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1
Karagun, Barbaros Sahin, Bulent Antmen, Ilgen Sasmaz, Kahraman Tanriverdi, Gulsum Ucar, and Yurdanur Kilinc. "Micro-RNA Profile of Childhood Acute Lymphoblastic Leukemia." Blood 120, no. 21 (November 16, 2012): 4824. http://dx.doi.org/10.1182/blood.v120.21.4824.4824.
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Abstract Abstract 4824 Micro-RNAs are functional, non-protein coding RNA molecules and their transcriptions provided by intron or exon regions of the genome and non-protein coding regions of RNA genes. The role of micro-RNAs in acute leukemia has become the subject of research increasingly. In this study we aimed to identify micro-RNA profiles in the childhood acute leukemia that one of hematologic malignancies. Fourty nine patients who were diagnosed with acute leukemia and admitted to Cukurova University Faculty of Medicine Department of Pediatric Hematology between December 2010 and September 2011. Blood samples were taken twice in patient groups at diagnosis and during remission and plasma samples were stored. Blood samples were taken once in the healthy group and plasma were separated. The plasma samples were investigated by PCR analysis of micro-RNA. Acute leukemia was diagnosed by cytomorphological, immuno histochemical and flow cytometric studies. Thirtyone patients who were diagnosed with ALL and fortyseven healthy children as a control group were included to study. miR20a, miR25, miR92a, miR30c, miR106b, miR203, miR150, miR192, miR302c, miR184, miR218, miR320, miR342-3p, miR223, miR328, miR483-5p, miR376a, miR381, miR451, miR576-3p, miR548a levels were increased in newly diagnosed ALL patients when compared to healthy controls (p <0.05). The miR20b, miR342-3p and miR548a levels were found higher in healthy controls than the newly diagnosed ALL patients group (p <0.05) Healthy control groups when compared with pediatric ALL patients whose in remission; miR769-3p, miR20a, miR92a, miR16, miR27b, miR192, miR320, miR223, miR484, miR451 levels were found higher in healthy control groups than the patients. Newly diagnosed pediatric ALL patients compared with patients whose in remission; miR30c, miR106b, miR25, miR184, miR218, miR302c, miR483-5p levels were increased in newly diagnosed pediatric ALL patients than ALL patients whose in remission (p<0.05). miRNAs are thought to be identified at a different level of expression in normal and pathological tissues can be determined between the miRNAs that are effective diagnosis and treatment of human cancers. We showed the microRNA profils that may play new roles treatment of acute leukemia in the futures. Disclosures: Kilinc: ApoPharma Inc.: Research Funding.
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Cao, Chunyu, Ruicai Long, Tiejun Zhang, Junmei Kang, Zhen Wang, Pingqing Wang, Hao Sun, Jie Yu, and Qingchuan Yang. "Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing." International Journal of Molecular Sciences 19, no. 12 (December 17, 2018): 4076. http://dx.doi.org/10.3390/ijms19124076.
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Saline-alkaline stress is a universal abiotic stress that adversely affects plant growth and productivity. Saline-alkaline conditions results in plant abnormal transcriptome expression finally manifesting as defective phenotypes. Considerable research has revealed the active role of microRNA in various stress conditions. This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 (Medicago truncatula). The miRNA contained in the total RNA extracted from Medicago truncatula seedlings (72 h) that had been treated with solutions mimicking saline and alkaline soils was subjected to miRNA deep sequencing. The Illumina HiSeq sequencing platform was used to analyze nine small RNA libraries of three treatment groups: distilled water, 20 mM NaCl + Na2SO4 and 5 mM Na2CO3 + NaHCO3. Sequencing revealed that 876 miRNAs including 664 known miRNAs and 212 potential novel miRNAs were present in all the libraries. The miR159 family, miR156 family, miR2086-3p, miR396, miR166, miR319, miR167, miR5213-5p, miR1510 and miR2643 were among the most expressed miRNAs in all libraries. The results of miRNAs expression under treatments were validated by reverse-transcription quantitative PCR (RT-qPCR). Target gene prediction through computational analysis and pathway annotation analysis revealed that the primary pathways affected by stress were related to plant development, including metabolic processes, single-organism processes and response to the stimulus. Our results provide valuable information towards elucidating the molecular mechanisms of salt/alkali tolerance in Medicago truncatula and provide insight into the putative role of miRNAs in plant stress resistance.
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Narducci, M. G., D. Arcelli, M. C. Picchio, C. Lazzeri, E. Pagani, F. Sampogna, E. Scala, et al. "MicroRNA profiling reveals that miR-21, miR486 and miR-214 are upregulated and involved in cell survival in Sézary syndrome." Cell Death & Disease 2, no. 4 (April 2011): e151-e151. http://dx.doi.org/10.1038/cddis.2011.32.
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Cao, Huiying, Xinyue Zhang, Yanye Ruan, Lijun Zhang, Zhenhai Cui, Xuxiao Li, and Bing Jia. "miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato." PLOS ONE 15, no. 12 (December 17, 2020): e0237690. http://dx.doi.org/10.1371/journal.pone.0237690.
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Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.
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Ding, Yueyun, Yinhui Hou, Zijing Ling, Qiong Chen, Tao Xu, Lifei Liu, Na Yu, et al. "Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes." International Journal of Molecular Sciences 23, no. 20 (October 20, 2022): 12596. http://dx.doi.org/10.3390/ijms232012596.
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Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.
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Ma, Jingyi, Pan Zhao, Shibiao Liu, Qi Yang, and Huihong Guo. "The Control of Developmental Phase Transitions by microRNAs and Their Targets in Seed Plants." International Journal of Molecular Sciences 21, no. 6 (March 13, 2020): 1971. http://dx.doi.org/10.3390/ijms21061971.
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Seed plants usually undergo various developmental phase transitions throughout their lifespan, mainly including juvenile-to-adult and vegetative-to-reproductive transitions, as well as developmental transitions within organ/tissue formation. MicroRNAs (miRNAs), as a class of small endogenous non-coding RNAs, are involved in the developmental phase transitions in plants by negatively regulating the expression of their target genes at the post-transcriptional level. In recent years, cumulative evidence has revealed that five miRNAs, miR156, miR159, miR166, miR172, and miR396, are key regulators of developmental phase transitions in plants. In this review, the advanced progress of the five miRNAs and their targets in regulating plant developmental transitions, especially in storage organ formation, are summarized and discussed, combining our own findings with the literature. In general, the functions of the five miRNAs and their targets are relatively conserved, but their functional divergences also emerge to some extent. In addition, potential research directions of miRNAs in regulating plant developmental phase transitions are prospected.
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Seyyedi, Samaneh Sadat, Masoud Soleimani, Marjan Yaghmaie, Monireh Ajami, Mansoureh Ajami, Shahram Pourbeyranvand, Kamran Alimoghaddam, and Seyed Mohammad Akrami. "Deregulation of miR-1, miR486, and let-7a in cytogenetically normal acute myeloid leukemia: association with NPM1 and FLT3 mutation and clinical characteristics." Tumor Biology 37, no. 4 (November 2, 2015): 4841–47. http://dx.doi.org/10.1007/s13277-015-4289-y.
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Puchta, Marta, Jolanta Groszyk, Magdalena Małecka, Marek D. Koter, Maciej Niedzielski, Monika Rakoczy-Trojanowska, and Maja Boczkowska. "Barley Seeds miRNome Stability during Long-Term Storage and Aging." International Journal of Molecular Sciences 22, no. 9 (April 21, 2021): 4315. http://dx.doi.org/10.3390/ijms22094315.
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Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.
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Salih, Haron, Wenfang Gong, Mtawa Mkulama, and Xiongming Du. "Genome-wide characterization, identification, and expression analysis of the WD40 protein family in cotton." Genome 61, no. 7 (July 2018): 539–47. http://dx.doi.org/10.1139/gen-2017-0237.
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WD40 repeat proteins are largely distributed across the plant kingdom and play an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization, and expression level analysis of WD40 genes in cotton. A total of 579, 318, and 313 WD40 genes were found in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during the initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950, and miR7505. The findings provide a stronger indication of WD40 gene function and their involvement in the regulation of cotton fiber development during the initiation and elongation stages.
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Gao, Shiwu, Yingying Yang, Yuting Yang, Xu Zhang, Yachun Su, Jinlong Guo, Youxiong Que, and Liping Xu. "Identification of Low-Nitrogen-Related miRNAs and Their Target Genes in Sugarcane and the Role of miR156 in Nitrogen Assimilation." International Journal of Molecular Sciences 23, no. 21 (October 29, 2022): 13187. http://dx.doi.org/10.3390/ijms232113187.
