title: High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.
abstract: High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2΄-O-ribose methylation sites. We thereby assigned the snoRNA guide to a known methylation site in the 18S rRNA, we uncovered a novel partially methylated site in the 28S ribosomal RNA, and we captured a site in the 28S rRNA in interaction with multiple snoRNAs. Although we also captured mRNAs in interaction with snoRNAs, we did not detect 2΄-O-methylation of these targets. Our study provides an integrated approach to the comprehensive characterization of 2΄-O-methylation targets of snoRNAs in species beyond those in which these interactions have been traditionally studied and contributes to the rapidly developing field of 'epitranscriptomics'.
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.|Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland.
authors.forename: Rafal
authors.initials: R
authors.lastname: Gumienny
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.
authors.forename: Dominik J
authors.initials: DJ
authors.lastname: Jedlinski
authors.affiliation: Proteomics Core Facility, Biozentrum, University of Basel, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.|Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland.
authors.forename: Foivos
authors.initials: F
authors.lastname: Gypas
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.
authors.forename: Georges
authors.initials: G
authors.lastname: Martin
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.
authors.forename: Arnau
authors.initials: A
authors.lastname: Vina-Vilaseca
authors.affiliation: Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.|Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland.
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D047468:Immunoprecipitation; D008745:Methylation; D011485:Protein Binding; D012337:RNA, Ribosomal, 18S / Q000235:genetics / Q000378:metabolism; D012339:RNA, Ribosomal, 28S / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000235:genetics* / Q000378:metabolism; D020718:Ribonucleoproteins, Small Nucleolar / Q000235:genetics* / Q000378:metabolism; D012266:Ribose / Q000378:metabolism; D012984:Software; D059467:Transcriptome; D000094704:RNA, Guide, CRISPR-Cas Systems
chemical_list: D003432:Cross-Linking Reagents; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S; D020537:RNA, Small Nucleolar; D020718:Ribonucleoproteins, Small Nucleolar; D012266:Ribose; D000094704:RNA, Guide, CRISPR-Cas Systems