School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
Nucleic Acids Res. 2012 Aug;40(14):6787-99. doi: 10.1093/nar/gks307. Epub 2012 Apr 9.
Deep sequencing studies frequently identify small RNA fragments of abundant RNAs. These fragments are thought to represent degradation products of their precursors. Using sequencing, computational analysis, and sensitive northern blot assays, we show that constitutively expressed non-coding RNAs such as tRNAs, snoRNAs, rRNAs and snRNAs preferentially produce small 5' and 3' end fragments. Similar to that of microRNA processing, these terminal fragments are generated in an asymmetric manner that predominantly favors either the 5' or 3' end. Terminal-specific and asymmetric processing of these small RNAs occurs in both mouse and human cells. In addition to the known processing of some 3' terminal tRNA-derived fragments (tRFs) by the RNase III endonuclease Dicer, we show that several RNase family members can produce tRFs, including Angiogenin that cleaves the TψC loop to generate 3' tRFs. The 3' terminal tRFs but not the 5' tRFs are highly complementary to human endogenous retroviral sequences in the genome. Despite their independence from Dicer processing, these tRFs associate with Ago2 and are capable of down regulating target genes by transcript cleavage in vitro. We suggest that endogenous 3' tRFs have a role in regulating the unwarranted expression of endogenous viruses through the RNA interference pathway.
深度测序研究经常鉴定出丰富 RNA 的小 RNA 片段。这些片段被认为代表其前体的降解产物。我们使用测序、计算分析和敏感的 northern blot 分析，表明如 tRNA、snoRNA、rRNA 和 snRNA 等组成型表达的非编码 RNA 优先产生小的 5' 和 3' 端片段。与 microRNA 加工类似，这些末端片段以不对称的方式产生，主要偏向 5' 或 3' 端。这些小 RNA 的末端特异性和不对称加工在小鼠和人类细胞中都发生。除了已知的某些 3' 末端 tRNA 衍生片段 (tRFs) 由 RNase III 内切酶 Dicer 加工外，我们还表明，包括血管生成素在内的几种 RNA 酶家族成员可以产生 tRFs，血管生成素可切割 TψC 环生成 3' tRFs。3' 末端 tRFs 而不是 5' tRFs 与基因组中人类内源性逆转录病毒序列高度互补。尽管它们独立于 Dicer 加工，但这些 tRFs 与 Ago2 结合，并能够通过体外转录切割来下调靶基因。我们认为，内源性 3' tRFs 通过 RNA 干扰途径在调节内源性病毒的不适当表达方面发挥作用。