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Chemical nitrogen (N) fertilizer is widely used in sugarcane production, especially in China and India. Understanding the molecular mechanisms and mining miRNAs and their target genes associated with nitrogen use efficiency (NUE) in sugarcane can aid in developing the N-efficient varieties, and thus is beneficial to reduce N fertilizer application. In this study, the root miRNA database of N-efficient sugarcane variety ROC22 under low N stress (0.3 mM NH4NO3) for 3 h was constructed, along with their transcriptome-rearranged data. KEGG analysis indicated that those candidate target genes, corresponding to differentially expressed miRNAs, were mainly enriched in N metabolism, amino acid metabolism, carbohydrate metabolism, photosynthesis, and hormone signal transduction pathways. It was found that under low N stress for 0–24 h, there was a negative correlation between miR168 and SPX, along with miR396 and acnA. Furthermore, the expression of miR156 in the roots of ROC22 was significantly up-regulated under low N treatment. Compared with the wild-type, the Arabidopsis plants overexpressing sugarcane miR156 exhibited significantly improved length and surface area of roots, while the expression of one NO3− transporter gene NRT1.1, three N assimilation key genes (NR1, NIR1, and GS), and the activity of two N assimilation key enzymes (NR and GS) were up-regulated under low N treatment. It can be reasonably deduced that sugarcane miR156 can enhance the nitrogen assimilation ability of the overexpressed Arabidopsis plants under low N application, and thus has a potential ability for improving sugarcane NUE. The present study should be helpful for understanding the molecular regulatory network in the N-efficient sugarcane genotype responding to low N stress and could provide the candidate miRNAs with a potential function in improving sugarcane NUE.
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Liu, LingLing, Chao Fang, YinZe Sun, and WuJun Liu. "Evaluation of key miRNAs during early pregnancy in Kazakh horse using RNA sequencing." PeerJ 9 (February 23, 2021): e10796. http://dx.doi.org/10.7717/peerj.10796.
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Background miRNA has an important role in cell differentiation, biological development, and physiology. Milk production is an important quantitative trait in livestock and miRNA plays a role in the amount of milk produced. Methods The role of regulatory miRNAs involved in equine milk production is not fully understood. We constructed two miRNA libraries for Kazakh horse milk production from higher-producing (H group) and lower-producing (L group) individuals, and used RNA-Seq technology to identify the differentially expressed miRNAs between the two milk phenotypes of Kazakh horses. Results A total of 341 known and 333 novel miRNAs were detected from the H and L groups, respectively. Eighty-three differentially expressed miRNAs were identified between the H and L group s, of which 32 were known miRNAs (27 were up-regulated, five were down-regulated) and 51 were novel miRNAs (nine were up-regulated, 42 were down-regulated). A total of 2,415 genes were identified. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that these genes were annotated to mammary gland development, mammary gland morphogenesis, tissue development and PI3K-Akt signaling pathways, insulin signaling pathway and TGF-beta signaling pathway, among others. Five miRNAs (miR-199a-3p, miR143, miR145, miR221, miR486-5p) were identified as affecting horse milk production and these five miRNAs were validated using qRT-PCR. Conclusions We described a methodology for the transcriptome-wide profiling of miRNAs in milk, which may help the design of new intervention strategies to improve the milk yield of Kazakh horses.
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Wang, Li-Sheng, Ling Li, Liang Li, Keh-Dong Shiang, Min Li, Su Chu, and Ravi Bhatia. "Role of MicroRNA-486-5p Overexpression In CML CD34+ Cells In Modulating BCR-ABL Mediated Hematopoietic Stem/Progenitor Cell Transformation and Imatinib Sensitivity." Blood 118, no. 21 (November 18, 2011): 1667. http://dx.doi.org/10.1182/blood.v118.21.1667.1667.
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Abstract Abstract 1667 MicroRNAs are key regulators of gene expression that regulate normal differentiation and contribute to malignant transformation of hematopoietic cells. Using microRNA microarrays we identified increased expression of miR-486 in chronic myeloid leukemia (CML) compared to normal CD34+ cells. In both normal and CML cells, miR-486 expression level was significantly higher in MEP compared to HSC, GMP and CMP populations. Treatment with Imatinib resulted in reduced expression of miR-486-5p in CML CD34+ cells, suggesting that upregulation of miR-486-5p expression was at least in part BCR-ABL kinase dependent. Consistent with this ectopic expression of BCR-ABL in cord blood CD34+ cells using retroviral vectors resulted in 4.2 fold increase in miR-486-5p expression. miR-486-5p is located within the last intron of the Ankyrin-1 gene on chromosome 8 and is enriched in muscle cells. However, the role of miR-486-5p in normal and leukemic hematopoiesis has not been evaluated. To explore the role of miR-486-5p in growth and differentiation of hematopoietic progenitor cells (HSPC), we first overexpressed hsa-miR-486-5p pre-microRNA in normal CD34+ cells using lentiviral vectors. CB CD34+ cells overexpressing miRNA-486-5p generated modestly increased numbers of cells (1.22 fold) in culture with SCF, IL-3, GM-CSF, G-CSF and EPO for 6 days compared to cells expressing control vectors, with increased numbers of erythroid cells and reduced numbers of myeloid cells. We further investigated the role of miR-486-5p on growth and differentiation of normal and leukemic HSPC by inhibiting miR-486-5p expression using a modified pmiRZip lentivirus vector expressing an anti-miR-486-5p sequence and comparing to cells expressing a control scrambled anti-miRNA sequence. Expression of anti-miR-486-5p resulted in reduced proliferation of normal CD34+ cells (32±10% inhibition) and BCR-ABL transformed CD34+ cells (38±7 % inhibition) with significantly greater inhibition of erythroid compared to myeloid cells. Anti-miR486-5p expression resulted in significantly increased apoptosis of BCR-ABL-transformed CD34+ cells but not normal CD34+ cells (CML CD34+ cells: scramble 11.1±2.4%, anti-miR-486-5p 14.7±1.7 % p=0.02; Normal CD34+ cells: scramble 9.7±5.4%, anti-486-5p 13.4±7.9% p=0.15). Importantly, anti-miR-486-5p significantly enhanced the sensitivity of BCR-ABL transformed CD34+ cells to imatinib-mediated apoptosis [combination of scramble with IM: 17.7±8.1%; anti-miR-486-5p with IM: 26.4±13%]. A search for conserved miR-486-5p target genes in the TargetScan database identified the important hematopoietic negative regulatory factors Foxo1 and Pten amongst the highest ranking targets. Using pMIR-REPORT constructs containing miR-486-5p seed sites within the Foxo1 and Pten 3'-UTR we showed that Foxo1 and Pten are direct targets of miR-486-5p. Expression of anti-miR-486-5p increased Foxo1 and Pten protein expression and decreased active Akt in normal and CML CD34+ cells. Knockdown of Foxo1 using shRNA partly blocked the suppressive effects of anti-miR486-5p on the growth of CD34+ cells. In summary, we have shown that miR-486-5p expression is modulated during hematopoietic differentiation and plays an important role in regulating hematopoietic progenitor growth and differentiation towards the erythroid lineage. We further show that miR-486-5p expression is enhanced in CML CD34+ cells, related at least in part to BCR-ABL kinase activity, and contributes to enhanced progenitor growth and survival. Inhibition of miR-486-5p results in enhanced sensitivity of CML CD34+ cells to IM-induced apoptosis. miR-486-5p effects are mediated at least in part through inhibition of Foxo1 and Pten expression. We conclude that miR-486-5p represents a novel regulatory mechanism that promotes erythroid differentiation in normal hematopoiesis and modulates Bcr-Abl-mediated transformation and tyrosine kinase inhibitor sensitivity in CML progenitors. Disclosures: No relevant conflicts of interest to declare.
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Perea-García, Ana, Amparo Andrés-Bordería, Peter Huijser, and Lola Peñarrubia. "The Copper-microRNA Pathway Is Integrated with Developmental and Environmental Stress Responses in Arabidopsis thaliana." International Journal of Molecular Sciences 22, no. 17 (September 2, 2021): 9547. http://dx.doi.org/10.3390/ijms22179547.
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As an essential nutrient, copper (Cu) scarcity causes a decrease in agricultural production. Cu deficiency responses include the induction of several microRNAs, known as Cu-miRNAs, which are responsible for degrading mRNAs from abundant and dispensable cuproproteins to economize copper when scarce. Cu-miRNAs, such as miR398 and miR408 are conserved, as well as the signal transduction pathway to induce them under Cu deficiency. The Arabidopsis thaliana SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) family member SPL7 binds to the cis-regulatory motifs present in the promoter regions of genes expressed under Cu deficiency, including Cu-miRNAs. The expression of several other SPL transcription factor family members is regulated by miR156. This regulatory miR156-SPL module plays a crucial role in developmental phase transitions while integrating internal and external cues. Here, we show that Cu deficiency also affects miR156 expression and that SPL3 overexpressing plants, resistant to miR156 regulation, show a severe decrease in SPL7-mediated Cu deficiency responses. These include the expression of Cu-miRNAs and their targets and is probably due to competition between SPL7 and miR156-regulated SPL3 in binding to cis-regulatory elements in Cu-miRNA promoters. Thus, the conserved SPL7-mediated Cu-miRNA pathway could generally be affected by the miR156-SPL module, thereby underscoring the integration of the Cu-miRNA pathway with developmental and environmental stress responses in Arabidopsis thaliana.
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López-Ruiz, Brenda A., Vasti T. Juárez-González, Estela Sandoval-Zapotitla, and Tzvetanka D. Dinkova. "Development-Related miRNA Expression and Target Regulation during Staggered In Vitro Plant Regeneration of Tuxpeño VS-535 Maize Cultivar." International Journal of Molecular Sciences 20, no. 9 (April 27, 2019): 2079. http://dx.doi.org/10.3390/ijms20092079.
