Mapping targets for small nucleolar RNAs in yeast.

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.