Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing

He, Xiangfeng; Shenkute, Awraris Getachew; Wang, Wenhe; Xu, Shufa

doi:10.1038/s41598-018-21193-4

Cited by 9 publications

(7 citation statements)

References 86 publications

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“…Total RNA in different cells and serum was extracted with TRIzol reagent. The extraction method was carried out according to the instruction [20]. Reverse transcription was performed using the Prime-Script RT kit (Takara, Tokyo, Japan) at 37°C for 30 min, followed by 42°C for 30 min and 75°C for 5 min.…”

Section: Rna Isolation and Qrt-pcrmentioning

confidence: 99%

MiR-221-3p as a Potential Biomarker for Patients with Psoriasis and Its Role in Inflammatory Responses in Keratinocytes

Meng

Qiu²,

Zhang

2021

Skin Pharmacol Physiol

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Introduction: This study investigated serum miR-221-3p levels in psoriatic patients and the characterization of serum miR-221-3p in keratinocyte inflammatory responses was further assessed. Methods: qRT-PCR was used to detect the expression level of miR-221-3p in the serum of 46 patients with psoriasis and 42 healthy controls. The receiver operating characteristic curve evaluated the diagnostic ability of miR-221-3p in psoriasis. The effect of miR-221-3p on HaCaT cell proliferation was detected by using a cell counting Kit-8 and Transwell. ELISA was used to detect serum and keratinocyte pro-inflammatory factors. Results: miR-221-3p was significantly increased in the serum of patients with psoriasis. The area under the curve was 0.861, the sensitivity was 80.4%, and the specificity was 85.7%. Serum miR-221-3p was positively correlated with the expression levels of tumor necrosis factor-α, interleukin (IL)-17A, and IL-22. Cell experiments showed that reducing the expression of miR-221-3p could significantly inhibit cell proliferation. Additionally, miR-221-3p downregulation also inhibited the release of some inflammatory factors in the HaCaT cells. Discussion/Conclusion: MiR-221-3p is a latent biomarker of psoriasis patients. Lower expression of miR-221-3p inhibits the cell proliferation and inflammatory responses of HaCaT cells, which offers a possible target for the therapeutic interventions of psoriasis.

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Section: Rna Isolation and Qrt-pcrmentioning

confidence: 99%

MiR-221-3p as a Potential Biomarker for Patients with Psoriasis and Its Role in Inflammatory Responses in Keratinocytes

Meng

Qiu²,

Zhang

2021

Skin Pharmacol Physiol

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“…Therefore, we believe that the pathways controlling these processes deserve intensive research focus. The commonly used NGS technique allows for comprehensive analyses of sRNAoms, transcriptoms, and degradomes, as well as identification of sRNAs and their target genes in both model and non-model plants, for example: tomato [58], soybean [59], Arabidopsis [60,61], oilseed rape [62], Brassica juncea [63], lily [64,65], peanut [66], orchardgrass [67] or wheat [68,69].…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Glazińska

Kulasek

Glinkowski

et al. 2019

Preprint

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Background Yellow lupine (Lupinus luteus L., Taper c.) is an important legume crop. However, its flower development and pod formation are often affected by excessive abscission. Organ detachment occurs within the abscission zone (AZ) and in L. luteus primarily affects flowers formed at the top of the inflorescence. The top flowers’ fate appears determined before anthesis. The organ development and abscission mechanisms utilize a complex molecular network, not yet not fully understood, especially as to the role of miRNAs and siRNAs. We aimed at identifying differentially expressed (DE) small ncRNAs in lupine by comparing small RNA-seq libraries generated from developing upper and lower raceme flowers, and flower pedicels with active and inactive AZs. Their target genes were also identified using transcriptome and degradome sequencing. Results Within all the libraries, 394 known and 28 novel miRNAs and 316 phased siRNAs were identified. In flowers at different stages of development, 30 miRNAs displayed DE in the upper and 29 in the lower parts of the raceme. In comparisons between upper and lower raceme flowers, a total of 46 DE miRNAs were identified. miR393 and miR160 were related to the upper and miR396 to the lower flowers and pedicels of non-abscising flowers. In flower pedicels we identified 34 DE miRNAs, with miR167 being the most abundant of all. Most siRNAs seem to play a marginal role in the processes studied herein, with the exception of tasiR-ARFs, which were DE in the developing flowers. The target genes of these miRNAs were predominantly categorized into the following Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways: ‘Metabolism’ (15,856), ‘Genetic information processing’ (5,267), and ‘Environmental information processing’ (1,517). Over 700 putative targets were categorized as belonging to the ‘Plant Hormone Signal Transduction pathway’. 26,230 target genes exhibited Gene Ontology (GO) terms: 23,092 genes were categorized into the ‘Cellular component’, 23,501 into the ‘Molecular function’, and 22,939 into the ’Biological process’. Conclusion Our results indicate that miRNAs and siRNAs in yellow lupine may influence the development of flowers and, consequently, their fate by repressing their target genes, particularly those associated with the homeostasis of phytohormones, mainly auxins.

