Two orthogonal cleavages separate subunit RNAs in mouse ribosome biogenesis

Nucleic Acids Res. 2014;42(17):11180-91. doi: 10.1093/nar/gku787. Epub 2014 Sep 4.


Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking down a ribosome synthesis factor produces a characteristic RAMP profile that exhibits consistency across a range of depletion levels. This facilitates the inference of affected steps and simplifies comparative analysis. We applied RAMP to examine how endonucleolytic cleavages of the mouse pre-rRNA transcript in the internal transcribed spacer 1 (ITS1) are affected by depletion of factors required for maturation of the small ribosomal subunit (Rcl1, Fcf1/Utp24, Utp23) and the large subunit (Pes1, Nog1). The data suggest that completion of early maturation in a subunit triggers its release from the common pre-rRNA transcript by stimulating cleavage at the proximal site in ITS1. We also find that splitting of pre-rRNA in the 3' region of ITS1 is prevalent in adult mouse tissues and quiescent cells, as it is in human cells. We propose a model for subunit separation during mammalian ribosome synthesis and discuss its implications for understanding pre-rRNA processing pathways.

Publication types

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

MeSH terms

  • Animals
  • BALB 3T3 Cells
  • Cells, Cultured
  • DNA, Ribosomal Spacer
  • Mice
  • Models, Genetic
  • NIH 3T3 Cells
  • RNA Cleavage
  • RNA Interference
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / metabolism*
  • RNA, Ribosomal, 18S / metabolism
  • Ribosomal Proteins / antagonists & inhibitors
  • Ribosome Subunits, Large, Eukaryotic / metabolism*
  • Ribosome Subunits, Small, Eukaryotic / metabolism*


  • DNA, Ribosomal Spacer
  • RNA Precursors
  • RNA, Ribosomal
  • RNA, Ribosomal, 18S
  • Ribosomal Proteins