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In vitro plant regeneration addresses basic questions of molecular reprogramming in the absence of embryonic positional cues. The process is highly dependent on the genotype and explant characteristics. However, the regulatory mechanisms operating during organ differentiation from in vitro cultures remain largely unknown. Recently, miRNAs have emerged as key regulators during embryogenic callus induction, plant differentiation, auxin responses and totipotency. Here, we explored how development-related miRNA switches the impact on their target regulation depending on physiological and molecular events taking place during maize Tuxpeño VS-535 in vitro plant regeneration. Three callus types with distinctive regeneration potential were characterized by microscopy and histological preparations. The embryogenic calli (EC) showed higher miRNA levels than non-embryogenic tissues (NEC). An inverse correlation for miR160 and miR166 targets was found during EC callus induction, whereas miR156, miR164 and miR394 displayed similar to their targets RNA accumulation levels. Most miRNA accumulation switches took place early at regenerative spots coincident with shoot apical meristem (SAM) establishment, whereas miR156, miR160 and miR166 increased at further differentiation stages. Our data uncover particular miRNA-mediated regulation operating for maize embryogenic tissues, supporting their regulatory role in early SAM establishment and basipetala growth during the in vitro regeneration process.
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Taier, Geli, Nan Hang, Tianran Shi, Yanrong Liu, Wenxin Ye, Wanjun Zhang, and Kehua Wang. "Ectopic Expression of Os-miR408 Improves Thermo-Tolerance of Perennial Ryegrass." Agronomy 11, no. 10 (September 26, 2021): 1930. http://dx.doi.org/10.3390/agronomy11101930.
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With global warming, high temperature stress has become a main threat to the growth of cool-season turfgrasses, including perennial ryegrass. As one of the conserved plant microRNA families, miR408s are known to play roles in various abiotic stresses, including cold, drought, salinity, and oxidative stress, but no report, thus far, was found for heat. Here, perennial ryegrass plants overexpressing rice Os-miR408 were used to investigate the role of miR408 in plant heat tolerance. Both wild type (WT) and miR408 transgenic perennial ryegrass plants (TG) were subjected to short-term heat stress at 38 °C for 72 h (experiment 1) or at 42 °C for 48 h (experiment 2), and then let recover for 7 days at optimum temperature. Morphological changes and physiological parameters, including antioxidative responses of TG and WT plants, were compared. The results showed that miR408 downregulated the expression of two putative target genes, PLASTOCYANIN and LAC3. Additionally, overexpression of Os-miR408 improved thermo-tolerance of perennial ryegrass, demonstrated by lower leaf lipid peroxidation and electrolyte leakage, and higher relative water content after both 38 and 42 °C heat stresses. In addition, the enhanced thermotolerance of TG plants could be associated with its morphological changes (e.g., narrower leaves, smaller tiller angles) and elevated antioxidative capacity. This study is the first that experimentally reported a positive role of miR408 in plant tolerance to heat stress, which provided useful information for further understanding the mechanism by which miR408 improved plant high-temperature tolerance, and offered a potential genetic resource for breeding heat-resistant cool-season turfgrass in the future.
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Liu, Hongyu, Ibrar Muhammad Khan, Yong Liu, Nazir Muhammad Khan, Kaiyuan Ji, Huiqun Yin, Wenliang Wang, Xinqi Zhou, and Yunhai Zhang. "A Comprehensive Sequencing Analysis of Testis-Born miRNAs in Immature and Mature Indigenous Wandong Cattle (Bos taurus)." Genes 13, no. 12 (November 23, 2022): 2185. http://dx.doi.org/10.3390/genes13122185.
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Micro RNAs (miRNAs) have been recognized as important regulators that are indispensable for testicular development and spermatogenesis. miRNAs are endogenous transcriptomic elements and mainly regulate the gene expression at post-transcriptional levels; however, the key role of miRNA in bovine testicular growth is not clearly understood. Thus, supposing to unveil the transcriptomics expression changes in the developmental processes of bovine testes, we selected three immature calves and three sexually mature bulls of the local Wandong breed for testicular-tissue sample collection. The cDNA libraries of experimental animals were established for RNA-sequencing analysis. We detected the miRNA expression in testes by using high-throughput sequencing technology, and bioinformatics analysis followed. The differentially expressed (DE) data showed that 151 miRNAs linked genes were significantly DE between immature and mature bull testes. Further, in detail, 64 were significantly up-regulated and 87 were down-regulated in the immature vs. mature testes (p-value < 0.05). Pathway analyses for miRNA-linked genes were performed and identified JAG2, BCL6, CFAP157, PHC2, TYRO3, SEPTIN6, and BSP3; these genes were involved in biological pathways such as TNF signaling, T cell receptor, PI3KAkt signaling, and functions affecting testes development and spermatogenesis. The DE miRNAs including MIR425, MIR98, MIR34C, MIR184, MIR18A, MIR136, MIR15A, MIR1388 and MIR210 were associated with cattle-bull sexual maturation and sperm production. RT-qPCR validation analysis showed a consistent correlation to the sequencing data findings. The current study provides a good framework for understanding the mechanism of miRNAs in the development of testes and spermatogenesis.
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Tang, Qi, Haozhe Lv, Qimeng Li, Xiaoyue Zhang, Le Li, Jie Xu, Fengkai Wu, Qingjun Wang, Xuanjun Feng, and Yanli Lu. "Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress." International Journal of Molecular Sciences 23, no. 9 (April 29, 2022): 4968. http://dx.doi.org/10.3390/ijms23094968.
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Maize (Zea mays) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress.
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Yrondi, Antoine, Laura M. Fiori, Benicio N. Frey, Raymond W. Lam, Glenda M. MacQueen, Roumen Milev, Daniel J. Müller, Jane A. Foster, Sidney H. Kennedy, and Gustavo Turecki. "Association Between Side Effects and Blood microRNA Expression Levels and Their Targeted Pathways in Patients With Major Depressive Disorder Treated by a Selective Serotonin Reuptake Inhibitor, Escitalopram: A CAN-BIND-1 Report." International Journal of Neuropsychopharmacology 23, no. 2 (December 10, 2019): 88–95. http://dx.doi.org/10.1093/ijnp/pyz066.
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Abstract Introduction Antidepressant drugs are effective therapies for major depressive disorder; however, they are frequently associated with side effects. Although there is some evidence for a relationship between genetic variation and side effects, little is known regarding the role of dynamic molecular factors as moderators of side effects. The aim of this study was to assess microRNA (miRNA) changes associated with side effects during escitalopram treatment and their downstream effects on target gene expression. Methods A total 160 patients with major depressive disorder from the CAN-BIND-1 cohort were included. Side effects were assessed with the Toronto Side Effect Scale after 2 weeks of treatment with escitalopram. We assessed the relationship between side effects and changes in peripheral expression of miRNAs between baseline and week 2. For miRNA whose expression changed, we used target prediction algorithms to identify putative messenger RNA (mRNA) targets and assessed their expression. Results Nausea was experienced by 42.5% of patients. We identified 45 miRNAs whose expression changed on initiation of escitalopram treatment, of which 10 displayed a negative association with intensity of nausea (miR15b-5p, miR17-5p, miR20a-5p, miR20b-5p, miR103a-3p, miR103b, miR106a-5p, miR182-5p, miR185-5p, and miR660-5p). Additionally, we found negative associations between 4 microRNAs (miR20a-5p, miR106a-5p, miR185-5p, miR660-5p) and mRNA targets. The expression of the miR185-5p target, CAMK2δ was significantly decreased [log 2 mean = −0.048 (0.233)] between weeks 0 and 2 (P = .01)]. Conclusions We identified an overexpression of miR185-5p during escitalopram treatment of major depressive disorder, which was negatively associated with intensity of nausea, and identified a potential mRNA target that may mediate this effect.
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Luo, Ming, Xinyuan Sun, Meng Xu, and Zhendong Tian. "Identification of miRNAs Involving Potato-Phytophthora infestans Interaction." Plants 12, no. 3 (January 19, 2023): 461. http://dx.doi.org/10.3390/plants12030461.
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sRNAs (small RNAs) play an important role in regulation of plant immunity against a variety of pathogens. In this study, sRNA sequencing analysis was performed to identify miRNAs (microRNAs) during the interaction of potato and Phytophthora infestans. Totally, 171 potato miRNAs were identified, 43 of which were annotated in the miRNA database and 128 were assigned as novel miRNAs in this study. Those potato miRNAs may target 878 potato genes and half of them encode resistance proteins. Fifty-three potato miRNAs may target 194 P. infestans genes. Three potato miRNAs (novel 72, 133, and 140) were predicted to have targets only in the P. infestans genome. miRNAs transient expression and P. infestans inoculation assay showed that miR396, miR166, miR6149-5P, novel133, or novel140 promoted P. infestans colonization, while miR394 inhibited colonization on Nicotiana benthamiana leaves. An artificial miRNA target (amiRNA) degradation experiment demonstrated that miR394 could target both potato gene (PGSC0003DMG400034305) and P. infestans genes. miR396 targets the multicystatin gene (PGSC0003DMG400026899) and miR6149-5p could shear the galactose oxidase F-box protein gene CPR30 (PGSC0003DMG400021641). This study provides new information on the aspect of cross-kingdom immune regulation in potato-P. infestans interaction at the sRNAs regulation level.