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“…By using RNA sequencing technology, stress-induced key genes can be identified and analyzed. These can then be manipulated by genetic methods to improve stress tolerance in crops [49], and provide new insights into physiological changes at the transcriptional level [51]. To date, considerable research focused on the transcriptional responses to cold stress in a number of lily species, including L. lancifolium [4,44,51], L. longiflorum [41], L. sorbonne [42,46], and L. pumilum [43].…”

Section: Introductionmentioning

confidence: 99%

“…These can then be manipulated by genetic methods to improve stress tolerance in crops [49], and provide new insights into physiological changes at the transcriptional level [51]. To date, considerable research focused on the transcriptional responses to cold stress in a number of lily species, including L. lancifolium [4,44,51], L. longiflorum [41], L. sorbonne [42,46], and L. pumilum [43]. These studies identified a large number of genes related to cold stress that are involved in a variety of biological processes [4], indicating that lilies have the ability to induce a series of transcriptome changes during the vernalization process [42][43]46].…”

Section: Introductionmentioning

confidence: 99%

Physiological and transcriptomic responses of Lanzhou Lily (Lilium davidii, var. unicolor) to cold stress

Tian

Xie

2020

PLoS ONE

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Low temperature induces changes in plants at physiological and molecular levels, thus affecting growth and development. The Lanzhou lily (Lilium davidii, var. unicolor) is an important medicinal plant with high economic value. However, the molecular mechanisms underlying its photosynthetic and antioxidation responses to low temperature still remain poorly understood. This study subjected the Lanzhou lily to the two temperatures of 20˚C (control) and 4˚C (low temperature) for 24 h. Physiological parameters related to membrane integrity, photosynthesis, antioxidant system, and differentially expressed genes were investigated. Compared with control, low temperature increased the relative electrical conductivity by 43.2%, while it decreased net photosynthesis rate, ratio of variable to maximal fluorescence, and catalase activity by 47.3%, 10.1%, and 11.1%, respectively. In addition, low temperature significantly increased the content of soluble protein, soluble sugar, and proline, as well as the activity of superoxide dismutase and peroxidase. Comparative transcriptome profiling showed that a total of 238,109 differentially expressed genes were detected. Among these, 3,566 were significantly upregulated while 2,982 were significantly downregulated in response to low temperature. Gene Ontology enrichment analysis indicated that in response to low temperature, the mostly significantly enriched differentially expressed genes were mainly involved in phosphorylation, membrane and protein kinase activity, as well as photosynthesis, light harvesting, light reaction, and alpha,alpha-trehalose-phosphate synthase activity. Kyoto Encyclopedia of Genes and Genomes enrichment analysis also indicated that the most significantly enriched pathways involved ribosome biogenesis in eukaryotes, phenylalanine metabolism, circadian rhythm, porphyrin and chlorophyll metabolism, photosynthesis of antenna proteins, photosynthesis, and carbon fixation in photosynthetic organisms. Moreover, the expression patterns of 10 randomly selected differentially expressed genes confirmed the RNA-Seq results. These results expand the understanding of the physiological and molecular mechanisms underlying the response of the Lanzhou lily to low temperature stress.

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Characterization of Conserved and Novel microRNAs in Lilium lancifolium Thunb. by High-Throughput Sequencing

Cited by 9 publications

References 86 publications

MiR-221-3p as a Potential Biomarker for Patients with Psoriasis and Its Role in Inflammatory Responses in Keratinocytes

MiR-221-3p as a Potential Biomarker for Patients with Psoriasis and Its Role in Inflammatory Responses in Keratinocytes

Integrated analysis of small RNA, transcriptome and degradome sequencing provides new insights into floral development and abscission in yellow lupine (Lupines luteus L.)

Physiological and transcriptomic responses of Lanzhou Lily (Lilium davidii, var. unicolor) to cold stress

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