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Journal articles on the topic 'MIR319C'

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Author: Grafiati
Published: 6 September 2023

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1

Hu, Ziwei, Tingting Liu, and Jiashu Cao. "Functional Similarity and Difference among Bra-MIR319 Family in Plant Development." Genes 10, no. 12 (November 21, 2019): 952. http://dx.doi.org/10.3390/genes10120952.

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miR319 was the first plant miRNA discovered via forward genetic mutation screening. In this study, we found that miR319 family members had similar sequences but different expression patterns in Brassica campestris and Arabidopsis thaliana. RT-PCR analysis revealed that Bra-MIR319a and Bra-MIR319c had similar expression patterns and were widely expressed in plant development, whereas Bra-MIR319b could only be detected in stems. The overexpression of each Bra-MIR319 family member in Arabidopsis could inhibit cell division and function in leaf and petal morphogenesis. Bra-miR319a formed a new regulatory relationship after whole genome triplication, and Bra-MIR319a overexpressing in Arabidopsis led to the degradation of pollen content and affected the formation of intine, thereby causing pollen abortion. Our results suggest that Bra-MIR319 family members have functional similarity and difference in plant development.
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2

Dmitriev, Alexey A., Anna V. Kudryavtseva, Nadezhda L. Bolsheva, Alexander V. Zyablitsin, Tatiana A. Rozhmina, Natalya V. Kishlyan, George S. Krasnov, et al. "miR319, miR390, and miR393 Are Involved in Aluminum Response in Flax (Linum usitatissimum L.)." BioMed Research International 2017 (2017): 1–6. http://dx.doi.org/10.1155/2017/4975146.

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Acid soils limit agricultural production worldwide. Major reason of crop losses in acid soils is the toxicity of aluminum (Al). In the present work, we investigated expression alterations of microRNAs in flax (Linum usitatissimum L.) plants under Al stress. Flax seedlings of resistant (TMP1919 and G1071/4_k) and sensitive (Lira and G1071/4_o) to Al cultivars and lines were exposed to AlCl3 solution for 4 and 24 hours. Twelve small RNA libraries were constructed and sequenced using Illumina platform. In total, 97 microRNAs from 18 conserved families were identified. miR319, miR390, and miR393 revealed expression alterations associated with Al treatment of flax plants. Moreover, for miR390 and miR393, the alterations were distinct in sensitive and resistant to Al genotypes. Expression level changes of miR319 and miR390 were confirmed using qPCR analysis. In flax, potential targets of miR319 are TCPs, miR390–TAS3 and GRF5, and miR393–AFB2-coding transcripts. TCPs, TAS3, GRF5, and AFB2 participate in regulation of plant growth and development. The involvement of miR319, miR390, and miR393 in response to Al stress in flax was shown here for the first time. We speculate that these microRNAs play an important role in Al response via regulation of growth processes in flax plants.
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3

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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4

Wu, Fangli, Jingyi Qi, Xin Meng, and Weibo Jin. "miR319c acts as a positive regulator of tomato against Botrytis cinerea infection by targeting TCP29." Plant Science 300 (November 2020): 110610. http://dx.doi.org/10.1016/j.plantsci.2020.110610.

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5

Dmitriev, Alexey A., Anna V. Kudryavtseva, Nadezhda L. Bolsheva, Alexander V. Zyablitsin, Tatiana A. Rozhmina, Natalya V. Kishlyan, George S. Krasnov, et al. "Erratum to “miR319, miR390, and miR393 Are Involved in Aluminum Response in Flax (Linum usitatissimum L.)”." BioMed Research International 2017 (2017): 1. http://dx.doi.org/10.1155/2017/6915898.

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6

Zhou, Bo, Yutong Kang, Jingtong Leng, and Qijiang Xu. "Genome-Wide Analysis of the miRNA–mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra." Genes 10, no. 6 (June 5, 2019): 430. http://dx.doi.org/10.3390/genes10060430.

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Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance.
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7

Fei, Yongjun, Caroline Luo, and Wei Tang. "Differential expression of microRNAs during root formation in Taxus chinensis var. mairei cultivars." Open Life Sciences 14, no. 1 (April 6, 2019): 97–109. http://dx.doi.org/10.1515/biol-2019-0011.

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AbstractMicroRNAs (miRNAs) have been shown to play key roles in the regulation of plant growth and development by modifying the expression of their target genes. However, the influence of miRNAs on root formation and development in woody plants, such as Taxus chinensis, remains largely unknown. In the current study, we explored the phytohormone-response and nutrition-response miRNA expression profiles during T. chinensis rooting by quantitative real-time PCR (qPCR). We identified six phytohormone-response miRNAs, namely, miR164a, miR165, miR167a, miR171b, miR319, and miR391, and eight nutrition-response miRNAs, namely, miR169b, miR395a, miR399c, miR408, miR826, miR827, miR857, and miR2111a, that were differentially expressed at different rooting phases of T. chinensis. Using northern blot analysis of the putative target genes of these miRNAs, we detected the relative gene expression changes of the target genes. Taken together, our results suggest that miRNAs are involved in root formation of T. chinensis and that miRNAs may play important regulatory roles in primary root, crown root, and root hair formation by targeting phytohormone and/or nutrition response genes in T. chinensis. For the first time, these results expand our understanding of the molecular mechanisms of plant root formation and development in a conifer species.
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8

Liu, Shengrui, Xiaozeng Mi, Ran Zhang, Yanlin An, Qiying Zhou, Tianyuan Yang, Xiaobo Xia, Rui Guo, Xuewen Wang, and Chaoling Wei. "Integrated analysis of miRNAs and their targets reveals that miR319c/TCP2 regulates apical bud burst in tea plant (Camellia sinensis)." Planta 250, no. 4 (June 6, 2019): 1111–29. http://dx.doi.org/10.1007/s00425-019-03207-1.