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de Vries, Sophie, Andreas Kukuk, Janina K. von Dahlen, Anika Schnake, Thorsten Kloesges, and Laura E. Rose. "Expression profiling across wild and cultivated tomatoes supports the relevance of early miR482/2118 suppression for Phytophthora resistance." Proceedings of the Royal Society B: Biological Sciences 285, no. 1873 (February 28, 2018): 20172560. http://dx.doi.org/10.1098/rspb.2017.2560.
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Plants possess a battery of specific pathogen resistance ( R- )genes. Precise R- gene regulation is important in the presence and absence of a pathogen. Recently, a microRNA family, miR482/2118, was shown to regulate the expression of a major class of R- genes , nucleotide-binding site leucine-rich repeats ( NBS-LRRs ). Furthermore, RNA silencing suppressor proteins, secreted by pathogens, prevent the accumulation of miR482/2118, leading to an upregulation of R- genes. Despite this transcriptional release of R -genes, RNA silencing suppressors positively contribute to the virulence of some pathogens . To investigate this paradox, we analysed how the regulation of NBS-LRRs by miR482/2118 has been shaped by the coevolution between Phytophthora infestans and cultivated and wild tomatoes. We used degradome analyses and qRT-PCR to evaluate and quantify the co-expression of miR482/2118 and their NBS-LRR targets. Our data show that miR482/2118-mediated targeting contributes to the regulation of NBS-LRRs in Solanum lycopersicum. Based on miR482/2118 expression profiling in two additional tomato species—with different coevolutionary histories with P. infestans —we hypothesize that pathogen-mediated RNA silencing suppression is most effective in the interaction between S. lycopersicum and P. infestans . Furthermore, an upregulation of miR482/2118 early in the infection may increase susceptibility to P. infestans .
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Kang, Qingzheng, Yin Tong, Vemana Gowd, Mingfu Wang, Feng Chen, and Ka-Wing Cheng. "Oral administration of EGCG solution equivalent to daily achievable dosages of regular tea drinkers effectively suppresses miR483-3p induced metastasis of hepatocellular carcinoma cells in mice." Food & Function 12, no. 8 (2021): 3381–92. http://dx.doi.org/10.1039/d1fo00664a.
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Yuan, Zhaodi, Jihong Pan, Congping Chen, Yulin Tang, Hongshan Zhang, Jia Guo, Xiaorong Yang, et al. "DRB2 Modulates Leaf Rolling by Regulating Accumulation of MicroRNAs Related to Leaf Development in Rice." International Journal of Molecular Sciences 23, no. 19 (September 22, 2022): 11147. http://dx.doi.org/10.3390/ijms231911147.
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As an important agronomic trait in rice (Oryza sativa), moderate leaf rolling helps to maintain the erectness of leaves and minimize shadowing between leaves, leading to improved photosynthetic efficiency and grain yield. However, the molecular mechanisms underlying rice leaf rolling still need to be elucidated. Here, we isolated a rice mutant, rl89, showing adaxially rolled leaf phenotype due to decreased number and size of bulliform cells. We confirmed that the rl89 phenotypes were caused by a single nucleotide substitution in OsDRB2 (LOC_Os10g33970) gene encoding DOUBLE-STRANDED RNA-BINDING2. This gene was constitutively expressed, and its encoded protein was localized to both nucleus and cytoplasm. Yeast two-hybrid assay showed that OsDRB2 could interact with DICER-LIKE1 (DCL1) and OsDRB1-2 respectively. qRT-PCR analysis of 29 related genes suggested that defects of the OsDRB2-miR166-OsHBs pathway could play an important role in formation of the rolled leaf phenotype of rl89, in which OsDRB2 mutation reduced miR166 accumulation, resulting in elevated expressions of the class III homeodomain-leucine zipper genes (such as OsHB1, 3 and 5) involved in leaf polarity and/or morphology development. Moreover, OsDRB2 mutation also reduced accumulation of miR160, miR319, miR390, and miR396, which could cause the abnormal leaf development in rl89 by regulating expressions of their target genes related to leaf development.
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Sun, Qiang, Xueyi Gong, Jianlong Wu, Zhipeng Hu, Qiao Zhang, Jingling Gong, and Xiaofeng Zhu. "Effect of lncRNA PVT1/miR186/KLF5 Axis on the Occurrence and Progression of Cholangiocarcinoma." BioMed Research International 2021 (July 10, 2021): 1–10. http://dx.doi.org/10.1155/2021/8893652.
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This study primarily focused on the effect of the long noncoding RNA (lncRNA) PVT1/miR186/KLF5 axis on the occurrence and progression of cholangiocarcinoma (CCA). miR186 was found both in the lncRNA PVT1 targeting miRNAs and KLF5 targeting miRNAs using bioinformatic analysis. The expression of lncRNA PVT1 and KLF5 in the TFK-1, QBC939, and HuCCT1 cell lines and normal biliary epithelial HIBEpiC cells was detected by RT-qPCR. The significance of lncRNA PVT1 and KLF5 on cell proliferation was analyzed using the MTT assay and clone formation assay in lncRNA PVT1 and KLF5 silencing HuCCT1 cell lines and lncRNA PVT1and KLF5 overexpressing TFK-1 and QBC939 cell lines, respectively. The potential role of lncRNA PVT1 and KLF5 in cell migration was detected using the transwell invasion assay in CCA cell lines and tumor formation assay. Additionally, lncRNA PVT1 and KLF5 were proved to be highly expressed in CCA tissues and cell lines. Silencing and overexpressing of lncRNA PVT1 or KLF5 markedly inhibited or increased the cell proliferation and cell invasion in CCA cell lines, respectively. Silencing and overexpressing of lncRNA PVT1 significantly inhibited and increased the expression of KLF5 in CCA cell lines, respectively. Silencing of lncRNA PVT1 increased the expression of miR186, and silencing of miR186 increased the expression of KLF5 in CCA cell lines. Cotransfection of lncRNA PVT1 and miR186 increased the expression of KLF5 compared with controls. Overall, these results demonstrated that the lncRNA PVT1/miR186/KLF5 axis might exert a key role in the occurrence and progression of CCA, and this axis might provide a new target for treating CCA.
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Ražná, Katarína, Janka Nôžková, Lucia Hlavačková, Nina Brutch, Elizaveta Porokhovinova, Tatiana Shelenga, and Andrey Pavlov. "Genotyping of Flax Genetic Resources by Mirna-Based Molecular Markers and Morphology." Agriculture (Polnohospodárstvo) 61, no. 4 (December 1, 2015): 129–38. http://dx.doi.org/10.1515/agri-2015-0018.
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Abstract MicroRNAs (miRNAs) are a class of non-coding RNAs about 20-24 nucleotides long. They play an important role in the gene regulation at the post-transcriptional level. They affect the plant genome response to environmental stress. The miRNA-based molecular markers is type of functional markers reported in very few plants. However, the information connected to the evaluation of genotypes by this type of markers within a single species is missing. Considering the stability, polymorphism, functionality and transferability potential of miRNA-based markers, the research was conducted to apply selected types of them (miR156b, miR408a and the combined type of miR156b/miR408a) for the genotyping analysis of eight flax genotypes of different origin together with the morphology analyses. A total of 145 miRNA loci were identified, of which 19 were unique. The highest numbers of miRNA loci (57) and unique fragments (9) as well as the highest percentage of polymorphism and the extent of polymerase chain reaction (PCR) amplification of miRNA fragments have been observed with the combination of miR156b-F and miR408-F markers. By means of the miRNA markers has been recorded the unique profile of the miRNA loci for individual accessions. The morphology study has shown that the genotypes are the same in the expression of selected morphological traits despite the different use and different places of origin. However, we have identified an interface between some of morphological traits and miRNA-based markers for genotyping the genetic resources of flax. By mutually linking these two types of markers, we were able to determine unique genotypes of flax.
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Canto-Pastor, Alex, Bruno A. M. C. Santos, Adrian A. Valli, William Summers, Sebastian Schornack, and David C. Baulcombe. "Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato." Proceedings of the National Academy of Sciences 116, no. 7 (January 24, 2019): 2755–60. http://dx.doi.org/10.1073/pnas.1814380116.
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Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family miRNAs that are in a distinct 22-nt class of miRNAs with a double mode of action. First, they cleave the target RNA, as with the canonical 21-nt miRNAs, and second, they trigger secondary siRNA production using the target RNA as a template. Here, we address the extent to which the miR482/2118 family affects expression of NLR mRNAs and disease resistance. We show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is a conserved motif in multiple NLR mRNAs, whereas for miR2118b, it is a noncoding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118, we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight, but nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars.
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Chen, Jin, Ao Pan, Shujun He, Pin Su, Xiaoling Yuan, Shengwei Zhu, and Zhi Liu. "Different MicroRNA Families Involved in Regulating High Temperature Stress Response during Cotton (Gossypium hirsutum L.) Anther Development." International Journal of Molecular Sciences 21, no. 4 (February 14, 2020): 1280. http://dx.doi.org/10.3390/ijms21041280.
