Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thycaud P O, Poojappura, Thiruvananthapuram, 695 014 Kerala, India.
Funct Integr Genomics. 2012 Jun;12(2):387-95. doi: 10.1007/s10142-012-0267-2. Epub 2012 Feb 25.
Plant miRNAs (18-24nt) are generated by the RNase III-type Dicer endonuclease from the endogenous hairpin precursors ('pre-miRNAs') with significant regulatory functions. The transcribed regions display a higher frequency of microsatellites, when compared to other regions of the genomic DNA. Simple sequence repeats (SSRs) resulting from replication slippage occurring in transcripts affect the expression of genes. The available experimental evidence for the incidence of SSRs in the miRNA precursors is limited. Considering the potential significance of SSRs in the miRNA genes, we carried out a preliminary analysis to verify the presence of SSRs in the pri-miRNAs of black pepper (Piper nigrum L.). We isolated a (CT) dinucleotide SSR bearing transcript using SMART strategy. The transcript was predicted to be a 'pri-miRNA candidate' with Dicer sites based on miRNA prediction tools and MFOLD structural predictions. The presence of this 'miRNA candidate' was confirmed by real-time TaqMan assays. The upstream sequence of the 'miRNA candidate' by genome walking when subjected to PlantCARE showed the presence of certain promoter elements, and the deduced amino acid showed significant similarity with NAP1 gene, which affects the transcription of many genes. Moreover the hairpin-like precursor overlapped the neighbouring NAP1 gene. In silico analysis revealed distinct putative functions for the 'miRNA candidate', of which majority were related to growth. Hence, we assume that this 'miRNA candidate' may get activated during transcription of NAP gene, thereby regulating the expression of many genes involved in developmental processes.
植物 microRNA（18-24nt）由 RNase III 型 Dicer 内切酶从具有重要调控功能的内源性发夹前体（“pre-miRNA”）中产生。与基因组 DNA 的其他区域相比，转录区域显示出更高频率的微卫星。由于在转录过程中发生的复制滑动而产生的简单重复序列（SSR）会影响基因的表达。关于 SSR 在 miRNA 前体中的发生的可用实验证据是有限的。考虑到 SSR 在 miRNA 基因中的潜在重要性，我们进行了初步分析，以验证黑胡椒（Piper nigrum L.）miRNA 前体中 SSR 的存在。我们使用 SMART 策略分离了一个含有（CT）二核苷酸 SSR 的转录本。该转录本基于 miRNA 预测工具和 MFOLD 结构预测，被预测为具有 Dicer 位点的“pri-miRNA 候选物”。通过实时 TaqMan 测定证实了这种“miRNA 候选物”的存在。通过基因组步移获得的“miRNA 候选物”的上游序列在 PlantCARE 中显示存在某些启动子元件，并且推导的氨基酸与影响许多基因转录的 NAP1 基因具有显著相似性。此外，发夹样前体与邻近的 NAP1 基因重叠。计算机分析揭示了“miRNA 候选物”的不同潜在功能，其中大多数与生长有关。因此，我们假设该“miRNA 候选物”可能在 NAP 基因转录过程中被激活，从而调节参与发育过程的许多基因的表达。
