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Mapping targets for small nucleolar RNAs in yeast.

Tatiana Dudnakova1, Hywel Dunn-Davies1, Rosie Peters1

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Summary

This study maps small nucleolar RNA (snoRNA) interactions in yeast, identifying new RNA targets and regulatory roles for snoRNAs in processes like rRNA methylation and mRNA expression.

Keywords:
RNA-RNA interactionRNA-protein interactionUV cross-linkingsmall nucleolar RNAsnoRNA

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Genetics

Background:

  • Dysregulation of box C/D small nucleolar RNAs (snoRNAs) is linked to human diseases.
  • Understanding snoRNA-target interactions is crucial for disease research.

Purpose of the Study:

  • To identify novel RNA targets for box C/D snoRNAs in budding yeast.
  • To develop bioinformatics tools for filtering functional snoRNA-target interactions.
  • To investigate the role of RNA helicase Mtr4 in snoRNA-target binding.

Main Methods:

  • UV crosslinking and sequencing of hybrids (CLASH) with key snoRNP proteins (Nop1, Nop56, Nop58).
  • Bioinformatics analysis to identify bona fide methylation guide interactions.
  • CLASH experiments involving the RNA helicase Mtr4.

Main Results:

  • Identified numerous high-confidence snoRNA interactions with ribosomal RNAs (rRNAs), including methylation sites.
  • Discovered potential regulatory snoRNA-rRNA binding distinct from methylation guidance.
  • Revealed snoRNA-snoRNA interactions suggesting cross-regulation.
  • Identified 1,368 snoRNA-mRNA interactions involving 39 snoRNAs and 382 mRNAs.
  • Observed that snoRNA depletion impacts mRNA levels, with CLASH targets being over-represented.

Conclusions:

  • Systematic mapping of snoRNA-target binding provides a comprehensive catalog of interactions.
  • Identified numerous potential regulatory roles for snoRNAs beyond rRNA modification.
  • The findings offer insights into snoRNA function and potential involvement in gene regulation.