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9

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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10

Li, Hansheng, Yuling Lin, Xiaohui Chen, Yu Bai, Congqiao Wang, Xiaoping Xu, Yun Wang, and Zhongxiong Lai. "Effects of blue light on flavonoid accumulation linked to the expression of miR393, miR394 and miR395 in longan embryogenic calli." PLOS ONE 13, no. 1 (January 30, 2018): e0191444. http://dx.doi.org/10.1371/journal.pone.0191444.

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11

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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12

Peng, Yan, Xianwen Zhang, Yuewu Liu, and Xinbo Chen. "Exploring Heat-Response Mechanisms of MicroRNAs Based on Microarray Data of Rice Post-meiosis Panicle." International Journal of Genomics 2020 (September 18, 2020): 1–13. http://dx.doi.org/10.1155/2020/7582612.

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To explore heat response mechanisms of mircoRNAs (miRNAs) in rice post-meiosis panicle, microarray analysis was performed on RNA isolated from rice post-meiosis panicles which were treated at 40°C for 0 min, 10 min, 20 min, 60 min, and 2 h. By integrating paired differentially expressed (DE) miRNAs and mRNA expression profiles, we found that the expression levels of 29 DE-miRNA families were negatively correlated to their 178 DE-target genes. Further analysis showed that the majority of miRNAs in 29 DE-miRNA families resisted the heat stress by downregulating their target genes and a time lag existed between expression of miRNAs and their target genes. Then, GO-Slim classification and functional identification of these 178 target genes showed that (1) miRNAs were mainly involved in a series of basic biological processes even under heat conditions; (2) some miRNAs might play important roles in the heat resistance (such as osa-miR164, osa-miR166, osa-miR169, osa-miR319, osa-miR390, osa-miR395, and osa-miR399); (3) osa-miR172 might play important roles in protecting the rice panicle under the heat stress, but osa-miR437, osa-miR418, osa-miR164, miR156, and miR529 might negatively affect rice fertility and panicle flower; and (4) osa-miR414 might inhibit the flowering gene expression by downregulation of LOC_Os 05g51830 to delay the heading of rice. Finally, a heat-induced miRNA-PPI (protein-protein interaction) network was constructed, and three miRNA coregulatory modules were discovered.
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13

Kuang, Liuhui, Jiahua Yu, Qiufang Shen, Liangbo Fu, and Liyuan Wu. "Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots." Plants 10, no. 12 (December 14, 2021): 2754. http://dx.doi.org/10.3390/plants10122754.

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Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley.
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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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15

Wang, Huiyan, Yizhong Zhang, Du Liang, Xiaojuan Zhang, Xinqi Fan, Qi Guo, Linfang Wang, Jingxue Wang, and Qingshan Liu. "Genome‑wide identification and characterization of miR396 family members and their target genes GRF in sorghum (Sorghum bicolor (L.) moench)." PLOS ONE 18, no. 5 (May 10, 2023): e0285494. http://dx.doi.org/10.1371/journal.pone.0285494.

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MicroRNAs (miRNAs) widely participate in plant growth and development. The miR396 family, one of the most conserved miRNA families, remains poorly understood in sorghum. To reveal the evolution and expression pattern of Sbi-miR396 gene family in sorghum, bioinformatics analysis and target gene prediction were performed on the sequences of the Sbi-miR396 gene family members. The results showed that five Sbi-miR396 members, located on chromosomes 4, 6, and 10, were identified at the whole-genome level. The secondary structure analysis showed that the precursor sequences of all five Sbi-miR396 potentially form a stable secondary stem–loop structure, and the mature miRNA sequences were generated on the 5′ arm of the precursors. Sequence analysis identified the mature sequences of the five sbi-miR396 genes were high identity, with differences only at the 1st, 9th and 21st bases at the 5’ end. Phylogenetic analysis revealed that Sbi-miR396a, Sbi-miR396b, and Sbi-miR396c were clustered into Group I, and Sbi-miR396d and Sbi-miR396e were clustered into Group II, and all five sbi-miR396 genes were closely related to those of maize and foxtail millet. Expression analysis of different tissue found that Sbi-miR396d/e and Sbi-miR396a/b/c were preferentially and barely expressed, respectively, in leaves, flowers, and panicles. Target gene prediction indicates that the growth-regulating factor family members (SbiGRF1/2/3/4/5/6/7/8/10) were target genes of Sbi-miR396d/e. Thus, Sbi-miR396d/e may affect the growth and development of sorghum by targeting SbiGRFs. In addition, expression analysis of different tissues and developmental stages found that all Sbi-miR396 target genes, SbiGRFs, were barely expressed in leaves, root and shoot, but were predominantly expressed in inflorescence and seed development stage, especially SbiGRF1/5/8. Therefore, inhibition the expression of sbi-miR396d/e may increase the expression of SbiGRF1/5/8, thereby affecting floral organ and seed development in sorghum. These findings provide the basis for studying the expression of the Sbi-mir396 family members and the function of their target genes.
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16

Cao, Biting, Hongfeng Wang, Jinjuan Bai, Xuan Wang, Xiaorong Li, Yanfeng Zhang, Suxin Yang, Yuke He, and Xiang Yu. "miR319-Regulated TCP3 Modulates Silique Development Associated with Seed Shattering in Brassicaceae." Cells 11, no. 19 (October 1, 2022): 3096. http://dx.doi.org/10.3390/cells11193096.

