High resolution landscape of ribosomal RNA processing and surveillance

Area of Science:

• Molecular Biology
• Genetics
• Biochemistry

Background:

• Ribosomal RNA (rRNA) processing is essential for ribosome biogenesis.
• Understanding rRNA processing pathways is crucial for cellular function and disease research.
• Existing methods have limitations in profiling rRNA processing intermediates at high resolution.

Purpose of the Study:

• To elucidate the mechanistic details of rRNA processing and surveillance pathways in yeast.
• To profile rRNA processing intermediates at single-molecule and single-nucleotide resolution.
• To investigate the role of polyadenylation in rRNA degradation.

Main Methods:

• Circularization, targeted amplification and deep sequencing (CircTA-seq) was employed.
• Single-molecule and single-nucleotide level profiling of rRNA processing intermediates.
• Analysis of pre-ribosomal RNA (pre-rRNA) polyadenylation profiles.

Main Results:

• Identified a unified processing pathway converting the long form of 5' end of 5.8S rRNA to the short form.
• Characterized the sequential trimming by Rex1, Rex2, and Trf4-mediated polyadenylation in 5.8S rRNA processing.
• Determined the role of four Rex proteins in the sequential digestion forming the 3' end of 25S rRNA.
• Observed intermediates with extended A1 sites during aberrant 18S rRNA precursor degradation.
• Demonstrated that polyadenylation length critically affects the degradation efficiency of 20S pre-rRNA by the exosome.

Conclusions:

• CircTA-seq provides significant mechanistic insights into yeast rRNA processing and surveillance.
• The processing of 5.8S and 25S rRNAs involves coordinated enzymatic activities.
• Polyadenylation plays a critical regulatory role in the degradation of pre-rRNA intermediates.