MepmiRDB: a medicinal plant microRNA database

Yu, Dongliang; Lu, Jiangjie; Shao, Weishan; Ma, Xiaoxia; Xie, Tian; Ito, Hidetaka; Wang, Tingzhang; Xu, Min; Huizhong, Wang; Meng, Yijun

doi:10.1093/database/baz070

Cited by 22 publications

(10 citation statements)

References 33 publications

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“…Recently, several computational approaches have been developed to elucidate the interactions of cross-species miRNAs and their targets in mammals. 14 , 15 However, miRNAs have selective distribution in different tissues, and even the same miRNA can play distinct roles in disease progression. 16 , 17 Thus, the biological roles of most exogenous plant miRNAs remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Exogenous Plant gma-miR-159a, Identified by miRNA Library Functional Screening, Ameliorated Hepatic Stellate Cell Activation and Inflammation via Inhibiting GSK-3β-Mediated Pathways

Yu¹,

Cai²,

Ying³

et al. 2021

JIR

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Plant-derived exogenous microRNAs (miRNAs) regulate human physiological functions by blocking the translation of target mRNAs. Although several computational approaches have been developed to elucidate the interactions of cross-species miRNAs and their targets in mammals, the number of verified plant miRNAs is still limited, and the biological roles of most exogenous plant miRNAs remain unknown. Methods: A miRNA mimic library-based phenotypic screening, which contained 8394 plant mature miRNAs published in the official database miRbase, was performed to identify more novel bioactive plant miRNAs for the prevention of hepatic fibrosis. Inhibition of candidates for the activation of hepatic stellate cells (HSCs) and the underlying mechanisms were evaluated in TGF-β1-and PDGF-exposed HSC models. The protective effects of the candidates against CCl 4 -induced liver fibrosis were evaluated in a mouse model. Results: Among the 8394 plant mature miRNAs reported in the official database miRBase, five candidates were found to effectively inhibit the differentiation of HSCs. gma-miR-159a (miR159a) exerted the strongest inhibitory activities on both TGF-β1-and PDGF-induced HSC activation and proliferation by inhibiting the GSK-3β-mediated NF-κB and TGF-β1 pathways. Moreover, miR159a was mainly accumulated in the liver after intravenous injection, and it reduced CCl 4 -induced hepatic fibrosis and inflammation in mice. Conclusion:Results indicated that miR159a has the therapeutic potential for preventing hepatic fibrosis. This study provides a novel strategy for achieving natural nucleic acid drugs.

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Section: Introductionmentioning

confidence: 99%

Exogenous Plant gma-miR-159a, Identified by miRNA Library Functional Screening, Ameliorated Hepatic Stellate Cell Activation and Inflammation via Inhibiting GSK-3β-Mediated Pathways

Yu¹,

Cai²,

Ying³

et al. 2021

JIR

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“…Intriguingly, several transcriptome-wide analyses in medicinal plants have well indicated that these ncRNAs whether siRNA or miRNA indeed have therapeutic properties which if harnessed systematically can help in the prevention of various chronic diseases such as cancer and influenza A virus infection [84]. In this context, a group of researchers have developed a miRNA database (MepmiRDB; medicinal plant microRNA database) devoted specifically for medicinal plants that provide plethora of information regarding gene sequence, expression levels and target miRNA for 30 different medicinal plants [85]. Besides, several software packages have also been developed such as sRNA-Seq-data, NATpipe, PLncPRO and CNIT that can greatly facilitate the identification ncRNAs, siRNAs and miRNAs in various medicinal plants as well as in crop plants that specifically involved in the regulation of secondary metabolites of therapeutic importance [85].…”

Section: Functional Genomics Approachmentioning

confidence: 99%

“…In this context, a group of researchers have developed a miRNA database (MepmiRDB; medicinal plant microRNA database) devoted specifically for medicinal plants that provide plethora of information regarding gene sequence, expression levels and target miRNA for 30 different medicinal plants [85]. Besides, several software packages have also been developed such as sRNA-Seq-data, NATpipe, PLncPRO and CNIT that can greatly facilitate the identification ncRNAs, siRNAs and miRNAs in various medicinal plants as well as in crop plants that specifically involved in the regulation of secondary metabolites of therapeutic importance [85].…”

Section: Functional Genomics Approachmentioning

confidence: 99%

Unlocking Pharmacological and Therapeutic Potential of Hyacinth Bean (Lablab purpureus L.): Role of OMICS Based Biology, Biotic and Abiotic Elicitors

