High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq

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'.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Cross-Linking Reagents / chemistry
  • Databases, Genetic
  • High-Throughput Nucleotide Sequencing / methods*
  • Immunoprecipitation
  • Methylation
  • Protein Binding
  • RNA, Guide, CRISPR-Cas Systems
  • RNA, Ribosomal, 18S / genetics
  • RNA, Ribosomal, 18S / metabolism
  • RNA, Ribosomal, 28S / genetics
  • RNA, Ribosomal, 28S / metabolism
  • RNA, Small Nucleolar / genetics*
  • RNA, Small Nucleolar / metabolism
  • Ribonucleoproteins, Small Nucleolar / genetics*
  • Ribonucleoproteins, Small Nucleolar / metabolism
  • Ribose / metabolism
  • Software
  • Transcriptome*


  • Cross-Linking Reagents
  • RNA, Ribosomal, 18S
  • RNA, Ribosomal, 28S
  • RNA, Small Nucleolar
  • Ribonucleoproteins, Small Nucleolar
  • Ribose