基因组之外：揭示丁香（Syzygium aromaticum L.）组织特异性非编码rna。

IF 2.6 4区生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

3 Biotech Pub Date : 2025-04-01 Epub Date: 2025-03-09 DOI:10.1007/s13205-025-04251-3

Nitesh Kumar Sharma, Dwijesh Chandra Mishra, Baibhav Kumar, Sudhir Srivastava, Krishna Kumar Chaturvedi, Awani Kumar Singh, Sharanbasappa D Madival, Neeraj Budhlakoti, Girish Kumar Jha

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引用次数: 0

摘要

丁香（Syzygium aromaticum）因其在食品保鲜和医药方面的作用而受到重视，近年来其非编码rna （ncRNAs）引起了人们的研究兴趣。本研究从公开的RNAseq数据中发现了3274个长链非编码rna （lncRNAs）和2404个环状rna （circRNAs）。我们通过miRNA-lncRNA-mRNA网络相互作用确定了834个基因的调控。此外，35个lncrna被预测为17个microrna （mirna）的前体，突出了它们在转录后调控中的作用。对circrna的组织特异性分析显示，它们与1047种mirna相互作用，并在2382种信使rna （mrna）上竞争结合位点。这些结果强调了它们参与复杂的监管网络。为了支持进一步的研究和开发，我们开发了SaroNcRDb (http://backlin.cabgrid.res.in/saroncrdb/)，这是一个网络资源，提供了对已确定的ncrna的类型、染色体位置、组织分布和相互作用的详细见解。这一发现为未来研究利用ncrna在改善丁香农艺性状和次生代谢物生产中的调节作用铺平了道路。

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Beyond the genome: unveiling tissue-specific non-coding RNAs in clove (Syzygium aromaticum L.).

Clove (Syzygium aromaticum), valued for its role in food preservation and medicine, has recently drawn research interest for its noncoding RNAs (ncRNAs). This study discovers 3274 long noncoding RNAs (lncRNAs) and 2404 circular RNAs (circRNAs) from publicly available RNAseq data. We identified the regulation of 834 genes through miRNA-lncRNA-mRNA network interactions. Additionally, 35 lncRNAs were predicted as precursors for 17 microRNAs (miRNAs), highlighting their role in post-transcriptional regulation. Tissue-specific analysis of circRNAs revealed their interaction with 1047 miRNAs and competing for binding sites on 2382 messenger RNAs (mRNAs). These results underscore their involvement in complex regulatory networks. To support further research and development, we developed SaroNcRDb (http://backlin.cabgrid.res.in/saroncrdb/), a web resource providing detailed insights into the types, chromosomal locations, tissue distributions, and interactions of identified ncRNAs. The findings pave the way for future studies to harness the regulatory roles of ncRNAs in improving Clove's agronomic traits and secondary metabolite production.

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来源期刊

3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)

CiteScore

6.00

自引率

0.00%

发文量

314

期刊介绍： 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.