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https://www.readbyqxmd.com/read/28633390/investigating-microrna-mediated-regulation-of-the-nascent-nuclear-transcripts-in-plants-a-bioinformatics-workflow
#1
Dongliang Yu, Zhonghai Tang, Chaogang Shao, Xiaoxia Ma, Taihe Xiang, Zhihong Fan, Huizhong Wang, Yijun Meng
Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs...
June 14, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28633325/malus-hupehensis-mir168-targets-to-argonaute1-and-contributes-to-the-resistance-against-botryosphaeria-dothidea-infection-by-altering-defense-responses
#2
Xinyi Yu, Yingjun Hou, Weiping Chen, Sanhong Wang, Peihong Wang, Shenchun Qu
MicroRNA-mediated post transcriptional regulation plays a fundamental role in various plant physiological processes, including responses to pathogens. MicroRNA168 has been implicated as an essential factor of miRNA pathways by targeting ARGONAUTE1 (AGO1), the core component of the RNA-induced silencing complex (RISC). A fluctuation in AGO1 expression influences various plant-pathogen interactions, and the homeostasis of AGO1 and miR168 accumulation is maintained by a complicated feedback regulatory loop. In this study, the connection between miR168 and the resistance of M...
June 13, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28632199/modulatory-effects-of-guarana-paullinia-cupana-on-adipogenesis
#3
Natália da Silva Lima, Erica de Paula Numata, Leonardo Mendes de Souza Mesquita, Pollyana Hammoud Dias, Wagner Vilegas, Alessandra Gambero, Marcelo Lima Ribeiro
Guarana (Paullinia cupana) is a plant originated in Brazil that presents a beneficial effect on body weight control and metabolic alterations. The aim of this study was to evaluate the effects of guarana on genes and miRNAs related to adipogenesis in 3T3L1 cells. The anti-adipogenic effect of guarana was evaluated by Oil Red-O staining. Gene and miRNA expression levels were determined by real time PCR. The Cebpα and β-catenin nuclear translocation were evaluated using immunocytochemistry. Our data indicated that the triglyceride-reducing effect of guarana was dose-dependent from 100 to 300 µg/mL (-12%, -20%, -24% and -40%, respectively, p < 0...
June 20, 2017: Nutrients
https://www.readbyqxmd.com/read/28624685/bacillus-subtilis-affects-mirnas-and-flavanoids-production-in-agrobacterium-tobacco-interaction
#4
Fahimeh Nazari, Naser Safaie, Bahram Mohammad Soltani, Masoud Shams-Bakhsh, Mohsen Sharifi
Agrobacterium tumefaciens is a very destructive plant pathogen. Selection of effective biological agents against this pathogen depends on more insight into molecular plant defence responses during the biocontrol agent-pathogen interaction. Auxin as a phytohormone is a key contributor in pathogenesis and plant defence and accumulation of auxin transport carriers are accompanied by increasing in flavonoid and miRNAs concentrations during plant interactions with bacteria. The aim of this research was molecular analysis of Bacillus subtilis (ATCC21332) biocontrol effect against A...
June 10, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28615713/exosomal-micrornas-in-giant-panda-ailuropoda-melanoleuca-breast-milk-potential-maternal-regulators-for-the-development-of-newborn-cubs
#5
Jideng Ma, Chengdong Wang, Keren Long, Hemin Zhang, Jinwei Zhang, Long Jin, Qianzi Tang, Anan Jiang, Xun Wang, Shilin Tian, Li Chen, Dafang He, Desheng Li, Shan Huang, Zhi Jiang, Mingzhou Li
The physiological role of miRNAs is widely understood to include fine-tuning the post-transcriptional regulation of a wide array of biological processes. Extensive studies have indicated that exosomal miRNAs in the bodily fluids of various organisms can be transferred between living cells for the delivery of gene silencing signals. Here, we illustrated the expression characteristics of exosomal miRNAs in giant panda breast milk during distinct lactation periods and highlighted the enrichment of immune- and development-related endogenous miRNAs in colostral and mature giant panda milk...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28611800/small-rna-sequencing-links-physiological-changes-and-rddm-process-to-vegetative-to-floral-transition-in-apple
#6
Xinwei Guo, Zeyang Ma, Zhonghui Zhang, Lailiang Cheng, Xiuren Zhang, Tianhong Li
Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28608334/in-vitro-analysis-of-argonaute-mediated-target-cleavage-and-translational-repression-in-plants
#7
Yukihide Tomari, Hiro-Oki Iwakawa
MicroRNAs (miRNAs) are endogenous small RNAs, which negatively regulate expression of complementary target genes at the post-transcriptional level. In plants, miRNAs are mainly loaded onto ARGONAUTE1 to form RNA-induced silencing complexes (RISCs), which mediate target mRNA cleavage as well as translational repression. The cell-free system derived from tobacco BY-2 protoplasts has become a powerful tool not only for the analysis of RISC assembly mechanism but also for mechanistic dissection of plant RISC functions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28608332/analysis-of-the-uridylation-of-both-argonaute-bound-mirnas-and-5-cleavage-products-of-their-target-rnas-in-plants
