Hajieghrari Behzad, Farrokhi Naser, Goliaei Bahram, Kavousi Kaveh
Department of Biotechnology, Faculty of New Technologies Engineering, Shahid Beheshti University G.C., Evin, Tehran, Iran.
Departments of Biophysics and Bioinformatics laboratories, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
Microrna. 2016;5(1):66-77. doi: 10.2174/2211536605666160622102619.
MicroRNAs (miRNAs) are endogenous small non-coding RNAs with 18-24 nucleotides in length, which have important roles in posttranscriptional gene regulation. The resemblance of miRNA biogenesis in unicellular green algae and those in plants suggests probable evolutionary conserved pathways. This conservation provides a ground towards prediction of new homologs via computational biology.
Here, conserved miRNA genes in Chlamydomonas reinhardtii and plants were examined through homology alignment. Previously known and unique plant miRNAs were BLASTed against expressed sequence tags (ESTs) and genomic survey sequences (GSSs) of C. reinhardtii. All candidate sequences with appropriate fold back structures were screened according to a series of miRNA filtering criteria.
Homologous miRNAs (17), belonging to 9 miRNA gene families were predicted. Interestingly and for the first time, a miRNA family of genes was localized to chloroplast. Again and for the first time, here we report identification of C. reinhardtii miRNA orthologs in plants and animals. miRNA target genes were identified based on their sequence complementarities to the respective miRNAs using psRNATarget against C. reinhardtii, Unigene, and DFCI Gene Index (CHRGI). Totally, 152 potential target sites were identified. From the predicted miRNAs, 7 miRNAs had no target sequence in C. reinhardtii protein coding genes.
Identifying miRNA and their target transcript(s) would be useful for other research concerned with the function and regulatory mechanisms of C. reinhardtii miRNAs and helps researchers to better understand the nature of its extensive metabolic flexibility and environmental compatibility to survive in distinct environmental niches and nutrient availability.
微小RNA（miRNA）是长度为18 - 24个核苷酸的内源性小非编码RNA，在转录后基因调控中发挥重要作用。单细胞绿藻与植物中miRNA生物合成的相似性表明可能存在进化上保守的途径。这种保守性为通过计算生物学预测新的同源物提供了基础。
在此，通过同源比对研究了莱茵衣藻和植物中保守的miRNA基因。将先前已知的独特植物miRNA与莱茵衣藻的表达序列标签（EST）和基因组勘测序列（GSS）进行BLAST比对。根据一系列miRNA筛选标准筛选出所有具有合适回折结构的候选序列。
预测出属于9个miRNA基因家族的同源miRNA（17个）。有趣的是，首次发现一个miRNA基因家族定位于叶绿体。同样也是首次，我们在此报告了在植物和动物中鉴定出莱茵衣藻miRNA的直系同源物。使用psRNATarget针对莱茵衣藻、单基因簇和DFCI基因索引（CHRGI），根据miRNA与各自靶基因的序列互补性鉴定miRNA靶基因。总共鉴定出152个潜在靶位点。在预测的miRNA中，有7个在莱茵衣藻蛋白质编码基因中没有靶序列。
鉴定miRNA及其靶转录本将有助于其他有关莱茵衣藻miRNA功能和调控机制的研究，并帮助研究人员更好地理解其广泛的代谢灵活性和环境适应性的本质，以便在不同的环境生态位和养分可利用性条件下生存。
