snoDB: an interactive database of human snoRNA sequences, abundance and interactions

Abstract

Small nucleolar RNAs (snoRNAs) are an abundant type of non-coding RNA with conserved functions in all known eukaryotes. Classified into two main families, the box C/D and H/ACA snoRNAs, they enact their most well characterized role of guiding site specific modifications in ribosomal RNA, through the formation of specific ribonucleoprotein complexes, with fundamental implications in ribosome biogenesis. However, it is becoming increasingly clear that the landscape of snoRNA cellular functionality is much broader than it once seemed with novel members, non-uniform expression patterns, new and diverse targets as well as several emerging non-canonical functions ranging from the modulation of alternative splicing to the regulation of chromatin architecture. In order to facilitate the further characterization of human snoRNAs in a holistic manner, we introduce an online interactive database tool: snoDB. Its purpose is to consolidate information on human snoRNAs from different sources such as sequence databases, target information, both canonical and non-canonical from the literature and from high-throughput RNA–RNA interaction datasets, as well as high-throughput sequencing data that can be visualized interactively.

Small nucleolar RNAs: continuing identification of novel members and increasing diversity of their molecular mechanisms of action

“…The use of reverse transcriptases from thermophilic bacteria has been shown to faithfully represent the abundance of highly structured RNAs such as transfer RNAs (tRNA) and snoRNAs [46,47]. Using thermostable group II intron reverse transcriptase sequencing on non-fragmented RNA samples, 25 nonannotated human snoRNAs were recently identified, including 22 box H/ACA snoRNA shown to be dependent on DKC1, the pseudouridine transferase H/ACA binding partner [4,48].…”

“…With ∼100-200 sites known to carry these modifications in rRNA, it was expected, two decades ago, that the complement of snoRNAs would number ∼200 in vertebrates [3]. However, diverse experimental and computational strategies have led to, and continue to result in the identification of novel snoRNAs, which now add up to between several hundreds and several thousands for many vertebrates, although not all have been shown to be expressed [4][5][6]. In parallel to the discovery of new members of the snoRNA family, the past decade has also led to the characterization of many diverse novel regulatory functions, affecting many cellular processes in addition to ribosome biogenesis [7].…”

Separated Siamese Twins: Intronic Small Nucleolar RNAs and Matched Host Genes May be Altered in Conjunction or Separately in Multiple Cancer Types

“…We calculated the overall percentage of samples with copy number alterations co-occurring in host genes and snoRNA that belonged to 295 pairs extracted from the snoDB database (http: //scottgroup.med.usherbrooke.ca/snoDB/) [27]. This provided us with alteration frequencies for each pair of host gene and snoRNA in ten human cancer types ( Supplementary Table S1).…”

“…We first compiled a sno-RNA/host gene shortlist starting from the snoDB public database (http://scottgroup.med.usherbrooke.ca/snoDB/) [27]. A total of 295 snoRNA-host gene couples were chosen on the basis of the following criteria: 1.…”

Unsupervised analysis of multi-experiment transcriptomic patterns with SegRNA identifies unannotated transcripts

“…A subset of snoRNAs have expression in specific tissues, particularly the brain 24,25 . Most snoRNAs, however, behave like housekeeping genes, having broad expression in To investigate whether SegRNA annotates broadly-expressed or tissue-specific snoRNAs, we compared SegRNA labels at snoRNA loci to expression data from snoDB 26 . SnoDB's data come from the low-structure-bias RNA-seq approach thermostable group II intron reverse transcriptase sequencing (TGIRT-seq).…”