In a study published in Nucleic Acids Research on July 12, a research team led by Prof. YE Keqiong from the Institute of Biophysics of the Chinese Academy of Sciences developed a high-throughput method consisting of RNA circularization, targeted amplification, and deep sequencing (CircTA-seq) to profile ribosomal RNA (rRNA) processing intermediates at single-molecule and single-nucleotide resolution.

The synthesis of rRNA is a critical, complex, and highly conserved cellular activity, and some steps in the rRNA processing pathway remain unresolved.

Using CircTA-seq high-throughput technology, the researchers quantitatively analyzed the effects of 15 mutants on yeast rRNA precursors, revealing several unknown mechanisms in the rRNA processing pathway.

They discovered that as rRNA processing progresses, the 5' extended end of 5.8S rRNA slowly converts to a short end, and proposed a unified model to explain its biogenesis.

In addition, they identified the initiation process of 3' end processing of 5.8S rRNA. They also sed that the 3' end of 25S rRNA is sequentially cleaved by four Rex nucleases.

The researchers accurately measured the distribution of polyadenylated tails on rRNA precursors, revealing the dependence of 20S precursor degradation efficiency on polyadenylated tail length, and found that degradation intermediates are often highly polyadenylated. They also discovered a novel intermediate generated by the 5' degradation process of defective 18S rRNA precursors.

This study advances the CircTA-seq high-throughput technology for identifying rRNA processing intermediates, reveals several novel mechanisms involved in rRNA processing and quality control processes, and significantly refines the classical rRNA processing pathway.

CircTA-seq technology discovers new mechanisms of ribosomal RNA processing and surveillance in yeast. (Image by YE Keqiong's group)