snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs

Abstract

snoDB is an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources. In the second edition of this database (snoDB 2.0), we added an entirely new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs with easy navigation between the different rRNA versions used in the literature and experimentally measured levels of modification. We also included new layers of information, including snoRNA motifs, secondary structure prediction, snoRNA–protein interactions, copy annotations and low structure bias expression data in a wide panel of tissues and cell lines to bolster functional probing of snoRNA biology. Version 2.0 features updated identifiers, more links to external resources and duplicate entry resolution. As a result, snoDB 2.0, which is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/, represents a one-stop shop for snoRNA features, rRNA modification targets, functional impact and potential regulators.

RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications

“…11 A total of 68 box H/ACA snoRNAs or scaRNAs modify these Ψ sites. 11 Pseudouridine is essential for ribosome maturation and function, clustering near functionally important regions of the ribosome. 6 Disruption in pseudouridine formation, caused by dysregulation of DKC1 or box H/ACA snoRNAs, can lead to ribosomal biogenesis defects and various human diseases.…”

“…RNA-guided 2′- O -methylation is the most prevalent modification in rRNAs as each ribosome harbors more than 100 sites . Among these, 157 box C/D snoRNAs or scaRNAs are involved in modifying specific sites within rRNAs .…”

“…RNA-guided pseudouridylation is abundant in rRNAs, with each ribosome having 95 Ψ sites . A total of 68 box H/ACA snoRNAs or scaRNAs modify these Ψ sites .…”

“…RNA-guided pseudouridylation is abundant in rRNAs, with each ribosome having 95 Ψ sites . A total of 68 box H/ACA snoRNAs or scaRNAs modify these Ψ sites . Pseudouridine is essential for ribosome maturation and function, clustering near functionally important regions of the ribosome .…”

“…11 Among these, 157 box C/D snoRNAs or scaRNAs are involved in modifying specific sites within rRNAs. 11 This modification plays a crucial role in ribosome assembly, ensuring proper folding of rRNA into its correct three-dimensional structure. Recent studies have revealed that the heterogeneity of rRNA 2′-O-methylation may contribute to functional specificity in human ribosomes and affect protein expression.…”