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MicroRNAs (miRNAs) are small molecule RNAs widely involved in responses to plant abiotic stresses. We performed small RNA sequencing of cotton anthers at four developmental stages under normal and high temperature (NT and HT, respectively) conditions to investigate the stress response characteristics of miRNA to HT. A total of 77 miRNAs, including 33 known miRNAs and 44 novel miRNAs, were identified, and 41 and 28 miRNAs were differentially expressed under NT and HT stress conditions, respectively. The sporogenous cell proliferation (SCP), meiotic phase (MP), microspore release period (MRP), and pollen maturity (PM) stages had 10 (including 12 miRNAs), four (including six miRNAs), four (including five miRNAs), and seven (including 11 miRNAs) HT stress-responsive miRNA families, respectively, which were identified after removing the changes in genotype-specific miRNAs under NT condition. Seven miRNA families (miR2949, miR167, and miR160 at the SCP stage; miR156 and miR172 at the MP stage; miR156 at the MRP stage; and miR393 and miR3476 at the PM stage), which had expression abundance of more than 10% of the total expression abundance, served as the main regulators responding to HT stress with positive or negative regulation patterns. These miRNAs orchestrated the expression of the corresponding target genes and led to different responses in the HT-tolerant and the HT-sensitive lines. The results revealed that the HT stress response of miRNAs in cotton anthers were stage-specific and differed with the development of anthers. Our study may enhance the understanding of the response of miRNAs to HT stress in cotton anthers and may clarify the mechanism of plant tolerance to HT stress.
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Yang, Fan, Dan Zhao, Haiyan Fan, Xiaofeng Zhu, Yuanyuan Wang, Xiaoyu Liu, Yuxi Duan, Yuanhu Xuan, and Lijie Chen. "Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita." International Journal of Molecular Sciences 21, no. 3 (January 30, 2020): 911. http://dx.doi.org/10.3390/ijms21030911.
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Root-knot nematodes (RKNs) severely affect plants growth and productivity, and several commercial biocontrol bacteria can improve plants resistance to RKNs. Pseudomonas putida Sneb821 isolate was found to induce tomatoes resistance against Meloidogyne incognita. However, the molecular functions behind induced resistance remains unclear. Long non-coding RNA (lncRNA) is considered to be a new component that regulates the molecular functions of plant immunity. We found lncRNA was involved in Sneb821-induced tomato resistance to M. incognita. Compared with tomato inoculated with M. incognita, high-throughput sequencing showed that 43 lncRNAs were upregulated, while 35 lncRNAs were downregulated in tomatoes previously inoculated with Sneb821. A regulation network of lncRNAs was constructed, and the results indicated that 12 lncRNAs were found to act as sponges of their corresponding miRNAs. By using qRT-PCR and the overexpression vector pBI121, we found the expression of lncRNA44664 correlated with miR396/GRFs (growth-regulating factors) and lncRNA48734 was correlated with miR156/SPL (squamosal promoter-binding protein-like) transcription factors. These observations provided a novel molecular model in biocontrol bacteria-induced tomato resistance to M. incognita.
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Shehzad, Muhammad, Zhongli Zhou, Allah Ditta, Majid Khan, Xiaoyan Cai, Yanchao Xu, Amir Maqbool, et al. "Identification and characterization of genes related to salt stress tolerance within segregation distortion regions of genetic map in F2 population of upland cotton." PLOS ONE 16, no. 3 (March 26, 2021): e0247593. http://dx.doi.org/10.1371/journal.pone.0247593.
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Segregation distortion (SD) is a genetic mechanism commonly found in segregating or stable populations. The principle behind this puzzles many researchers. The F2generation developed from wildGossypium darwiniiandG.hirsutumCCRI12 species was used to investigate the possible transcription factors within the segregation distortion regions (SDRs). The 384 out of 2763 markers were distorted in 29 SDRs on 18 chromosomes. Good collinearity was observed among genetic and physical maps ofG.hirsutumandG.barbadensesyntenic blocks. Total 568 genes were identified from SDRs of 18 chromosomes. Out of these genes, 128 belonged to three top-ranked salt-tolerant gene families. The DUF597 contained 8 uncharacterized genes linked to Pkinase (PF00069) gene family in the phylogenetic tree, while 15 uncharacterized genes clustered with the zinc finger gene family. Two hundred thirty four miRNAs targeted numerous genes, including ghr-miR156, ghr-miR399 and ghr-miR482, while others targeted top-ranked stress-responsive transcription factors. Moreover, these genes were involved in the regulation of numerous stress-responsive cis-regulatory elements. The RNA sequence data of fifteen upregulated genes were verified through the RT-qPCR. The expression profiles of two highly upregulated genes (Gh_D01G2015andGh_A01G1773) in salt-tolerantG.darwiniishowed antagonistic expression inG.hirsutum. The results indicated that salt-tolerant genes have been possibly transferred from the wildG.darwiniispecies. A detailed functional analysis of these genes can be carried out which might be helpful in the future for gene cloning, transformation, gene editing and the development of salt-resistant cotton varieties.
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Bakhshi, Behnam, and Ehsan Mohseni Fard. "Whole Aegilops tauschii Transcriptome Investigation Revealed Nine Novel miRNAs Involved in Stress Response." Current Bioinformatics 15, no. 5 (October 14, 2020): 455–62. http://dx.doi.org/10.2174/1574893614666191017151708.
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Background: Aegilops tauschii is a wild relative of bread wheat. This species has been reported as the donor of bread wheat D genome. There are also several reports that mentioned the importance of Ae. tauschii in biotic and abiotic stress tolerance. On the other hands, miRNAs have been reported as the essential regulatory elements in stress response. Objective: Therefore, it is important to discover novel miRNAs involved in stress tolerance in this species. The aim of the current study was to predict novel miRNAs in Ae. tauschii and also uncover their potential role in stress response. Methods: For this purpose, ESTs, TSAs, and miRBase databases were obtained and used to predict new miRNAs. Results: Our results discovered nine novel stem-loop miRNAs. These predicted miRNAs could be introduced as the new members of previously identified miRNA families in Ae. tauschii, including miR156, miR168, miR169, and miR319. The result indicating that miR397 and miR530 are novel families in this species. Furthermore, several novel stem-loop miRNAs predicted for T. aestivum showed remarkable similarities to novel Ae. tauschii stem-loops. Conclusion: Our results demonstrated that predicted novel miRNAs could play a significant role in stress response.
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Gorshkov, Oleg, Tatyana Chernova, Natalia Mokshina, Natalia Gogoleva, Dmitry Suslov, Alexander Tkachenko, and Tatyana Gorshkova. "Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles." Plants 8, no. 2 (February 19, 2019): 47. http://dx.doi.org/10.3390/plants8020047.
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Phloem fibers are important elements of plant architecture and the target product of many fiber crops. A key stage in fiber development is intrusive elongation, the mechanisms of which are largely unknown. Integrated analysis of miRNA and mRNA expression profiles in intrusivelygrowing fibers obtained by laser microdissection from flax (Linum usitatissimum L.) stem revealed all 124 known flax miRNA from 23 gene families and the potential targets of differentially expressed miRNAs. A comparison of the expression between phloem fibers at different developmental stages, and parenchyma and xylem tissues demonstrated that members of miR159, miR166, miR167, miR319, miR396 families were down-regulated in intrusively growing fibers. Some putative target genes of these miRNA families, such as those putatively encoding growth-regulating factors, an argonaute family protein, and a homeobox-leucine zipper family protein were up-regulated in elongating fibers. miR160, miR169, miR390, and miR394 showed increased expression. Changes in the expression levels of miRNAs and their target genes did not match expectations for the majority of predicted target genes. Taken together, poorly understood intrusive fiber elongation, the key process of phloem fiber development, was characterized from a miRNA-target point of view, giving new insights into its regulation.
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Xu, Pan, Quanqing Li, Weiqing Liang, Yijuan Hu, Rubing Chen, Kelang Lou, Lianghui Zhan, Xiaojun Wu, and Jinbao Pu. "A tissue-specific profile of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia lactiflora Pall. by transcriptome, small RNAs and degradome sequencing." PLOS ONE 18, no. 1 (January 26, 2023): e0279992. http://dx.doi.org/10.1371/journal.pone.0279992.
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Paeonia lactiflora Pall. (Paeonia) has aroused many concerns due to its extensive medicinal value, in which monoterpene glucoside paeoniflorin and its derivatives are the active chemical components. However, little is known in the molecular mechanism of monoterpenoids biosynthesis, and the regulation network between small RNAs and mRNAs in monoterpenoids biosynthesis has not been investigated yet. Herein, we attempted to reveal the tissue-specific regulation network of miRNAs and their targets related to paeoniaflorin and monoterpenoids biosynthesis in Paeonia by combining mRNA and miRNA expression data with degradome analysis. In all, 289 miRNAs and 30177 unigenes were identified, of which nine miRNAs from seven miRNA families including miR396, miR393, miR835, miR1144, miR3638, miR5794 and miR9555 were verified as monoterpenoids biosynthesis-related miRNAs by degradome sequencing. Moreover, the co-expression network analysis showed that four monoterpenoids-regulating TFs, namely AP2, MYBC1, SPL12 and TCP2, were putatively regulated by five miRNAs including miR172, miR828, miR858, miR156 and miR319, respectively. The present study will improve our knowledge of the molecular mechanisms of the paeoniaflorin and monoterpenoids biosynthesis mediated by miRNA to a new level, and provide a valuable resource for further study on Paeonia.