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Seed shattering is an undesirable trait that leads to crop yield loss. Improving silique resistance to shattering is critical for grain and oil crops. In this study, we found that miR319-targeted TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTOR (TCPs) inhibited the process of post-fertilized fruits (silique) elongation and dehiscence via regulation of FRUITFULL (FUL) expression in Arabidopsis thaliana and Brassica napus. AtMIR319a activation resulted in a longer silique with thickened and lignified replum, whereas overexpression of an miR319a-resistant version of AtTCP3 (mTCP3) led to a short silique with narrow and less lignified replum. Further genetic and expressional analysis suggested that FUL acted downstream of TCP3 to negatively regulate silique development. Moreover, hyper-activation of BnTCP3.A8, a B. napus homolog of AtTCP3, in rapeseed resulted in an enhanced silique resistance to shattering due to attenuated replum development. Taken together, our findings advance our knowledge of TCP-regulated silique development and provide a potential target for genetic manipulation to reduce silique shattering in Brassica crops.
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17

Li, Lihong, Huilan Yi, Meizhao Xue, and Min Yi. "miR398 and miR395 are involved in response to SO2 stress in Arabidopsis thaliana." Ecotoxicology 26, no. 9 (August 17, 2017): 1181–87. http://dx.doi.org/10.1007/s10646-017-1843-y.

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18

Dong, Weiguo, Wenqing Ren, Xuan Wang, Yanfei Mao, and Yuke He. "MicroRNA319a regulates plant resistance to Sclerotinia stem rot." Journal of Experimental Botany 72, no. 10 (February 19, 2021): 3540–53. http://dx.doi.org/10.1093/jxb/erab070.

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Abstract MicroRNA319a (miR319a) controls cell division arrest in plant leaves by inhibiting the expression of TCP (TEOSINTE BRANCHED 1/CYCLOIDEA/PCF) family genes. However, it is unclear whether miR319a influences infection by necrotrophic pathogens and host susceptibility. In this study, we revealed that miR319a affects plant resistance to stem rot disease caused by Sclerotinia sclerotiorum. In Brassica rapa plants infected with S. sclerotiorum, miR319a levels increased while the expression levels of several BraTCP genes significantly decreased compared with those of uninfected plants. Overexpression of BraMIR319a in B. rapa increased the susceptibility of the plants to S. sclerotiorum and aggravated stem rot disease, whereas overexpression of BraTCP4-1 promoted plant resistance. RNA sequencing data revealed a potential relationship between miR319a and pathogen-related WRKY genes. Chromatin immunoprecipitation, electrophoretic mobility shift, and reporter transaction assays showed that BraTCP4-1 could bind to the promoters of WRKY75, WRKY70, and WRKY33 and directly activate these pathogen-related genes. Moreover, the expression levels of WRKY75, WRKY70, and WRKY33 in plants overexpressing BraMIR319a decreased significantly, whereas those of plants overexpressing BraTCP4-1 increased significantly, relative to the wild type. These results suggest that miR319a and its target gene BraTCP4 control stem rot resistance through pathways of WRKY genes.
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Köster, Tino, Katja Meyer, Claus Weinholdt, Lisa M. Smith, Martina Lummer, Corinna Speth, Ivo Grosse, Detlef Weigel, and Dorothee Staiger. "Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis." Nucleic Acids Research 42, no. 15 (August 7, 2014): 9925–36. http://dx.doi.org/10.1093/nar/gku716.

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Abstract The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log2 fold change of ±0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing.
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Li, Mingna, Lei Xu, Lixia Zhang, Xiao Li, Chunyu Cao, Lin Chen, Junmei Kang, et al. "Overexpression of Mtr-miR319a Contributes to Leaf Curl and Salt Stress Adaptation in Arabidopsis thaliana and Medicago truncatula." International Journal of Molecular Sciences 24, no. 1 (December 27, 2022): 429. http://dx.doi.org/10.3390/ijms24010429.

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Salt stress is a worldwide agronomic issue that limits crop yield and quality. Improving salt stress tolerance via genetic modification is the most efficient method to conquer soil salinization problems in crops. Crop miRNAs have been declared to be tightly associated with responding and adapting to salt stress and are advantageous for salt tolerance modification. However, very few studies have validated vital salt tolerance miRNAs and coupled potent target genes in Medicago species, the most economically important forage legume species. In this study, Mtr-miR319a, a miRNA that was identified from the previous next-generation sequencing assay of salt-treated Medicago truncatula, was overexpressed in M. truncatula and Arabidopsis thaliana, inducing the curly leaves and salt stress tolerance phenotypes. Combining the elevated expression level of Mtr-miR319a in the M. truncatula overexpression lines under normal and salt-treatment conditions, the regulatory roles of Mtr-miR319a in leaf development and salt stress adaptation were demonstrated. Several predicted target genes of Mtr-miR319a were also regulated by Mtr-miR319a and were associated with the aforementioned phenotypes in M. truncatula plants, most notably MtTCP4. Our study clarified the functional role of Mtr-miR319a and its target genes in regulating leaf development and defending salt stress, which can help to inform crop breeding efforts for improving salt tolerance via genetic engineering.
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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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Wang, Wanxu, Ting Shi, Xiaopeng Ni, Yanshuai Xu, Shenchun Qu, and Zhihong Gao. "The role of miR319a and its target gene TCP4 in the regulation of pistil development in Prunus mume." Genome 61, no. 1 (January 2018): 43–48. http://dx.doi.org/10.1139/gen-2017-0118.

