The Profile and Biological Functions of 28s rRNA 5' Terminus-Derived Small RNA

The recent advancements in small RNA high-throughput sequencing have vastly enhanced our understanding of the small RNA repertoire, and it has been revealed that some housekeeping non-coding RNAs, including tRNA and rRNA, act as sources of small RNAs. In this study, we re-analyzed publicly accessible PANDORA-seq data to uncover 28s5-rtsRNA, the small RNA originating from the first nucleotide at the 5' terminus of 28s rRNA, as the most prevalent small RNA class across multiple tissues. Furthermore, we discovered a novel category termed ‘28s5-rtsRNA half,’ which is highly expressed in sperm. When paired with 5.8s rRNA 3' terminus-derived small RNA or complementary single-stranded RNA, 28s5-rtsRNA duplexes elevate the 28s/18s rRNA ratios and decrease the mRNA levels of several ribosomal proteins, whereas single-stranded 28s5-rtsRNA alone lacks these effects. Mutational scanning analysis pinpointed the first seven nucleotides of 28s5-rtsRNA as essential for its biological functions. Our findings highlight the abundance of 28s5-rtsRNA across tissues and its potential role in regulating ribosomal protein mRNA levels, paving the way for future studies to comprehensively elucidate the mechanisms and functions of 28s5-rtsRNA in diverse biological processes.