides the identification of a full scope of sncRNAs in a size range that excludes well-characterized and abundant mature miRNAs and piRNAs as well as 5S RNA in a given cell type, followed by a thorough procedure of experimental validation of the candidate new snoRNAs. This study points out the potential of intergenic snoRNAs as indicators of the presence of not yet annotated transcription units
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
