突变狼疮lncRNA的分析及其在干旱反应中的潜在作用。

IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Manuel Hidalgo, Cynthia Ramos, Gaston Zolla
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引用次数: 0

摘要

突变狼疮是一种具有高农艺潜力和可用转录组数据的豆类,其lncRNA尚未研究。因此,我们的目的是鉴定、表征和验证突变乳杆菌中的干旱响应lncRNA。为了实现这一点,我们使用了一种基于lncRNA预测、注释、亚细胞定位、热力学表征、结构守恒和验证的多级方法。因此,通过至少两种lncRNA鉴定算法鉴定了590个lncRNA。PLncDB数据库的注释显示,在28个植物科中,有571个tarwi特有的lncRNA和19个具有同源性的lncRNAs,包括茄科(19)、豆科(17)、十字花科(17),芸香科(17。总共有12个lncRNA在40多个物种中具有同源性。共有67%的lncRNA位于细胞质中,33%位于外泌体中。S03的热力学表征显示出稳定的二级结构,为-105.67kcal/mol。该结构包括三个区域,其中一个多分支环包含一个带有类似SECIS元素的发夹。CROSSalign对结构保守性的评估揭示了突变乳杆菌(S03)和番茄(Solyc04r022210.1)之间的部分相似性。RT-PCR验证表明,S03在突变乳杆菌的耐旱登录中上调。最后,这些结果强调了lncRNA在干旱条件下改善tarwi的重要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Analysis of lncRNAs in <i>Lupinus mutabilis</i> (Tarwi) and Their Potential Role in Drought Response.

Analysis of lncRNAs in <i>Lupinus mutabilis</i> (Tarwi) and Their Potential Role in Drought Response.

Analysis of lncRNAs in <i>Lupinus mutabilis</i> (Tarwi) and Their Potential Role in Drought Response.

Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response.

Lupinus mutabilis is a legume with high agronomic potential and available transcriptomic data for which lncRNAs have not been studied. Therefore, our objective was to identify, characterize, and validate the drought-responsive lncRNAs in L. mutabilis. To achieve this, we used a multilevel approach based on lncRNA prediction, annotation, subcellular location, thermodynamic characterization, structural conservation, and validation. Thus, 590 lncRNAs were identified by at least two algorithms of lncRNA identification. Annotation with the PLncDB database showed 571 lncRNAs unique to tarwi and 19 lncRNAs with homology in 28 botanical families including Solanaceae (19), Fabaceae (17), Brassicaceae (17), Rutaceae (17), Rosaceae (16), and Malvaceae (16), among others. In total, 12 lncRNAs had homology in more than 40 species. A total of 67% of lncRNAs were located in the cytoplasm and 33% in exosomes. Thermodynamic characterization of S03 showed a stable secondary structure with -105.67 kcal/mol. This structure included three regions, with a multibranch loop containing a hairpin with a SECIS-like element. Evaluation of the structural conservation by CROSSalign revealed partial similarities between L. mutabilis (S03) and S. lycopersicum (Solyc04r022210.1). RT-PCR validation demonstrated that S03 was upregulated in a drought-tolerant accession of L. mutabilis. Finally, these results highlighted the importance of lncRNAs in tarwi improvement under drought conditions.

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来源期刊
Non-Coding RNA
Non-Coding RNA Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
6.70
自引率
4.70%
发文量
74
审稿时长
10 weeks
期刊介绍: Functional studies dealing with identification, structure-function relationships or biological activity of: small regulatory RNAs (miRNAs, siRNAs and piRNAs) associated with the RNA interference pathway small nuclear RNAs, small nucleolar and tRNAs derived small RNAs other types of small RNAs, such as those associated with splice junctions and transcription start sites long non-coding RNAs, including antisense RNAs, long ''intergenic'' RNAs, intronic RNAs and ''enhancer'' RNAs other classes of RNAs such as vault RNAs, scaRNAs, circular RNAs, 7SL RNAs, telomeric and centromeric RNAs regulatory functions of mRNAs and UTR-derived RNAs catalytic and allosteric (riboswitch) RNAs viral, transposon and repeat-derived RNAs bacterial regulatory RNAs, including CRISPR RNAS Analysis of RNA processing, RNA binding proteins, RNA signaling and RNA interaction pathways: DICER AGO, PIWI and PIWI-like proteins other classes of RNA binding and RNA transport proteins RNA interactions with chromatin-modifying complexes RNA interactions with DNA and other RNAs the role of RNA in the formation and function of specialized subnuclear organelles and other aspects of cell biology intercellular and intergenerational RNA signaling RNA processing structure-function relationships in RNA complexes RNA analyses, informatics, tools and technologies: transcriptomic analyses and technologies development of tools and technologies for RNA biology and therapeutics Translational studies involving long and short non-coding RNAs: identification of biomarkers development of new therapies involving microRNAs and other ncRNAs clinical studies involving microRNAs and other ncRNAs.
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