Two featured series of rRNA-derived RNA fragments (rRFs) constitute a novel class of small RNAs

In this study, we reported two featured series of rRNA-derived RNA fragments (rRFs) from the small RNA sequencing (sRNA-seq) data of Amblyomma testudinarium using the Illunima platform. Two series of rRFs (rRF5 and rRF3) were precisely aligned to the 5' and 3' ends of the 5.8S and 28S rRNA gene. The rRF5 and rRF3 series were significantly more highly expressed than the rRFs located in the body of the rRNA genes. These series contained perfectly aligned reads, the lengths of which varied progressively with 1-bp differences. The rRF5 and rRF3 series in the same expression pattern exist ubiquitously from ticks to human. The cellular experiments showed the RNAi knockdown of one 20-nt rRF3 induced the cell apoptosis and inhibited the cell proliferation. In addition, the RNAi knockdown resulted in a significant decrease of H1299 cells in the G2 phase of the cell cycle. These results indicated the rRF5 and rRF3 series were not random intermediates or products during rRNA degradation, but could constitute a new class of small RNAs that deserves further investigation.本研究基于Illumina测序平台获得的龟形花蜱（Amblyomma testudinarium）小RNA测序（small RNA sequencing, sRNA-seq）数据，报道了两类特征性的核糖体RNA来源RNA片段（rRNA-derived RNA fragments, rRFs）。两类rRFs（rRF5与rRF3）可精准比对至5.8S及28S核糖体RNA基因的5'端与3'端。rRF5与rRF3系列的表达水平显著高于位于核糖体RNA基因内部区域的rRFs。该两类rRFs均包含完全匹配的测序读段，其长度以1碱基为间隔呈渐进式变化。具有相同表达模式的rRF5与rRF3系列广泛存在于从蜱类到人类的多个物种中。细胞实验结果显示，对一条20核苷酸（nt）长度的rRF3进行RNA干扰（RNAi）敲降，可诱导细胞凋亡并抑制细胞增殖。此外，该RNA干扰敲降处理导致H1299细胞的细胞周期G2期占比显著降低。上述结果表明，rRF5与rRF3系列并非核糖体RNA降解过程中的随机中间产物或降解产物，而是一类值得开展深入研究的新型小RNA。