Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs

Nucleic Acids Res. 2022 Oct 14;50(18):10695-10716. doi: 10.1093/nar/gkac817.


5-Methylcytosine (m5C) is a base modification broadly found on various RNAs in the human transcriptome. In eukaryotes, m5C is catalyzed by enzymes of the NSUN family composed of seven human members (NSUN1-7). NOP2/NSUN1 has been primarily characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S ribosomal RNA (rRNA). Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions and substrates remain poorly characterized. Here, we used a miCLIP-seq approach to identify human NOP2/NSUN1 RNA substrates. Our analysis revealed that NOP2/NSUN1 catalyzes the deposition of m5C at position 4447 on the 28S rRNA. We also find that NOP2/NSUN1 binds to the 5'ETS region of the pre-rRNA transcript and regulates pre-rRNA processing through non-catalytic complex formation with box C/D snoRNAs. We provide evidence that NOP2/NSUN1 facilitates the recruitment of U3 and U8 snoRNAs to pre-90S ribosomal particles and their stable assembly into snoRNP complexes. Remarkably, expression of both WT and catalytically inactive NOP2/NSUN1 in knockdown background rescues the rRNA processing defects and the stable assembly of box C/D snoRNP complexes, suggesting that NOP2/NSUN1-mediated deposition of m5C on rRNA is not required for ribosome synthesis.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • 5-Methylcytosine / metabolism
  • Humans
  • Nuclear Proteins / metabolism*
  • RNA Precursors / metabolism
  • RNA, Ribosomal / metabolism
  • RNA, Ribosomal, 28S / metabolism
  • RNA, Small Nucleolar / metabolism
  • Ribonucleoproteins, Small Nucleolar* / genetics
  • Ribonucleoproteins, Small Nucleolar* / metabolism
  • Ribosomes / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • tRNA Methyltransferases / metabolism*


  • Nuclear Proteins
  • RNA Precursors
  • RNA, Ribosomal
  • RNA, Ribosomal, 28S
  • RNA, Small Nucleolar
  • Ribonucleoproteins, Small Nucleolar
  • Saccharomyces cerevisiae Proteins
  • 5-Methylcytosine
  • NOP2 protein, human
  • tRNA Methyltransferases