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The microRNAs (miRNAs) comprise a broad class of non-coding small endogenous RNAs that are associated with many biological processes through the regulation of target genes, such as leaf morphogenesis and polarity, biotic and abiotic stress responses, and root and flower development. We identified a miRNA that affects flower development, miR319a, in Prunus mume. The Pm-miR319a target, Pm-TCP4, was validated by 5′RACE. The higher expression of Pm-TCP4 in imperfect flowers showed that Pm-TCP4 might promote pistil abortion. Further experiments showed that Pm-miR319a negatively regulates the expression of Pm-TCP4 mRNAs and affected pistil development. Sixteen downstream genes of Pm-TCP4 related to flower development were predicted. Previous studies have shown that they have an impact on the development of pistils. In this study it was established that Pm-miR319a indirectly regulates the development of pistils by regulating its target gene Pm-TCP4.
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Mo, Xiaowei, Haolang Chen, Xiaolan Yang, Beixin Mo, Lei Gao, and Yu Yu. "Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha." International Journal of Molecular Sciences 23, no. 18 (September 13, 2022): 10596. http://dx.doi.org/10.3390/ijms231810596.

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M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.
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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 and miR399 Expression Modules Alters the Response of Arabidopsis thaliana to Phosphate Stress." Plants 10, no. 12 (November 24, 2021): 2570. http://dx.doi.org/10.3390/plants10122570.

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In plant cells, the molecular and metabolic processes of nucleic acid synthesis, phospholipid production, coenzyme activation and the generation of the vast amount of chemical energy required to drive these processes relies on an adequate supply of the essential macronutrient, phosphorous (P). The requirement of an appropriate level of P in plant cells is evidenced by the intricately linked molecular mechanisms of P sensing, signaling and transport. One such mechanism is the posttranscriptional regulation of the P response pathway by the highly conserved plant microRNA (miRNA), miR399. In addition to miR399, numerous other plant miRNAs are also required to respond to environmental stress, including miR396. Here, we exposed Arabidopsis thaliana (Arabidopsis) transformant lines which harbor molecular modifications to the miR396 and miR399 expression modules to phosphate (PO4) starvation. We show that molecular alteration of either miR396 or miR399 abundance afforded the Arabidopsis transformant lines different degrees of tolerance to PO4 starvation. Furthermore, RT-qPCR assessment of PO4-starved miR396 and miR399 transformants revealed that the tolerance displayed by these plant lines to this form of abiotic stress most likely stemmed from the altered expression of the target genes of these two miRNAs. Therefore, this study forms an early step towards the future development of molecularly modified plant lines which possess a degree of tolerance to growth in a PO4 deficient environment.
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Chang, Kuo-Wei, Wan-Wen Hung, Chung-Hsien Chou, Hsi-Feng Tu, Shi-Rou Chang, Ying-Chieh Liu, Chung-Ji Liu, and Shu-Chun Lin. "LncRNA MIR31HG Drives Oncogenicity by Inhibiting the Limb-Bud and Heart Development Gene (LBH) during Oral Carcinoma." International Journal of Molecular Sciences 22, no. 16 (August 4, 2021): 8383. http://dx.doi.org/10.3390/ijms22168383.

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The miR-31 host gene (MIR31HG) encodes a long non-coding RNA (LncRNA) that harbors miR-31 in its intron 2; miR-31 promotes malignant neoplastic progression. Overexpression of MIR31HG and of miR-31 occurs during oral squamous cell carcinoma (OSCC). However, the downstream effectors modulated by MIR31HG during OSCC pathogenesis remain unclear. The present study identifies up-regulation of MIR31HG expression during the potentially premalignant disorder stage of oral carcinogenesis. The potential of MIR31HG to enhance oncogenicity and to activate Wnt and FAK was identified when there was exogenous MIR31HG expression in OSCC cells. Furthermore, OSCC cell subclones with MIR31HG deleted were established using a Crispr/Cas9 strategy. RNA sequencing data obtained from cells expressing MIR31HG, cells with MIR31HG deleted and cells with miR-31 deleted identified 17 candidate genes that seem to be modulated by MIR31HG in OSCC cells. A TCGA database algorithm pinpointed MMP1, BMP2 and Limb-Bud and Heart development (LBH) as effector genes controlled by MIR31HG during OSCC. Exogenous LBH expression decreases tumor cell invasiveness, while knockdown of LBH reverses the oncogenic suppression present in MIR31HG deletion subclones. The study provides novel insights demonstrating the contribution of the MIR31HG-LBH cascade to oral carcinogenesis.
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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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Du, Kun, Yang Yang, Jinping Li, Ming Wang, Jinjin Jiang, Jian Wu, Yujie Fang, Yang Xiang, and Youping Wang. "Functional Analysis of Bna-miR399c-PHO2 Regulatory Module Involved in Phosphorus Stress in Brassica napus." Life 13, no. 2 (January 22, 2023): 310. http://dx.doi.org/10.3390/life13020310.

