In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.

Kohnehrouz, Bahram Baghban; Bastami, Meysam; Nayeri, Shahnoush

doi:10.1007/s12539-017-0240-9

Cited by 10 publications

(4 citation statements)

References 72 publications

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“…Onion contains ESTs and GSSs deposited in the National Centre for Biotechnology Information (NCBI), which could be used as the starting material for predicting miRNAs in this economically important plant species. A previous study had reported 9 onion miRNAs using the ESTs datasets [14]. In the present study, we used a robust homology based comparative algorithm approach for the detection of onion miRNAs and their targets from the EST and GSS datasets.…”

Section: Introductionmentioning

confidence: 99%

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

et al. 2019

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MicroRNAs are small non-coding RNAs of 21-24 nucleotides in length that acts as important modulators of gene expression related to numerous biological processes including development and defense response in eukaryotes. However, only a limited report on onion (Allium cepa) miRNAs is available and their associated role in growth and development of onion is not yet clear. Therefore, it is of interest to identify miRNAs and their targets in Allium cepa using the genome survey sequences (GSSs) and expressed sequence tags (ESTs) and deduce the functions of the target genes using gene ontology (GO) terms. We report 14 potential miRNAs belonging to 13 different families (miR162, miR168, miR172c, miR172e, miR398, miR400, miR414, miR1134, miR1223, miR6219, miR7725, miR8570, miR8703 and miR8752). BLAST analysis using psRNATarget server predicted 39 potential targets for the identified miRNAs majority of which were transcription factors implicated in plant growth, development, hormone signaling and stress responses. These data forms the basis for further analysis and verification towards understanding the miRNA mediated regulatory mechanism in Allium cepa.

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Section: Introductionmentioning

confidence: 99%

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

et al. 2019

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“…miRNAs regulate gene expression through translational repression or target mRNA degradation ( Chekulaeva & Filipowicz, 2009 ) . Among Allium crops, two reports have reported discovery of miRNA in garlic and onion by using the in silico approach ( Panda et al, 2014 ; Kohnehrouz, Bastami & Nayeri, 2018 ). Fusarium oxysporum f. sp.…”

Section: Survey Methodologymentioning

confidence: 99%

Omics approaches inAlliumresearch: Progress and way ahead

Khandagale

Krishna

Roylawar

et al. 2020

PeerJ

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Background The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. Method In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. Results Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. Conclusion All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

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“…MicroRNAs (miRNAs) are small non-coding endogenous RNAs containing 20-25 nucleotides that regulate gene expression at the post-transcriptional level via sequencespecific interactions with 3'-untranslatedregions (UTRs) in miRNAs and also via inhibition of translation or degradation of miRNAs (1)(2)(3). miRNAs play a significant role in crucial biological processes, such as cell proliferation, apoptosis, development, differentiation, and metabolism, and miRNAs are especially associated with carcinogenesis (4)(5)(6)(7)(8). Several studies have indicated that aberrantly expressed miRNAs might serve as oncogenes or tumor suppressor genes in cancers (9)(10)(11)(12).…”

Section: Introductionmentioning

confidence: 99%

MicroRNA analysis of NCI-60 human cancer cells indicates that miR-720 and miR-887 are potential therapeutic biomarkers for breast cancer

Wang

Zhao

et al. 2020

DD&T

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miRNA, NCI-60, lineage-specific, miR-720, miR-887 MicroRNAs (miRNAs) play a vital role in many biological processes, including cell growth, differentiation, apoptosis, development, differentiation, and carcinogenesis. Since miRNAs might play a part in cancer initiation and progression, they comprise an original class of promising diagnostic and prognostic molecular markers. In order to systematically understand the regulation of miRNA expression in cancers, the current study analyzed the miRNA expression profile in NCI-60 human cancer cell lines. Over 300 miRNAs exhibited unique expression profiles in cell lines derived from the same lineage. This study identified 9 lineage-specific miRNA expression patterns. Moreover, results indicated that miR-720 and miR-887 are expressed at relatively high levels in breast cancer cell lines compared to other types of cancer. Ultimately, matching NCI-60 drug response data to miR-720 and miR-887 expression profiles revealed that several FDAapproved drugs were inversely related to miR-720 and miR-887. Furthermore, the anti-cancer effect of perifosine was significantly enhanced by inhibiting miR-720 and decreased by miR-720 precursor treatment in breast cancer cell lines. 5-Fu treatment was enhanced by inhibiting miR-887 and decreased by miR-887 precursor treatment. The current results offer insight into the relationship between miRNA expression and their lineage types, and the approach used here represents a potential cancer therapy with the help of miRNAs.

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In Silico Identification of Novel microRNAs and Targets Using EST Analysis in Allium cepa L.

Cited by 10 publications

References 72 publications

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

Analysis of microRNAs and their targets from onion (Allium cepa) using genome survey sequences (GSS) and expressed sequence tags (ESTs)

Omics approaches inAlliumresearch: Progress and way ahead

MicroRNA analysis of NCI-60 human cancer cells indicates that miR-720 and miR-887 are potential therapeutic biomarkers for breast cancer

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