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Jia, Fan, and Christopher D. Rock. "Jacalin LectinAt5g28520Is Regulated By ABA and miR846." Plant Signaling & Behavior 8, no. 6 (June 2013): e24563. http://dx.doi.org/10.4161/psb.24563.
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Dalmadi, Ágnes, Fabio Miloro, Jeannette Bálint, Éva Várallyay, and Zoltán Havelda. "Controlled RISC loading efficiency of miR168 defined by miRNA duplex structure adjusts ARGONAUTE1 homeostasis." Nucleic Acids Research 49, no. 22 (November 24, 2021): 12912–28. http://dx.doi.org/10.1093/nar/gkab1138.
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Abstract Micro RNAs (miRNAs) are processed from precursor RNA molecules with precisely defined secondary stem-loop structures. ARGONAUTE1 (AGO1) is the main executor component of miRNA pathway and its expression is controlled via the auto-regulatory feedback loop activity of miR168 in plants. Previously we have shown that AGO1 loading of miR168 is strongly restricted leading to abundant cytoplasmic accumulation of AGO-unbound miR168. Here, we report, that intrinsic RNA secondary structure of MIR168a precursor not only defines the processing of miR168, but also precisely adjusts AGO1 loading efficiency determining the biologically active subset of miR168 pool. Our results show, that modification of miRNA duplex structure of MIR168a precursor fragment or expression from artificial precursors can alter the finely adjusted loading efficiency of miR168. In dcl1-9 mutant where, except for miR168, production of most miRNAs is severely reduced this mechanism ensures the elimination of unloaded AGO1 proteins via enhanced AGO1 loading of miR168. Based on this data, we propose a new competitive loading mechanism model for miR168 action: the miR168 surplus functions as a molecular buffer for controlled AGO1 loading continuously adjusting the amount of AGO1 protein in accordance with the changing size of the cellular miRNA pool.
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Feng, Yaxing, Nawei Qi, Piao Lei, Yuanyuan Wang, Yuanhu Xuan, Xiaoyu Liu, Haiyan Fan, Lijie Chen, Yuxi Duan, and Xiaofeng Zhu. "Gma-miR408 Enhances Soybean Cyst Nematode Susceptibility by Suppressing Reactive Oxygen Species Accumulation." International Journal of Molecular Sciences 23, no. 22 (November 14, 2022): 14022. http://dx.doi.org/10.3390/ijms232214022.
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Soybean cyst nematode (SCN, Heterodera glycine) is a serious damaging disease in soybean worldwide, thus resulting in severe yield losses. MicroRNA408 (miR408) is an ancient and highly conserved miRNA involved in regulating plant growth, development, biotic and abiotic stress response. Here, we analyzed the evolution of miR408 in plants and verified four miR408 members in Glycine max. In the current research, highly upregulated gma-miR408 expressing was detected during nematode migration and syncytium formation response to soybean cyst nematode infection. Overexpressing and silencing miR408 vectors were transformed to soybean to confirm its potential role in plant and nematode interaction. Significant variations were observed in the MAPK signaling pathway with low OXI1, PR1, and wounding of the overexpressing lines. Overexpressing miR408 could negatively regulate soybean resistance to SCN by suppressing reactive oxygen species accumulation. Conversely, silencing miR408 positively regulates soybean resistance to SCN. Overall, gma-miR408 enhances soybean cyst nematode susceptibility by suppressing reactive oxygen species accumulation.
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Vijayaraghavan, Bhooma, Sridharan Jeyamohan, Giri Padmanabhan, Antony Joseph Velangann, and Kumaresan Ramanathan. "Circulatory microRNA expression profile for coronary artery calcification in chronic kidney disease patients." African Health Sciences 21, no. 2 (August 2, 2021): 728–34. http://dx.doi.org/10.4314/ahs.v21i2.31.
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Background & Aim: Coronary artery disease (CAD) is the primary cause of mortality in patients with end stage renal disease (ESRD). MicroRNA profiling is proven as a powerful tool in the diagnosis of any disease at the molecular level. Hence, the present study aimed to profile the microRNA expression for CAD especially coronary artery calcification in CKD patients.
Materials and Methods: Two hundread patients with CKD stages 3 to 5 without dialysis and healthy controls were includ- ed in this study. All two hundred patients underwent 1024 multi sliceardiac computed tomography (CT) scan for calcium scoring. The calcium scoring more than 100 have been included in the study. We performed miRNA microarray analysis from serum samples of seven high calcium scored with CKD patients and one control patients.
Results: Seven patients have observed circulating miRNAs has significantly upregulated and downregulated when compared with control patients. mir21, mir 67, mir 390, mir 56, mir 250, mir 65 and mir 13 were up regulated and mir235, mir256, mir226, mir207, mir255, mir193 were downregulated. There was no significant difference in left ventricle function.
Conclusion: 13 microRNAs play a potential role in coronary artery calcification in CKD patients.
Keywords: CKD; CAD; microRNA; coronary artery calcification.
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Mo, Zhenghai, Gang Feng, Wenchuan Su, Zhuangzhuang Liu, and Fangren Peng. "Identification of miRNAs Associated with Graft Union Development in Pecan [Carya illinoinensis (Wangenh.) K. Koch]." Forests 9, no. 8 (August 3, 2018): 472. http://dx.doi.org/10.3390/f9080472.
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Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a high-value fruit tree with a long juvenile period. The fruiting process of pecan seedlings can be largely accelerated through grafting. As non-coding small RNAs, plant miRNAs participate in various biological processes through negative regulation of gene expression. To reveal the roles of miRNAs in the graft union development of pecan, four small RNA libraries were constructed from the graft union at days 0, 8, 15, and 30 after grafting. A total of 47 conserved miRNAs belonging to 31 families and 39 novel miRNAs were identified. For identified miRNAs, 584 target genes were bioinformatically predicted, and 266 of them were annotated; 29 miRNAs (including 16 conserved and 13 novel miRNAs) were differentially expressed during the graft process. The expression profiles of 12 miRNA were further validated by quantitative reverse transcription PCR (qRT-PCR). In addition, qRT-PCR revealed that the expression levels of 3 target genes were negatively correlated with their corresponding miRNAs. We found that miRS26 might be involved in callus formation; miR156, miR160, miR164, miR166, and miRS10 might be associated with vascular bundle formation. These results indicate that the miRNA-mediated gene regulations play important roles in the graft union development of pecan.
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Ražná, Katarína, Vladimír Rataj, Miroslav Macák, and Jana Galambošová. "MicroRNA-based markers as a tool to monitor the barley (Hordeum vulgare L.) response to soil compaction." Acta fytotechnica et zootechnica 23, no. 3 (September 30, 2020): 139–46. http://dx.doi.org/10.15414/afz.2020.23.03.139-146.
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Plants are often exposed to adverse environmental conditions that can significantly interfere with their genomic response. Soil compaction induced by heavy field machinery represents a major problem for crop production mainly due to restricted root growth and penetration into soil and therefore reduced water and nutrient uptake by the plants. Tested hypotheses were to declare whether the plant‘s genome responds to soil compaction and whether the microRNA-based markers are suitable to determine this response. A long term field scale experiment was established in 2009 where different levels of soil compaction are researched from the soil and crop point of view. The analyzed barley (Hordeum vulgare L.) plants were collected during the growing season in 2019. The effect of soil compaction was analysed by four different DNA-based markers corresponding to miRNA sequences of dehydratation stress-responsive barley miRNAs (hvu-miR156, and hvu-miR408) and nutrition-sensitive markers (hvu-miR399 and hvu-miR827), within the leaf, stem and root tissues of barley plants. Our preliminary data support hypotheses that plant genome response was tissue-specific due to significant induction of the biomarkers to dehydratation and nutrition stress. The most affected part of the plant by dehydration, were roots and lack of nutrient supply was most pronounced on leaves.
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Bortolotti, Daria, Irene Soffritti, Maria D’Accolti, Valentina Gentili, Dario Di Luca, Roberta Rizzo, and Elisabetta Caselli. "HHV-6A Infection of Endometrial Epithelial Cells Affects miRNA Expression and Trophoblast Cell Attachment." Reproductive Sciences 27, no. 3 (January 1, 2020): 779–86. http://dx.doi.org/10.1007/s43032-019-00102-8.
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AbstractWe recently reported that human herpesvirus 6 (HHV-6) infection is frequently present in endometrial tissue of women with unexplained infertility, and that virus infection induces a profound remodulation of miRNA expression in human cells of different origin. Since specific miRNA patterns have been associated with specific pregnancy outcomes, we aimed to analyze the impact of HHV-6A infection on miRNAs expression and trophoblast receptivity in human endometrial cells. To this purpose, a human endometrial cell line (HEC-1A) was infected with HHV-6A and analyzed for alterations in the expression of miRNAs and for permissiveness to the attachment of a human choriocarcinoma trophoblast cell line (JEG-3). The results showed that HHV-6A infection of endometrial cells up-modulates miR22 (26-fold), miR15 (19.5-fold), and miR196-5p (12.1 fold), that are correlated with implant failure, and down-modulates miR18 (11.4 fold), miR101-3p (4.6 fold), miR181-5p (4.9 fold), miR92 (3.3 fold), and miR1207-5p (3.9 fold), characterized by a low expression in preeclampsia. Moreover, HHV-6A-infected endometrial cells infected resulted less permissive to the attachment of trophoblast cells. In conclusion, collected data suggest that HHV-6A infection could modify miRNA expression pattern and control of trophoblast cell adhesion of endometrial cells, undermining a correct trophoblast cell attachment on endometrial cells.
