title: snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions.
abstract: Among thousands of non-protein-coding RNAs which have been found in humans, a significant group represents snoRNA molecules that guide other types of RNAs to specific chemical modifications, cleavages, or proper folding. Yet, hundreds of mammalian snoRNAs have unknown function and are referred to as "orphan" molecules. In 2006, for the first time, it was shown that a particular orphan snoRNA (HBII-52) plays an important role in the regulation of alternative splicing of the serotonin receptor gene in humans and other mammals. In order to facilitate the investigation of possible involvement of snoRNAs in the regulation of pre-mRNA processing, we developed a new computational web resource, snoTARGET, which searches for possible guiding sites for snoRNAs among the entire set of human and rodent exonic and intronic sequences. Application of snoTARGET for finding possible guiding sites for a number of human and rodent orphan C/D-box snoRNAs showed that another subgroup of these molecules (HBII-85) have statistically elevated guiding preferences toward exons compared to introns. Moreover, these energetically favorable putative targets of HBII-85 snoRNAs are non-randomly associated with genes producing alternatively spliced mRNA isoforms. The snoTARGET resource is freely available at: (http://hsc.utoledo.edu/depts/bioinfo/snotarget.html).
authors.affiliation: Program in Bioinformatics and Proteomics/Genomics, University of Toledo Health Science Campus, Toledo, OH 43614, USA.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Bazeley
authors.forename: Valery
authors.initials: V
authors.lastname: Shepelev
authors.forename: Zohreh
authors.initials: Z
authors.lastname: Talebizadeh
authors.forename: Merlin G
authors.initials: MG
authors.lastname: Butler
authors.forename: Larisa
authors.initials: L
authors.lastname: Fedorova
authors.forename: Vadim
authors.initials: V
authors.lastname: Filatov
authors.forename: Alexei
authors.initials: A
authors.lastname: Fedorov
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D001483:Base Sequence; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D022821:RNA Splice Sites; D020537:RNA, Small Nucleolar / Q000378:metabolism*; D012984:Software
chemical_list: D022821:RNA Splice Sites; D020537:RNA, Small Nucleolar