Byeon Boseon, Bilichak Andriy, Kovalchuk Igor
Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.
Noncoding RNA. 2017 Mar 24;3(2):17. doi: 10.3390/ncrna3020017.
Recently, a novel type of non-coding RNA (ncRNA), known as ncRNA fragments or ncRFs, has been characterised in various organisms, including plants. The biogenesis mechanism, function and abundance of ncRFs stemming from various ncRNAs are poorly understood, especially in plants. In this work, we have computationally analysed the composition of ncRNAs and the fragments that derive from them in various tissues of plants, including leaves, meristem tissue, pollen, unfertilized and fertilized ova, embryo and endosperm. Detailed analysis of transfer RNA (tRNA) fragments (tRFs), ribosomal RNA (rRNA) fragments (rRFs), small nucleolar RNA (snoRNA) fragments (snoRFs) and small nuclear RNA (snRNA) fragments (snRFs) showed a predominance of tRFs, with the 26 nucleotides (nt) fraction being the largest. Mapping ncRF reads to full-length mature ncRNAs showed a strong bias for one or both termini. tRFs mapped predominantly to the 5' end, whereas snRFs mapped to the 3' end, suggesting that there may be specific biogenesis and retention mechanisms. In the case of tRFs, specific isoacceptors were enriched, including tRNA and tRF. The analysis showed that the processing of 26-nt tRF5' occurred by cleavage at the last unpaired nucleotide of the loop between the D arm and the anticodon arm. Further support for the functionality of ncRFs comes from the analysis of binding between ncRFs and their potential targets. A higher average percentage of binding at the first half of fragments was observed, with the highest percentage being at 2-6 nt. To summarise, our analysis showed that ncRFs in are abundantly produced in a tissue-specific manner, with bias toward a terminus, the bias toward the size of generated fragments and the bias toward the targeting of specific biological processes.
最近，一种新型非编码RNA（ncRNA），即ncRNA片段或ncRFs，已在包括植物在内的各种生物体中得到表征。源自各种ncRNA的ncRFs的生物发生机制、功能和丰度尚不清楚，尤其是在植物中。在这项工作中，我们通过计算分析了植物各种组织（包括叶片、分生组织、花粉、未受精和受精的卵子、胚胎和胚乳）中ncRNA及其衍生片段的组成。对转移RNA（tRNA）片段（tRFs）、核糖体RNA（rRNA）片段（rRFs）、小核仁RNA（snoRNA）片段（snoRFs）和小核RNA（snRNA）片段（snRFs）的详细分析表明，tRFs占主导地位，其中26个核苷酸（nt）的部分最大。将ncRF读数映射到全长成熟ncRNA显示，对一个或两个末端存在强烈偏向。tRFs主要映射到5'端，而snRFs映射到3'端，这表明可能存在特定的生物发生和保留机制。就tRFs而言，特定的同工受体富集，包括tRNA和tRF。分析表明，26-nt tRF5'的加工是通过在D臂和反密码子臂之间环的最后一个未配对核苷酸处切割发生的。对ncRFs功能的进一步支持来自对ncRFs与其潜在靶标之间结合的分析。在片段的前半部分观察到更高的平均结合百分比，最高百分比在2-6 nt处。总之，我们的分析表明，植物中的ncRFs以组织特异性方式大量产生，对末端存在偏向，对产生片段的大小存在偏向，对特定生物过程的靶向存在偏向。
