Gumienny Rafal, Jedlinski Dominik J, Schmidt Alexander, Gypas Foivos, Martin Georges, Vina-Vilaseca Arnau, Zavolan Mihaela
Computational and Systems Biology, Biozentrum, University of Basel, Switzerland.
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Switzerland.
Nucleic Acids Res. 2017 Mar 17;45(5):2341-2353. doi: 10.1093/nar/gkw1321.
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'.
高通量测序极大地推动了长链和短链非编码RNA（ncRNAs）的发现，这些非编码RNA常常引导核糖核蛋白复合体作用于RNA靶标，从而调节其代谢和表达。然而，对于许多ncRNAs而言，其靶标仍有待发现。在本研究中，我们开发了计算方法，利用来自核心小核仁核糖核蛋白交联和免疫沉淀的数据以及全转录组范围的2'-O-核糖甲基化位点图谱来定位C/D盒小核仁RNA（snoRNA）的靶位点。我们据此将snoRNA引导序列定位到18S rRNA中的一个已知甲基化位点，在28S核糖体RNA中发现了一个新的部分甲基化位点，并捕捉到28S rRNA中一个与多个snoRNAs相互作用的位点。尽管我们也捕捉到了与snoRNAs相互作用的mRNA，但未检测到这些靶标的2'-O-甲基化。我们的研究提供了一种综合方法，用于全面表征传统研究之外物种中snoRNAs的2'-O-甲基化靶标，并为迅速发展的“表观转录组学”领域做出了贡献。