#8
Guodong Ren, Xiaoyan Wang, Bin Yu
Uridylation (3' untemplated uridine addition) provides a mechanism to trigger the degradation of miRNAs and the 5' cleavage products (5' CP) that are produced from miRNA-directed ARGONAUTE (AGO) cleavage of target RNAs. We have recently shown that HEN1 SUPPRESSOR 1 (HESO1), a terminal uridylyltransferase, and its homolog UTP:RNA uridylyltransferase 1 (URT1) catalyze the uridylation of miRNAs and 5' CPs within the AGO complex in higher plants. In this chapter, we describe detailed protocols for analyzing 3' end uridylation of both AGO-bound miRNAs and 5' CP...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28604625/association-of-mir-938g-a-polymorphisms-with-primary-ovarian-insufficiency-poi-related-gene-expression
#9
Sung Hwan Cho, Eun Hee Ahn, Hui Jeong An, Ji Hyang Kim, Jung Jae Ko, Young Ran Kim, Woo Sik Lee, Nam Keun Kim
MicroRNAs (miRNAs) post-transcriptionally regulate gene expression in animals and plants. The aim of this study was to investigate whether polymorphisms in miR-938 are associated with the risk of primary ovarian insufficiency (POI) and POI-related target gene regulation. We identified the miR-938G>A polymorphisms within the seed sequence of mature miRNA and aligned the seed sequence with the 3' untranslated region (UTR) of the gonadotropin-releasing hormone receptor (GnRHR) mRNA, a miR-938 target gene. We found that the binding of miR-938 to the 3'-UTR of GnRHR mRNA was significantly different between normal and variant alleles...
June 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28596514/genome-wide-identification-and-characterization-of-phased-small-interfering-rna-genes-in-response-to-botrytis-cinerea-infection-in-solanum-lycopersicum
#10
Fangli Wu, Yue Chen, Xing Tian, Xiaole Zhu, Weibo Jin
Phased small interfering RNAs (phasiRNAs) are encoded by a novel class of genes known as phasiRNA producing (PHAS) genes. These genes play important regulatory roles by targeting protein coding transcripts in plant species. In this study, 91 regions were identified as potential PHAS loci in tomato, with additional evidence that seven of them can be triggered by five miRNAs. Among the identified loci, 51 were located in genic regions, and the remaining 40 were located in intergenic regions. The transient overexpression of PHAS15 and PHAS26 demonstrated that phasiRNAs predicted by PhaseTank were indeed generated from their respective PHAS loci...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28588605/mir397-laccase-gene-mediated-network-improves-tolerance-to-fenoxaprop-p-ethyl-in-beckmannia-syzigachne-and-oryza-sativa
#11
Lang Pan, Hongwei Zhao, Qin Yu, Lianyang Bai, Liyao Dong
Herbicide resistance can be either target-site or non-target-site based. The molecular mechanisms underlying non-target-site resistance (NTSR) are poorly understood, especially at the level of gene expression regulation. MicroRNAs (miRNAs) represent key post-transcriptional regulators of eukaryotic gene expression and play important roles in stress responses. In this study, the miR397 gene from Beckmannia syzigachne (referred to as bsy-miR397) was functionally characterized to determine its role in regulating fenoxaprop-P-ethyl resistance...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28587281/genome-wide-identification-and-characterization-of-salinity-stress-responsive-mirnas-in-wild-emmer-wheat-triticum-turgidum-ssp-dicoccoides
#12
Kewei Feng, Xiaojun Nie, Licao Cui, Pingchuan Deng, Mengxing Wang, Weining Song
MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs which regulate diverse molecular and biochemical processes at a post-transcriptional level in plants. As the ancestor of domesticated wheat, wild emmer wheat (Triticum turgidum ssp. dicoccoides) has great genetic potential for wheat improvement. However, little is known about miRNAs and their functions on salinity stress in wild emmer. To obtain more information on miRNAs in wild emmer, we systematically investigated and characterized the salinity-responsive miRNAs using deep sequencing technology...
June 6, 2017: Genes
https://www.readbyqxmd.com/read/28587194/cross-kingdom-regulation-of-putative-mirnas-derived-from-happy-tree-in-cancer-pathway-a-systems-biology-approach
#13
Dinesh Kumar, Swapnil Kumar, Garima Ayachit, Shivarudrappa B Bhairappanavar, Afzal Ansari, Priyanka Sharma, Subhash Soni, Jayashankar Das
MicroRNAs (miRNAs) are well-known key regulators of gene expression primarily at the post-transcriptional level. Plant-derived miRNAs may pass through the gastrointestinal tract, entering into the body fluid and regulate the expression of endogenous mRNAs. Camptotheca acuminata, a highly important medicinal plant known for its anti-cancer potential was selected to investigate cross-kingdom regulatory mechanism and involvement of miRNAs derived from this plant in cancer-associated pathways through in silico systems biology approach...
