Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read Nanopore sequencing

Abstract

Ribosome biogenesis requires the synthesis and processing of precursor rRNAs (pre-rRNAs) into mature rRNAs. Traditional methods like northern blotting and metabolic labeling offer limited resolution. We present NanoRibolyzer, a nanopore-based, long-read sequencing approach that enables ab initio identification and quantification of rRNA precursors. Using both supervised and unsupervised mapping, it detects known and novel pre-rRNA species and defines cleavage sites at single-nucleotide resolution. A simple cell fractionation protocol provides spatial separation of nuclear and cytoplasmic pre-rRNAs. Targeted knockdowns quantify intermediate accumulations, revealing condition-specific processing fingerprints with biomarker potential. Pseudouridine mapping shows that the primary 47S transcript is extensively modified, while aberrant products are not. With its high resolution and unique mapping strategy, NanoRibolyzer offers new insights into rRNA processing and modification, enhancing our understanding of ribosome biogenesis.