Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs that guide the post-transcriptional processing of other non-coding RNAs (mostly ribosomal RNAs), but have also been implicated in processes ranging from microRNA-dependent gene silencing to alternative splicing.
In order to construct an up-to-date catalog of human snoRNAs researchers at the University of Basel have combined data from various databases, de novo prediction and extensive literature review. In total, they list more than 750 curated genomic loci that give rise to snoRNA and snoRNA-like genes. Utilizing small RNA-seq data from the ENCODE project, this study characterizes the plasticity of snoRNA expression identifying both constitutively as well as cell type specific expressed snoRNAs. Especially, the comparison of malignant to non-malignant tissues and cell types shows a dramatic perturbation of the snoRNA expression profile. Finally, the researchers developed a high-throughput variant of the reverse-transcriptase-based method for identifying 2′-O-methyl modifications in RNAs termed RimSeq. Using the data from this and other high-throughput protocols together with previously reported modification sites and state-of-the-art target prediction methods they re-estimate the snoRNA target RNA interaction network. Their current results assign a reliable modification site to 83% of the canonical snoRNAs, leaving only 76 snoRNA sequences as orphan.
Outline of the snoRNA annotation strategy used in this study
The researchers combined de novo search on ENCODE sRNA-seq expressed regions with snoRNA genes and predictions from various databases. All predicted candidate sequences were checked for a supportive sRNA-seq read pattern to identify high confidence, currently not annotated snoRNA genes. Finally, snoRNAs from all sources were merged and filtered for redundancy to establish a comprehensive map of human snoRNA loci.
Availability – The data collected in this study is publicly accessible via http://www.bioinf.uni-leipzig.de/publications/supplements/15-065