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Guo, Xiaorong, Junfeng Niu, and Xiaoyan Cao. "Heterologous Expression of Salvia miltiorrhiza MicroRNA408 Enhances Tolerance to Salt Stress in Nicotiana benthamiana." International Journal of Molecular Sciences 19, no. 12 (December 11, 2018): 3985. http://dx.doi.org/10.3390/ijms19123985.
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MicroRNAs (miRNAs) are a class of endogenous small RNAs that regulate the expression of target genes post-transcriptionally; they are known to play major roles in development and responses to abiotic stress. MicroRNA408 (miR408) is a conserved small RNA in plants; it was reported that miR408 genes were involved in abiotic stress in Arabidopsis. However, miR408 in Salvia miltiorrhiza has been rarely investigated. In this study, we cloned Sm-MIR408, the miR408 precursor sequence, and its promoter sequence from S. miltiorrhiza and the role in tolerance to salt stress is described. The effects of salt stress on miR408 expression were studied by using β-glucuronidase (GUS) staining. Our data indicated that transgenic tobacco overexpressing Sm-MIR408 promoted seed germination and reduced the accumulation of reactive oxygen species under salt stress. Transcript levels of antioxidative genes, i.e., NbSOD, NbPOD, and NbCAT, and their enzyme activities increased in salinity-stressed transgenic tobacco plants, suggesting a better antioxidant system to cope the oxidative damage caused by salinity stress. Taken together, these findings indicated that miR408 functions in positive responses to salt tolerance in tobacco.
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Gao, Yu, Baohua Feng, Caixia Gao, Huiquan Zhang, Fengting Wen, Longxing Tao, Guanfu Fu, and Jie Xiong. "The Evolution and Functional Roles of miR408 and Its Targets in Plants." International Journal of Molecular Sciences 23, no. 1 (January 4, 2022): 530. http://dx.doi.org/10.3390/ijms23010530.
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MicroRNA408 (miR408) is an ancient and highly conserved miRNA, which is involved in the regulation of plant growth, development and stress response. However, previous research results on the evolution and functional roles of miR408 and its targets are relatively scattered, and there is a lack of a systematic comparison and comprehensive summary of the detailed evolutionary pathways and regulatory mechanisms of miR408 and its targets in plants. Here, we analyzed the evolutionary pathway of miR408 in plants, and summarized the functions of miR408 and its targets in regulating plant growth and development and plant responses to various abiotic and biotic stresses. The evolutionary analysis shows that miR408 is an ancient and highly conserved microRNA, which is widely distributed in different plants. miR408 regulates the growth and development of different plants by down-regulating its targets, encoding blue copper (Cu) proteins, and by transporting Cu to plastocyanin (PC), which affects photosynthesis and ultimately promotes grain yield. In addition, miR408 improves tolerance to stress by down-regulating target genes and enhancing cellular antioxidants, thereby increasing the antioxidant capacity of plants. This review expands and promotes an in-depth understanding of the evolutionary and regulatory roles of miR408 and its targets in plants.
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Szczygieł-Sommer and Gaj. "The miR396–GRF Regulatory Module Controls the Embryogenic Response in Arabidopsis via an Auxin-Related Pathway." International Journal of Molecular Sciences 20, no. 20 (October 21, 2019): 5221. http://dx.doi.org/10.3390/ijms20205221.
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In plants, microRNAs have been indicated to control various developmental processes, including somatic embryogenesis (SE), which is triggered in the in vitro cultured somatic cells of plants. Although a transcriptomic analysis has indicated that numerous MIRNAs are differentially expressed in the SE of different plants, the role of specific miRNAs in the embryogenic reprogramming of the somatic cell transcriptome is still poorly understood. In this study, we focused on performing a functional analysis of miR396 in SE given that the transcripts of MIR396 genes and the mature molecules of miR396 were found to be increased during an SE culture of Arabidopsis [1]. In terms of miR396 in embryogenic induction, we observed the SE-associated expression pattern of MIR396b in explants of the β-glucuronidase (GUS) reporter line. In order to gain insight into the miR396-controlled mechanism that is involved in SE induction, the embryogenic response of mir396 mutants and the 35S:MIR396b overexpressor line to media with different 2,4-Dichlorophenoxyacetic acid (2,4-D) concentrations was evaluated. The results suggested that miR396 might contribute to SE induction by controlling the sensitivity of tissues to auxin treatment. Within the targets of miR396 that are associated with SE induction, we identified genes encoding the GROWTH-REGULATING FACTOR (GRF) transcription factors, including GRF1, GRF4, GRF7, GRF8, and GRF9. Moreover, the study suggested a regulatory relationship between miR396, GRF, and the PLETHORA (PLT1 and PLT2) genes during SE induction. A complex regulatory relationship within the miR396–GRF1/4/8/9–PLT1/2 module that involves the negative and positive control of GRFs and PLT (respectively) by miR396 might be assumed.
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Kong, Demao, and Xia Wang. "miR126-Mediated Signal Transducer and Activator of Transcription 3 Signaling Pathway Regulates the Malignant Biological Behavior of Pancreatic Cancer Cells." Journal of Biomaterials and Tissue Engineering 10, no. 8 (August 1, 2020): 1199–205. http://dx.doi.org/10.1166/jbt.2020.2401.
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Background and purpose: As a type of non-coding genetic material widely existing in eukaryotes, a growing amount of research have confirmed that it have close connection with the occurrence and progression of various malignancies. MicroRNA126 is increased in non-small-cell lung cancer, liver cancer and gastric carcinoma. The up-regulation of miR126 in cervical cancer is closely associated with the clinical staging, histological grade, depth of invasion and early metastasis of the tumor, and it is also of great value in predicting the survival prognosis of the tumor. However, there is little known about the relationship between miR126 and pancreatic carcinoma. Therefore, this study explored the miR126-mediated STAT3 signaling pathway in medicating pancreatic cancer cell multiplication, migration, cell cycle and apoptosis in vitro . Methods: PANC-1 cell (human pancreatic cancer cell line) was selected for routine resuscitation and subculture. The experiment is grouped as: blank control group (NC group), empty plasmid transfection group (miR126-NC group), miR126mimic transfection group (overexpression Group) and miR126 inhibition plasmid transfection group (low expression group); cell viability of each group for 12 h, 24 h, 48 h and 72 h was detected using MTT assay. Wound healing assay was used to evaluated the ability of cell migration. Flow cytometry was performed to analyze cell cycle. The mRNA expression of Caspase-3 was determined by reverse transcription PCR (RT-PCR). STAT3 protein was evaluated by western blot. Results: miR126 overexpression significantly increased cell proliferation at 12 h, 24 h, 48 h, and 72 h, while the cell proliferation rates of the low expression group at each time point were significantly reduced in comparision with those of the NC group and the miR126-NC group (P < 0 05). miR126 overexpression significantly induced cell migration, while miR126 low-expression significantly inhibited cell migration (P < 0 05). miR126 overexpression significantly enhanced the percentage of G2/M, while the percentage of G2/M in the low-expressed group was remarkably reduced in comparision with those of the NC group and the miR126-NC group (P < 0 05). The mRNA expression of Caspase-3 was significantly inhibited in miR126 overexpression group, while the expression of Caspase-3 mRNA in the cells with miR126 low expression was remarkably increased (P < 0 05). The protein expression of STAT3 in miR126 overexpression group was notably up-regulated, while the expression level of STAT3 protein in the low expression group was prominently down-regulated (P <0 05). Conclusion: MiR126 overexpression may induces the STAT3 signaling pathway and then regulates cell proliferation, cell migration, cell cycle arrest and cell apoptosis in pancreatic carcinoma.
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Zhao, Xian, Yanli Wang, Rong Deng, Hailong Zhang, Jinzhuo Dou, Haihua Yuan, Guofang Hou, Yuzhang Du, Qin Chen, and Jianxiu Yu. "miR186 suppresses prostate cancer progression by targeting Twist1." Oncotarget 7, no. 22 (April 21, 2016): 33136–51. http://dx.doi.org/10.18632/oncotarget.8887.
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Pegler, Joseph L., Duc Quan Nguyen, Jackson M. J. Oultram, Christopher P. L. Grof, and Andrew L. Eamens. "Molecular Manipulation of the MiR396/GRF Expression Module Alters the Salt Stress Response of Arabidopsis thaliana." Agronomy 11, no. 9 (August 31, 2021): 1751. http://dx.doi.org/10.3390/agronomy11091751.
