Department of Biotechnology, Panjab University, 160014, Chandigarh, India.
National Institute of Animal Biotechnology (NIAB), D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Opp. to Talkie Town, Miyapur, Hyderabad, 500 049, Telangana, India.
Sci Rep. 2019 Mar 5;9(1):3552. doi: 10.1038/s41598-019-38989-7.
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes-i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like 'photosynthesis' and 'oxidative phosphorylation'. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
长非编码 RNA（lncRNA）是长度大于 200 个核苷酸的转录物，它们作为动态调节分子而引人注目。我们利用来自叶片、花序和浆果组织的 10 个发育阶段的 RNA-seq 数据，通过计算方法，在葡萄（Vitis vinifera）中鉴定和描述了 56441 个 lncRNA。我们进行了差异表达分析，并确定了葡萄中 lncRNA 的组织和发育阶段特异性，这表明它们具有时空调节功能。通过共表达分析进行的功能注释表明，它们参与了与转录因子（TFs）同步的发育转变的调节。此外，途径富集分析显示，lncRNA 与生物合成和次生代谢途径有关。此外，我们鉴定了 115、560 和 133 个 lncRNA 分别作为潜在的 miRNA 前体、靶标和内源性靶标模拟物，这为调节 RNA 的相互作用提供了一个视角。我们还探索了 lncRNA 对染色体外基因的调节，即线粒体和叶绿体编码序列，并观察到它们参与了关键的生物学过程，如“光合作用”和“氧化磷酸化”。简而言之，这些转录本通过与编码和非编码 RNA 以及 TF 的相互作用，在葡萄中协调重要的生物学功能。我们的研究将有助于未来在这个具有经济重要性的水果作物中阐明发育的调节机制的实验。