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Phosphorus stress is one of the important factors restricting plant growth and development, and the microRNA (miRNA) family is involved in the regulation of the response to plant nutrient stress by repressing the expression of target genes at the post-transcriptional or translational level. miR399 is involved in the transportation of phosphate in multiple plants by improving tolerance to low Pi conditions. However, the effect of miR399 on the response of low Pi stress in rapeseed (Brassica napus L.) is unclear. The present study showed a significant increase in taproot length and lateral root number of plants overexpressing Bna-miR399c, while the biomass and Pi accumulation in shoots and roots increased, and the anthocyanin content decreased and chlorophyll content improved under low Pi stress. The results illustrate that Bna-miR399c could enhance the uptake and transportation of Pi in soil, thus making B. napus more tolerant to low Pi stress. Furthermore, we confirmed that BnPHO2 is one of the targets of Bna-miR399c, and the rejection of Pi in rapeseed seedlings increased due to the overexpression of BnPHO2. Hence, we suggest that miR399c-PHO2 module can effectively regulate the homeostasis of Pi in B. napus. Our study can also provide the theoretical basis for germplasm innovation and the design of intelligent crops with low nutrient input and high yield to achieve the dual objectives of income and yield increase and environmental protection in B. napus.
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Mazhar, Muhammad Waqar, Nik Yusnoraini Yusof, Tayyaba Shaheen, Saira Saif, Ahmad Raza, and Fatima Mazhar. "Sequence, Secondary Structure, and Phylogenetic Conservation of MicroRNAs in Arabidopsis thaliana." Bioinformatics and Biology Insights 16 (January 2022): 117793222211421. http://dx.doi.org/10.1177/11779322221142116.

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MicroRNAs are small non-coding RNA molecules that are produced in a cell endogenously. They are made up of 18 to 26 nucleotides in strength. Due to their evolutionary conserved nature, most of the miRNAs provide a logical basis for the prediction of novel miRNAs and their clusters in plants such as sunflowers related to the Asteraceae family. In addition, they participate in different biological processes of plants, including cell signaling and metabolism, development, growth, and tolerance to (biotic and abiotic) stresses. In this study profiling, conservation and characterization of novel miRNA possessing conserved nature in various plants and their targets annotation in sunflower (Asteraceae) were obtained by using various computational tools and software. As a result, we looked at 152 microRNAs in Arabidopsis thaliana that had already been predicted. Drought tolerance stress is mediated by these 152 non-coding RNAs. Following that, we used local alignment to predict novel microRNAs that were specific to Helianthus annuus. We used BLAST to do a local alignment, and we chose sequences with an identity of 80% to 100%. MIR156a, MIR164a, MIR165a, MIR170, MIR172a, MIR172b, MIR319a, MIR393a, MIR394a, MIR399a, MIR156h, and MIR414 are the new anticipated miRNAs. We used MFold to predict the secondary structure of new microRNAs. We used conservation analysis and phylogenetic analysis against a variety of organisms, including Gossypium hirsutum, H. annuus, A. thaliana, Triticum aestivum, Saccharum officinarum, Zea mays, Brassica napus, Solanum tuberosum, Solanum lycopersicum, and Oryza sativa, to determine the evolutionary history of these novel non-coding RNAs. Clustal W was used to analyze the evolutionary history of discovered miRNAs.
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Liu, Yanrong, Dayong Li, Jianping Yan, Kexin Wang, Hong Luo, and Wanjun Zhang. "MiR319 mediated salt tolerance by ethylene." Plant Biotechnology Journal 17, no. 12 (June 7, 2019): 2370–83. http://dx.doi.org/10.1111/pbi.13154.

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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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Chen, Kai, Bo Zhang, and Zhongjie Sun. "MicroRNA 379 Regulates Klotho Deficiency–Induced Cardiomyocyte Apoptosis Via Repression of Smurf1." Hypertension 78, no. 2 (August 2021): 342–52. http://dx.doi.org/10.1161/hypertensionaha.120.16888.

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Klotho is an aging-suppressor gene. Klotho gene deficiency impairs heart function leading to heart failure, but the underlying mechanism remains poorly understood. MicroRNAs are increasingly recognized to play important roles in the pathogenesis of cardiomyopathy. The objective of this study is to investigate whether microRNA 379 (Mir379) regulates Klotho deficiency-associated cardiomyocyte apoptosis. Using inducible Cre-Loxp recombination technology, we first found that kidney-specific deletion of the Klotho gene caused heart failure. Using microRNA sequencing analysis, we found that Mir379 may be a target of Klotho. In cultured H9c2 heart cells, we found that treatment with Klotho-free medium increased Mir379 levels and induced apoptosis. To test whether Mir379 mediates Klotho deficiency–induced apoptosis, H9c2 cells were transfected with Mir379 inhibitor. Interestingly, Mir379 inhibitor (anti-Mir379) prevented Klotho deficiency–induced H9c2 cell apoptosis. On the contrary, Mir379 mimic itself caused apoptosis in H9c2 cells. These findings suggest that Mir379 may mediate Klotho deficiency–induced apoptosis in H9C2 cells. Using the mRNA-miRNA target interaction assay, we found that Smurf1(SMAD specific E3 ubiquitin protein ligase 1) mRNA contained the 3-UTR binding site for Mir379. Importantly, Mir379 mimic suppressed Smurf1 expression, and the Mir379 mimic–induced apoptosis can be rescued by treatment with exogenous Smurf1 protein. Therefore, Smurf1 repression may be involved in Mir379–induced H9c2 cells apoptosis. In conclusion, Mir379 may mediate Klotho deficiency-associated cardiomyocyte apoptosis through repression of Smurf1 which is required for Mir379-induced apoptotic cell death. Mir379 may be a potential therapeutic target for cardiomyocyte apoptosis-associated heart failure due to Klotho deficiency.
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Fan, Zhengyang, Bianbian Zhao, Ruilian Lai, Huan Wu, Liang Jia, Xiaobing Zhao, Jie Luo, et al. "Genome-Wide Identification of the MPK Gene Family and Expression Analysis under Low-Temperature Stress in the Banana." Plants 12, no. 16 (August 12, 2023): 2926. http://dx.doi.org/10.3390/plants12162926.