Kumar¹,

Rai²,

Pandey-Rai³

2022

Legumes Research - Volume 2

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Hyacinth bean also known as Indian bean is multipurpose legume crops consumed both as food by humans and as forage by animals. Being a rich source of protein, it also produces distinct secondary metabolites such as flavonoids, phenols and tyrosinase which not only help strengthened plant’s own innate immunity against abiotic/biotrophic attackers but also play important therapeutic role in the treatment of various chronic diseases. However, despite its immense therapeutic and nutritional attributes in strengthening food, nutrition and therapeutic security in many developing countries, it is still considered as an “orphan crop” for unravelling its genetic potential and underlying molecular mechanisms for enhancing secondary metabolite production. Several lines of literatures have well documented the use of OMICS based techniques and biotic and abiotic elicitors for stimulating secondary metabolite production particularly in model as well as in few economically important crops. However, only limited reports have described their application for stimulating secondary metabolite production in underutilised crops. Therefore, the present chapter will decipher different dimensions of multi-omics tools and their integration with other conventional techniques (biotic and abiotic elicitors) for unlocking hidden genetic potential of hyacinth bean for elevating the production of secondary metabolites having pharmaceutical and therapeutic application. Additionally, the study will also provide valuable insights about how these advance OMICS tools can be successfully exploited for accelerating functional genomics and breeding research for unravelling their hidden pharmaceutical and therapeutic potential thereby ensuring food and therapeutic security for the betterment of mankind.

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“…Apart from these common tools, many plant miRNAs databases were also developed e.g. PmiREN: a comprehensive encyclopaedia of plant miRNAs [97], PMRD: plant miRNA database, PmiRExAt: : plant miRNA expression atlas database [98], MepmiRDB: : a medicinal plant miRNA database [99] etc. These databases can also be used as knowledge resource for plant based dietary miRNAs [100].…”

Section: Databases To Study Dietary/food-borne Mirnasmentioning

confidence: 99%

<strong>Diet-Derived Exogenous miRNAs As Functional Food Components: Facts and New Perspectives</strong>

Khurana¹,

Gupta²,

Varshney³

2021

Preprint

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Exogenous miRNAs derived from dietary substances have been shown to be orally transferred to the mammalian system and proven to remain active to regulate host-gene expression. This way they have become an active area of research as functional food components and aspects for dietary supplementation. They are being studied as a new class of metabolically targeted therapeutics that work through diet manipulation and may hold promise for a therapeutic approach in reducing the risk of life-threatening diseases. However, a substantial amount of evidence also defies this dietary miRNA concept in terms of their absorption, bioavailability, cellular uptake and its physiological effects in the mammalian system. But recent advances in the identification of some unique sequence and structural characteristics of dietary miRNAs and a deeper understanding of their stability in host peripheral blood for its cellular uptake have strengthened the whole concept. The review comprehensively summarizes the mechanism for miRNA extracellular transport, absorption through the gastrointestinal tract (GI), stability in peripheral blood, and cellular uptake in mammalian cells. It recapitulates the shreds of evidence, related to the influence of dietary miRNAs on gene expression based on the source of the origin (plant vs animal), and compares their cross-kingdom behaviour in terms of their unique sequence and stem-loop structure properties that help them to get stabilized in the mammalian system. The review also summarizes the parameters required for maintaining the sustainable uptake and bioavailability of the dietary miRNAs with existing examples of successful in-vivo and in-vitro delivery of dietary miRNA for augmented therapy. Lastly, it provides an overview of the available and required databases, webserver, and tools that can be used for the successful identification of potential dietary miRNA candidates.

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MepmiRDB: a medicinal plant microRNA database

Cited by 22 publications

References 33 publications

Exogenous Plant gma-miR-159a, Identified by miRNA Library Functional Screening, Ameliorated Hepatic Stellate Cell Activation and Inflammation via Inhibiting GSK-3β-Mediated Pathways

Exogenous Plant gma-miR-159a, Identified by miRNA Library Functional Screening, Ameliorated Hepatic Stellate Cell Activation and Inflammation via Inhibiting GSK-3β-Mediated Pathways

Unlocking Pharmacological and Therapeutic Potential of Hyacinth Bean (Lablab purpureus L.): Role of OMICS Based Biology, Biotic and Abiotic Elicitors

<strong>Diet-Derived Exogenous miRNAs As Functional Food Components: Facts and New Perspectives</strong>

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