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We previously demonstrated that microRNA396 (miR396) abundance is altered in 15-day-old Arabidopsis thaliana (Arabidopsis) whole seedlings following their exposure to a 7-day salt stress treatment regime. We, therefore, used a molecular modification approach to generate two new Arabidopsis transformant populations with reduced (MIM396 plants) and elevated (MIR396 plants) miR396 abundance. The exposure of 8-day-old wild-type Arabidopsis whole seedlings and a representative plant line of the MIM396 and MIR396 transformant populations to a 7-day salt stress treatment regime revealed unique phenotypic and physiological responses to the imposed stress by unmodified wild-type Arabidopsis plants and the MIM396 and MIR396 transformat lines. A quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) approach was, therefore, applied to demonstrate that the plant line specific responses to salt stress likely stemmed from the unique molecular profile of each of the GROWTH REGULATING FACTOR (GRF) transcription factor gene family members which form posttranscriptional targets of miR396-directed expression regulation. RT-qPCR additionally revealed that, in 15-day-old Arabidopsis whole seedlings, the three previously identified putative target genes of miR396 belonging to the NEUTRAL/ALKALINE NONLYSOSOMAL CERAMIDASE-LIKE (NCER) gene family, including NCER1, NCER2, and NCER3, do not form targets of miR396-directed expression regulation at the posttranscriptional level. Taken together, the phenotypic and molecular analyses presented here demonstrate that alteration of the miR396/GRF expression module is central to the molecular response of Arabidopsis to salt stress.
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Jin, Hong-Yi, Xin-Guang Qiu, and Bo Yang. "The MicroRNA3686 Inhibits the Proliferation of Pancreas Carcinoma Cell Line by Targeting the Polo-Like Kinase 1." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/954870.
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The Polo-like kinase 1 (PLK1) is one member of the so-called Polo-like kinase family which plays an important role in tumorigenesis. By analyzing the potential complementary microRNA (miRNA) targeting sequence of PLK1, we identified that miRNA-3686 (hereby and thereafter mir3696) could be the potential regulator for PLK1. Real-time PCR demonstrated that the mir3686 has a relatively higher expression in the immortalized pancreas cell HPDE6C7 than pancreas carcinoma derived cell line PANC1. The upregulation of mir3686 in HPDE6C7 cell corresponded with the low expression of PLK1 as well. Both luciferase based reporter assay and evaluation of endogenous PLK1 expression demonstrated that mir3686 regulated PLK1, which confirms our speculation. Moreover, we found that transfection of mir3686 in PANC1 cell could lead to proliferation inhibition and promote apoptosis. Further analysis demonstrated that mir3686 transfection in PANC1 cell also inhibited cell invasion, and clone formation in cell invasion assay and clonogenic cell survival assay, respectively. In contrast, inhibition of mir3686 expression in HPDE6C7 cell enhanced the capability of proliferation, cell invasion and clone formation. Taken together, our results indicated that mir3686 could target PLK1 to inhibit the cell proliferation in pancreas cancer derived cell line and mir3686 could be a new therapeutic target for pancreas cancer treatment.
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Li, Hongshun, Yiwei Luo, Bi Ma, Jianqiong Hu, Zhiyuan Lv, Wuqi Wei, Haiye Hao, Jianglian Yuan, and Ningjia He. "Hierarchical Action of Mulberry miR156 in the Vegetative Phase Transition." International Journal of Molecular Sciences 22, no. 11 (May 24, 2021): 5550. http://dx.doi.org/10.3390/ijms22115550.
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The vegetative phase transition is a prerequisite for flowering in angiosperm plants. Mulberry miR156 has been confirmed to be a crucial factor in the vegetative phase transition in Arabidopsis thaliana. The over-expression of miR156 in transgenic Populus × canadensis dramatically prolongs the juvenile phase. Here, we find that the expression of mno-miR156 decreases with age in all tissues in mulberry, which led us to study the hierarchical action of miR156 in mulberry. Utilizing degradome sequencing and dual-luciferase reporter assays, nine MnSPLs were shown to be directly regulated by miR156. The results of yeast one-hybrid and dual-luciferase reporter assays also revealed that six MnSPLs could recognize the promoter sequences of mno-miR172 and activate its expression. Our results demonstrate that mno-miR156 performs its role by repressing MnSPL/mno-miR172 pathway expression in mulberry. This work uncovered a miR156/SPLs/miR172 regulation pathway in the development of mulberry and fills a gap in our knowledge about the molecular mechanism of vegetative phase transition in perennial woody plants.
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Li, Meng, Ting Chen, Ran Wang, Jun-Yi Luo, Jia-Jian He, Rui-Song Ye, Mei-Ying Xie, et al. "Plant MIR156 regulates intestinal growth in mammals by targeting the Wnt/β-catenin pathway." American Journal of Physiology-Cell Physiology 317, no. 3 (September 1, 2019): C434—C448. http://dx.doi.org/10.1152/ajpcell.00030.2019.
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MicroRNAs (miRNAs) are important negative regulators of genes involved in physiological and pathological processes in plants and animals. Recent studies have shown that miRNAs might regulate gene expression among different species in a cross-kingdom manner. However, the specific roles of plant miRNAs in animals remain poorly understood and somewhat. Herein, we found that plant MIR156 regulates proliferation of intestinal cells both in vitro and in vivo. Continuous administration of a high plant miRNA diet or synthetic MIR156 elevated MIR156 levels and inhibited the Wnt/β-catenin signaling pathway in mouse intestine. Bioinformatics predictions and luciferase reporter assays indicated that MIR156 targets Wnt10b. In vitro, MIR156 suppressed proliferation by downregulating the Wnt10b protein and upregulating β-catenin phosphorylation in the porcine jejunum epithelial (IPEC-J2) cell line. Lithium chloride and an MIR156 inhibitor relieved this inhibition. This research is the first to demonstrate that plant MIR156 inhibits intestinal cell proliferation by targeting Wnt10b. More importantly, plant miRNAs may represent a new class of bioactive molecules that act as epigenetic regulators in humans and other animals.
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Xie, Qi, Xufeng Wang, Juan He, Ting Lan, Jiayu Zheng, Yupeng Li, Jinkang Pan, et al. "Distinct Evolutionary Profiles and Functions of microRNA156 and microRNA529 in Land Plants." International Journal of Molecular Sciences 22, no. 20 (October 14, 2021): 11100. http://dx.doi.org/10.3390/ijms222011100.
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MicroRNA156 (miR156) and miR529 have high sequence similarity and recognize overlapping sites in the same target genes, SQUAMOSA promoter binding protein-like (SPL or SBP box) genes, making it difficult to accurately distinguish their roles in regulatory networks that affect numerous biological functions. Here, we collected data about miR156 and miR529 family members from representative land plants and performed sequence comparisons, phylogenetic analysis, small RNA sequencing, and parallel analysis of RNA ends (PARE) analysis to dissect their evolutionary and functional differences. Although miR156 and miR529 are highly similar, there are differences in their mismatch-sensitive regions, which are essential for target recognition. In land plants, miR156 precursors are conserved mainly within the hairpin region, whereas miR529 precursors are conserved outside the hairpin region, including both the 5’ and 3’ arms. Phylogenetic analysis showed that MIR156 and MIR529 evolved independently, through divergent evolutionary patterns. The two genes also exhibit different expression patterns, with MIR529 preferentially expressed in reproductive tissues and MIR156 in other tissues. PARE analysis revealed that miR156 and miR529 possess specific targets in addition to common targets in maize, pointing to functional differences between them. Based on our findings, we developed a method for the rapid identification of miR529 and miR156 family members and uncovered the evolutionary divergence of these families, providing insights into their different regulatory roles in plant growth and development.
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Pegler, Joseph L., Duc Quan Nguyen, Christopher P. L. Grof, and Andrew L. Eamens. "Profiling of the Salt Stress Responsive MicroRNA Landscape of C4 Genetic Model Species Setaria viridis (L.) Beauv." Agronomy 10, no. 6 (June 12, 2020): 837. http://dx.doi.org/10.3390/agronomy10060837.
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Setaria viridis has recently emerged as an ideal model species to genetically characterize the C4 monocotyledonous grasses via a molecular modification approach. Soil salinization has become a compelling agricultural problem globally with salinity adversely impacting the yield potential of many of the major cereals. Small regulatory molecules of RNA, termed microRNAs (miRNAs), were originally demonstrated crucial for developmental gene expression regulation in plants, however, miRNAs have since been shown to additionally command a central regulatory role in abiotic stress adaptation. Therefore, a small RNA sequencing approach was employed to profile the salt stress responsive miRNA landscapes of the shoot and root tissues of two Setaria viridis accessions (A10 and ME034V) amenable to molecular modification. Small RNA sequencing-identified abundance alterations for miRNAs, miR169, miR395, miR396, miR397, miR398 and miR408, were experimentally validated via RT-qPCR. RT-qPCR was further applied to profile the molecular response of the miR160 and miR167 regulatory modules to salt stress. This analysis revealed accession- and tissue-specific responses for the miR160 and miR167 regulatory modules in A10 and ME034V shoot and root tissues exposed to salt stress. The findings reported here form the first crucial step in the identification of the miRNA regulatory modules to target for molecular manipulation to determine if such modification provides S. viridis with an improved tolerance to salt stress.
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Liu, Junying, Huiyan Fan, Ying Wang, Chenggui Han, Xianbing Wang, Jialin Yu, Dawei Li, and Yongliang Zhang. "Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection." Viruses 12, no. 3 (March 12, 2020): 310. http://dx.doi.org/10.3390/v12030310.
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Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.