Faculty of Engineering and Natural Sciences, Sabanci University, Orhanlı, Tuzla, Istanbul, Turkey.
PLoS One. 2013 Jul 23;8(7):e69801. doi: 10.1371/journal.pone.0069801. Print 2013.
MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow-sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat.
miRNAs 是一类短的、非编码的、单链 RNA，作为基因表达的转录后调控因子。对小麦 5D 染色体的 miRNA 进行了分析，在经过流式分选的 454GSFLXTi 序列中，对 5D 染色体进行了分析，总共有 3208630 个高质量读数，分别代表短臂（5DS）和长臂（5DL）的 1.34x 和 1.61x 覆盖率。在计算机和结构分析中，共发现了 55 个 miRNA；在 5DL 和 5DS 上分别发现了 48 个和 42 个 miRNA，其中 35 个 miRNA 是两个染色体臂共有的，而 13 个 miRNA 是 5DL 特有的，7 个 miRNA 是 5DS 特有的。总共，有 14 个预测的 miRNA 是首次在小麦中发现的。预测的 miRNA 的代表（每个 miRNA 的拷贝数）在 5DL（1949）中也高于 5DS（1191）。对每个 miRNA 进行了靶标预测，而表达分析则证明了 55 个 miRNA 中的 6 个表达。在 Brachypodiumdistachyon 和 Oryzasativa 基因组序列中也发现了相同的 miRNA 的出现，以鉴定同线性 miRNA 编码序列。基于此分析，在小麦 5DS 的 B.distaschyon 同线性区域中检测到了另外两个 miRNA：miR1133 和 miR167。预测的 miRNA 编码区中有 5 个（miR6220、miR5070、miR169、miR5085、miR2118）通过实验被验证位于 5D 染色体上，其中 3 个：miR2118、miR169 和 miR5085，被证明是 5D 特异性的。此外，miR2118 在春小麦的成年叶片中表达。本研究中鉴定的 miRNA 基因将扩展我们对面包小麦基因调控的理解。