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Mitogen-activated protein kinases (MAPKs and MPKs) are important in the process of resisting plant stress. In this study, 21, 12, 18, 16, and 10 MPKs were identified from Musa acuminata, Musa balbisiana, Musa itinerans, Musa schizocarpa, and Musa textilis, respectively. These MPKs were divided into Group A, B, C, and D. Phylogenetic analysis revealed that this difference in number was due to the gene shrinkage of the Group B subfamily of Musa balbisiana and Musa textilis. KEGG annotations revealed that K14512, which is involved in plant hormone signal transduction and the plant–pathogen interaction, was the most conserved pathway of the MPKs. The results of promoter cis-acting element prediction and focTR4 (Fusarium oxysporum f. sp. cubense tropical race 4) transcriptome expression analysis preliminarily confirmed that MPKs were relevant to plant hormone and biotic stress, respectively. The expression of MPKs in Group A was significantly upregulated at 4 °C, and dramatically, the MPKs in the root were affected by low temperature. miR172, miR319, miR395, miR398, and miR399 may be the miRNAs that regulate MPKs during low-temperature stress, with miR172 being the most critical. miRNA prediction and qRT-PCR results indicated that miR172 may negatively regulate MPKs. Therefore, we deduced that MPKs might coordinate with miR172 to participate in the process of the resistance to low-temperature stress in the roots of the banana. This study will provide a theoretical basis for further analysis of the mechanism of MPKs under low-temperature stress of bananas, and this study could be applied to molecular breeding of bananas in the future.
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Ko, Ching-Chung, Yao-Yu Hsieh, and Pei-Ming Yang. "Long Non-Coding RNA MIR31HG Promotes the Transforming Growth Factor β-Induced Epithelial-Mesenchymal Transition in Pancreatic Ductal Adenocarcinoma Cells." International Journal of Molecular Sciences 23, no. 12 (June 12, 2022): 6559. http://dx.doi.org/10.3390/ijms23126559.

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The epithelial-to-mesenchymal transition (EMT) describes a biological process in which polarized epithelial cells are converted into highly motile mesenchymal cells. It promotes cancer cell dissemination, allowing them to form distal metastases, and also involves drug resistance in metastatic cancers. Transforming growth factor β (TGFβ) is a multifunctional cytokine that plays essential roles in development and carcinogenesis. It is a major inducer of the EMT. The MIR31 host gene (MIR31HG) is a newly identified long non-coding (lnc)RNA that exhibits ambiguous roles in cancer. In this study, a cancer genomics analysis predicted that MIR31HG overexpression was positively correlated with poorer disease-free survival of pancreatic ductal adenocarcinoma (PDAC) patients, which was associated with upregulation of genes related to TGFβ signaling and the EMT. In vitro evidence demonstrated that TGFβ induced MIR31HG expression in PDAC cells, and knockdown of MIR31HG expression reversed TGFβ-induced EMT phenotypes and cancer cell migration. Therefore, MIR31HG has an oncogenic role in PDAC by promoting the EMT.
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Xia, Zihao, Zhenxing Zhao, Xinran Gao, Zhiyuan Jiao, Yuanhua Wu, Tao Zhou, and Zaifeng Fan. "Characterization of Maize miRNAs in Response to Synergistic Infection of Maize Chlorotic Mottle Virus and Sugarcane Mosaic Virus." International Journal of Molecular Sciences 20, no. 13 (June 27, 2019): 3146. http://dx.doi.org/10.3390/ijms20133146.

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The synergistic infection of maize chlorotic mottle virus (MCMV) and sugarcane mosaic virus (SCMV) causes maize lethal necrosis, with considerable losses to global maize production. microRNAs (miRNAs) are conserved non-coding small RNAs that play essential regulatory roles in plant development and environmental stress responses, including virus infection. However, the characterization of maize miRNAs in response to synergistic infection of MCMV and SCMV remains largely unknown. In this study, the profiles of small RNAs from MCMV and SCMV single- and co-infected (S + M) maize plants were obtained by high-throughput sequencing. A total of 173 known miRNAs, belonging to 26 miRNA families, and 49 novel miRNAs were profiled. The expression patterns of most miRNAs in S + M-infected maize plants were similar to that in SCMV-infected maize plants, probably due to the existence of RNA silencing suppressor HC-Pro. Northern blotting and quantitative real-time PCR were performed to validate the accumulation of miRNAs and their targets in different experimental treatments, respectively. The down-regulation of miR159, miR393, and miR394 might be involved in antiviral defense to synergistic infection. These results provide novel insights into the regulatory networks of miRNAs in maize plants in response to the synergistic infection of MCMV and SCMV.
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Huang, Jing-Hao, Xiong-Jie Lin, Ling-Yuan Zhang, Xian-Da Wang, Guo-Cheng Fan, and Li-Song Chen. "MicroRNA Sequencing Revealed Citrus Adaptation to Long-Term Boron Toxicity through Modulation of Root Development by miR319 and miR171." International Journal of Molecular Sciences 20, no. 6 (March 21, 2019): 1422. http://dx.doi.org/10.3390/ijms20061422.

