Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing

J Cell Biol. 2013 Mar 4;200(5):577-88. doi: 10.1083/jcb.201207131. Epub 2013 Feb 25.


Human ribosome production is up-regulated during tumorogenesis and is defective in many genetic diseases (ribosomopathies). We have undertaken a detailed analysis of human precursor ribosomal RNA (pre-rRNA) processing because surprisingly little is known about this important pathway. Processing in internal transcribed spacer 1 (ITS1) is a key step that separates the rRNA components of the large and small ribosomal subunits. We report that this was initiated by endonuclease cleavage, which required large subunit biogenesis factors. This was followed by 3' to 5' exonucleolytic processing by RRP6 and the exosome, an enzyme complex not previously linked to ITS1 removal. In contrast, RNA interference-mediated knockdown of the endoribonuclease MRP did not result in a clear defect in ITS1 processing. Despite the apparently high evolutionary conservation of the pre-rRNA processing pathway and ribosome synthesis factors, each of these features of human ITS1 processing is distinct from those in budding yeast. These results also provide significant insight into the links between ribosomopathies and ribosome production in human cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Endoribonucleases / genetics
  • Endoribonucleases / metabolism*
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism*
  • Exosome Multienzyme Ribonuclease Complex / genetics
  • Exosome Multienzyme Ribonuclease Complex / metabolism*
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Proteins / metabolism
  • RNA Interference
  • RNA Precursors / metabolism*
  • RNA Processing, Post-Transcriptional*
  • RNA, Fungal / metabolism
  • RNA, Ribosomal / metabolism*
  • RNA, Ribosomal, 18S / metabolism
  • RNA-Binding Proteins / metabolism
  • Ribosomes / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Transfection


  • BOP1 protein, human
  • Proteins
  • RBM28 protein, human
  • RNA Precursors
  • RNA, Fungal
  • RNA, Ribosomal
  • RNA, Ribosomal, 18S
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins
  • Endoribonucleases
  • Exoribonucleases
  • Exosome Multienzyme Ribonuclease Complex
  • mitochondrial RNA-processing endoribonuclease
  • EXOSC10 protein, human