Structural insight into the mechanism of stabilization of the 7SK small nuclear RNA by LARP7

Nucleic Acids Res. 2015 Mar 31;43(6):3373-88. doi: 10.1093/nar/gkv173. Epub 2015 Mar 9.

Abstract

The non-coding RNA 7SK is the scaffold for a small nuclear ribonucleoprotein (7SKsnRNP) which regulates the function of the positive transcription elongation factor P-TEFb in the control of RNA polymerase II elongation in metazoans. The La-related protein LARP7 is a component of the 7SKsnRNP required for stability and function of the RNA. To address the function of LARP7 we determined the crystal structure of its La module, which binds a stretch of uridines at the 3'-end of 7SK. The structure shows that the penultimate uridine is tethered by the two domains, the La-motif and the RNA-recognition motif (RRM1), and reveals that the RRM1 is significantly smaller and more exposed than in the La protein. Sequence analysis suggests that this impacts interaction with 7SK. Binding assays, footprinting and small-angle scattering experiments show that a second RRM domain located at the C-terminus binds the apical loop of the 3' hairpin of 7SK, while the N-terminal domains bind at its foot. Our results suggest that LARP7 uses both its N- and C-terminal domains to stabilize 7SK in a closed structure, which forms by joining conserved sequences at the 5'-end with the foot of the 3' hairpin and has thus functional implications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Conformation
  • Protein Interaction Domains and Motifs
  • RNA Stability
  • RNA, Small Nuclear / chemistry*
  • RNA, Small Nuclear / genetics
  • RNA, Small Nuclear / metabolism
  • Ribonucleoproteins / chemistry*
  • Ribonucleoproteins / genetics
  • Ribonucleoproteins / metabolism
  • Ribonucleoside Diphosphate Reductase / chemistry
  • Ribonucleoside Diphosphate Reductase / metabolism
  • Scattering, Small Angle
  • Sequence Homology, Amino Acid
  • Static Electricity
  • Tumor Suppressor Proteins / chemistry
  • Tumor Suppressor Proteins / metabolism
  • Uridine / chemistry
  • X-Ray Diffraction

Substances

  • Larp7 protein, human
  • RNA, Small Nuclear
  • Ribonucleoproteins
  • Tumor Suppressor Proteins
  • ribonucleotide reductase M2
  • RRM1 protein, human
  • Ribonucleoside Diphosphate Reductase
  • Uridine