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Boron (B) toxicity in Citrus is a common physiological disorder leading to reductions in both productivity and quality. Studies on how Citrus roots evade B toxicity may provide new insight into plant tolerance to B toxicity. Here, using Illumina sequencing, differentially expressed microRNAs (miRNAs) were identified in B toxicity-treated Citrus sinensis (tolerant) and C. grandis (intolerant) roots. The results showed that 37 miRNAs in C. grandis and 11 miRNAs in C. sinensis were differentially expressed when exposed to B toxicity. Among them, miR319, miR171, and miR396g-5p were confirmed via 5′-RACE and qRT-PCR to target a myeloblastosis (MYB) transcription factor gene, a SCARECROW-like protein gene, and a cation transporting ATPase gene, respectively. Maintenance of SCARECROW expression in B treated Citrus roots might fulfill stem cell maintenance, quiescent center, and endodermis specification, thus allowing regular root elongation under B-toxic stress. Down-regulation of MYB due to up-regulation of miR319 in B toxicity-treated C. grandis roots might decrease the number of root tips, thereby dramatically changing root system architecture. Our findings suggested that miR319 and miR171 play a pivotal role in Citrus adaptation to long-term B toxicity by targeting MYB and SCARECROW, respectively, both of which are responsible for root growth and development.
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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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Zhou, Yi, Yanghua Fan, Xi Zhou, Anna Mou, Yu He, Fu Wang, and Yong Liu. "Significance of lncRNA MIR31HG in predicting the prognosis for Chinese patients with cancer: a meta-analysis." Biomarkers in Medicine 14, no. 4 (March 2020): 303–16. http://dx.doi.org/10.2217/bmm-2019-0145.

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It is important to clarify the significance of long noncoding RNA MIR31 host gene (lncRNA MIR31HG) in predicting the prognosis for malignant tumors through meta-analysis. Electronic databases were systemically searched, from inception until 2 January 2019, to identify related articles. Meanwhile, the hazard ratios (odds ratios) and 95% CIs were computed for exploring the association between the expression of lncRNA MIR31HG and the survival (pathological variables). Eleven studies with 1041 cases were enrolled into the current meta-analysis. Low expression of lncRNA MIR31HG showed correlation with the dismal overall survival, disease-free survival, high tumor stage and lymph node metastasis among patients with digestive system cancers. Low expression of lncRNA MIR31HG may serve as a potential novel factor to indicate the dismal prognosis and metastasis in patients with digestive system cancers.
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LUO, Mao, Zhi-Ming ZHANG, Jian GAO, Xing ZENG, and Guang-Tang PAN. "The role of miR319 in plant development regulation." Hereditas (Beijing) 33, no. 11 (December 2, 2011): 1203–11. http://dx.doi.org/10.3724/sp.j.1005.2011.01203.

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THIEBAUT, FLÁVIA, CRISTIAN A. ROJAS, KARLA L. ALMEIDA, CLÍCIA GRATIVOL, GISELLI C. DOMICIANO, CAREN REGINA C. LAMB, JANICE DE ALMEIDA ENGLER, ADRIANA S. HEMERLY, and PAULO C. G. FERREIRA. "Regulation of miR319 during cold stress in sugarcane." Plant, Cell & Environment 35, no. 3 (October 24, 2011): 502–12. http://dx.doi.org/10.1111/j.1365-3040.2011.02430.x.

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Schommer, Carla, Juan M. Debernardi, Edgardo G. Bresso, Ramiro E. Rodriguez, and Javier F. Palatnik. "Repression of Cell Proliferation by miR319-Regulated TCP4." Molecular Plant 7, no. 10 (October 2014): 1533–44. http://dx.doi.org/10.1093/mp/ssu084.

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41

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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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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43

Krivmane, Baiba, Kaiva Solvita Ruņģe, Ineta Samsone, and Dainis Edgars Ruņģis. "Differentially Expressed Conserved Plant Vegetative Phase-Change-Related microRNAs in Mature and Rejuvenated Silver Birch In Vitro Propagated Tissues." Plants 12, no. 10 (May 16, 2023): 1993. http://dx.doi.org/10.3390/plants12101993.

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In plants, phase change from the juvenile stage to maturity involves physiological and anatomical changes, which are initiated and controlled by evolutionary highly conserved microRNAs. This process is of particular significance for the in vitro propagation of woody plant species, as individuals or tissues that have undergone the transition to vegetative maturity are recalcitrant to propagation. Conserved miRNAs differentially expressed between juvenile (including rejuvenated) and mature silver birch tissues were identified using high-throughput sequencing of small RNA libraries. Expression of some miR156 isoforms was high in juvenile tissues and has been previously reported to regulate phase transitions in a range of species. Additional miRNAs, such as miR394 and miR396, that were previously reported to be highly expressed in juvenile woody plant tissues were also differentially expressed in this study. However, expression of miR172, previously reported to be highly expressed in mature tissues, was low in all sample types in this study. The obtained results will provide insight for further investigation of the molecular mechanisms regulating vegetative phase change in silver birch and other perennial woody plant species, by analysing a wider range of genotypes, tissue types and maturation stages. This knowledge can potentially assist in identification of rejuvenated material at an earlier stage than currently possible, increasing the efficiency of silver birch in vitro propagation.
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Rong, Hao, Xin Han, Yue Xin, Zhouxian Ni, Wangxiang Zhang, and Li’an Xu. "Small RNA and Degradome Sequencing Reveal Roles of miRNAs in the Petal Color Fading of Malus Crabapple." International Journal of Molecular Sciences 24, no. 14 (July 13, 2023): 11384. http://dx.doi.org/10.3390/ijms241411384.

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The Malus crabapple is an important woody ornamental plant. The fading of petals during its development significantly affects their ornamental value. Petal color is related to anthocyanin content and miRNAs play an important role in the post-transcriptional regulation of anthocyanin synthesis. However, the mechanisms underlying miRNA regulation of petal fading have rarely been studied. Transcriptome and small RNA sequencing of petals from the blooming phases of Malus. ‘Indian Summer’ varieties S1 (small bud), S2 (initial-flowering), and S3 (late-flowering) allowed us to identify 230 known miRNAs and 17 novel miRNAs, including 52 differentially expressed miRNAs which targeted 494 genes and formed 823 miRNA–target pairs. Based on the target gene annotation results, miRNA–target pairs were screened that may be involved in the fading process of Malus crabapple petals through three different pathways: anthocyanin synthesis, transport, and degradation, involving mcr-miR858-MYB1\MYB5 and mcr-miR396-McCHI inhibiting anthocyanin synthesis; mcr-miR167, mcr-miR390, mcr-miR535, and mcr-miR858 inhibiting anthocyanin transport from the cytoplasm to the vacuole by targeting ABC transporter genes (ABCB, ABCC, ABCD, and ABCG); and mcr-miR398 targeting the superoxide dismutase genes (CZSOD2 and CCS) to accelerate anthocyanin degradation. These findings offer a novel approach to understanding the mechanism of petal fading and serve as a reference for other plants with floral fading.
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45

Krasnikova, M. S., I. A. Milyutina, V. K. Bobrova, L. V. Ozerova, A. V. Troitsky, A. G. Solovyev, and S. Y. Morozov. "Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis." Journal of Biomedicine and Biotechnology 2009 (2009): 1–9. http://dx.doi.org/10.1155/2009/952304.

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TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor inArabidopsis thalianais controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the5′-terminal miR390 target site.
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46

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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Li, Ying, Naresh Vasupalli, Ou Cai, Xiaofang Lin, and Hongyu Wu. "Network of miR396-mRNA in Tissue Differentiation in Moso Bamboo (Phyllostachys edulis)." Plants 12, no. 5 (March 1, 2023): 1103. http://dx.doi.org/10.3390/plants12051103.

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MiR396 plays an essential role in various developmental processes. However, the miR396-mRNA molecular network in bamboo vascular tissue differentiation during primary thickening has not been elucidated. Here, we revealed that three of the five members from the miR396 family were overexpressed in the underground thickening shoots collected from Moso bamboo. Furthermore, the predicted target genes were up/down-regulated in the early (S2), middle (S3) and late (S4) developmental samples. Mechanistically, we found that several of the genes encoding protein kinases (PKs), growth-regulating factors (GRF), transcription factors (TFs), and transcription regulators (TRs) were the potential targets of miR396 members. Moreover, we identified QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) d omains in five PeGRF homologs and a Lipase_3 domain and a K_trans domain in another two potential targets, where the cleavage targets were identified via degradome sequencing (p < 0.05). The sequence alignment indicated many mutations in the precursor sequence of miR396d between Moso bamboo and rice. Our dual-luciferase assay revealed that ped-miR396d-5p binds to a PeGRF6 homolog. Thus, the miR396-GRF module was associated with Moso bamboo shoot development. Fluorescence in situ hybridization localized miR396 in the vascular tissues of the leaves, stems, and roots of pot Moso bamboo seedlings at the age of two months. Collectively, these experiments revealed that miR396 functions as a regulator of vascular tissue differentiation in Moso bamboo. Additionally, we propose that miR396 members are targets for bamboo improvement and breeding.
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Schommer, Carla, Javier F. Palatnik, Pooja Aggarwal, Aurore Chételat, Pilar Cubas, Edward E. Farmer, Utpal Nath, and Detlef Weigel. "Control of Jasmonate Biosynthesis and Senescence by miR319 Targets." PLoS Biology 6, no. 9 (September 23, 2008): e230. http://dx.doi.org/10.1371/journal.pbio.0060230.

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49

Beltramino, Matías, Juan Manuel Debernardi, Antonella Ferela, and Javier F. Palatnik. "ARF2 represses expression of plant GRF transcription factors in a complementary mechanism to microRNA miR396." Plant Physiology 185, no. 4 (January 25, 2021): 1798–812. http://dx.doi.org/10.1093/plphys/kiab014.

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Abstract Members of the GROWTH REGULATING FACTOR (GRF) family of transcription factors play key roles in the promotion of plant growth and development. Many GRFs are post-transcriptionally repressed by microRNA (miRNA) miR396, an evolutionarily conserved small RNA, which restricts their expression to proliferative tissue. We performed a comprehensive analysis of the GRF family in eudicot plants and found that in many species all the GRFs have a miR396-binding site. Yet, we also identified GRFs with mutations in the sequence recognized by miR396, suggesting a partial or complete release of their post-transcriptional repression. Interestingly, Brassicaceae species share a group of GRFs that lack miR396 regulation, including Arabidopsis GRF5 and GRF6. We show that instead of miR396-mediated post-transcriptional regulation, the spatiotemporal control of GRF5 is achieved through evolutionarily conserved promoter sequences, and that AUXIN RESPONSE FACTOR 2 (ARF2) binds to such conserved sequences to repress GRF5 expression. Furthermore, we demonstrate that the unchecked expression of GRF5 in arf2 mutants is responsible for the increased cell number of arf2 leaves. The results describe a switch in the repression mechanisms that control the expression of GRFs and mechanistically link the control of leaf growth by miR396, GRFs, and ARF2 transcription factors.
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50

Nag, Anwesha, Stacey King, and Thomas Jack. "miR319a targeting ofTCP4is critical for petal growth and development inArabidopsis." Proceedings of the National Academy of Sciences 106, no. 52 (December 10, 2009): 22534–39. http://dx.doi.org/10.1073/pnas.0908718106.

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