June 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28586645/the-protein-phosphatase-4-and-smek1-complex-dephosphorylates-hyl1-to-promote-mirna-biogenesis-by-antagonizing-the-mapk-cascade-in-arabidopsis
#14
Chuanbin Su, Ziwei Li, Jinping Cheng, Lei Li, Songxiao Zhong, Li Liu, Yun Zheng, Binglian Zheng
Phosphorylation plays an essential role in microRNA (miRNA) processing by regulating co-factors of the miRNA biogenesis machinery. HYL1 (Hyponastic Leaves 1), a core co-factor in plant miRNA biogenesis, is a short-lived phosphoprotein. However, the precise balance and regulatory mechanism of the stability and phosphorylation of HYL1 remain unclear. Here, we show that a highly conserved PP4 (Protein Phosphatase 4) and SMEK1 (Suppressor of MEK 1) complex dephosphorylates HYL1 to promote miRNA biogenesis, by antagonizing the MAPK cascade in Arabidopsis...
June 5, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28578021/transcriptome-profiling-of-the-floral-buds-and-discovery-of-genes-related-to-sex-differentiation-in-the-dioecious-cucurbit-coccinia-grandis-l-voigt
#15
Jatindra Nath Mohanty, Sanghamitra Nayak, Sumita Jha, Raj Kumar Joshi
Dioecious species offer an inclusive structure to study the molecular basis of sexual dimorphism in angiosperms. Despite having a small genome and heteromorphic sex chromosomes, Coccinia grandis is a highly neglected dioecious species with little information available on its physical state, genetic orientation and key sex-defining elements. In the present study, we performed RNA-Seq and DGE analysis of male (MB) and female (FB) buds in C. grandis to gain insights into the molecular basis of sex determination in this plant...
May 31, 2017: Gene
https://www.readbyqxmd.com/read/28575745/the-contrasting-microrna-content-of-a-drought-tolerant-and-a-drought-susceptible-wheat-cultivar
#16
Behnam Bakhshi, Ehsan Mohseni Fard, Javad Gharechahi, Mahdieh Safarzadeh, Nava Nikpay, Reza Fotovat, Mohammad Reza Azimi, Ghasem Hosseini Salekdeh
Drought stress represents one of the most common stresses affecting the productivity of crop plants. A rather recently discovered component of the plant response to drought is the cellular population of microRNAs. Here, the microRNA content was revealed of two bread wheat cultivars contrasting strongly with respect to the ability to withstand drought stress. A total of 1813 miRNAs was identified, grouped into 106 families. Some 104 of these miRNAs were predicted to match 212 novel miRNA precursors. In the drought tolerant cultivar (SM), 105 (33 known and 72 novel) miRNAs were altered in abundance by the imposition of drought stress, while the equivalent number in the more sensitive cultivar (SW) was 51 (20 and 31)...
May 21, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28575144/cernas-in-plants-computational-approaches-and-associated-challenges-for-target-mimic-research
#17
Alexandre Rossi Paschoal, Irma Lozada-Chávez, Douglas Silva Domingues, Peter F Stadler
The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions...
May 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28574638/amplification-and-quantification-of-cold-associated-micrornas-in-the-colorado-potato-beetle-leptinotarsa-decemlineata-agricultural-pest
#18
M D Morin, J J Frigault, P J Lyons, N Crapoulet, S Boquel, K B Storey, P Jr Morin
The Colorado potato beetle [Leptinotarsa decemlineata (Say)] is an important insect pest that can inflict considerable damage to potato plants. This insect can survive extended periods of cold exposure, and yet the molecular switches underlying this phenomenon have not been fully elucidated. A better characterization of this process would highlight novel vulnerabilities associated with L. decemlineata that could serve as targets for the management of this devastating pest. Using high-throughput sequencing, the current work reveals a cold-associated signature group of microRNAs (miRNAs) in control (15 °C) and -5 °C-exposed L...
June 2, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28572808/transcriptome-wide-analysis-of-botrytis-elliptica-responsive-micrornas-and-their-targets-in-lilium-regale-wilson-by-high-throughput-sequencing-and-degradome-analysis
#19
Xue Gao, Qi Cui, Qin-Zheng Cao, Qiang Liu, Heng-Bin He, Dong-Mei Zhang, Gui-Xia Jia
MicroRNAs, as master regulators of gene expression, have been widely identified and play crucial roles in plant-pathogen interactions. A fatal pathogen, Botrytis elliptica, causes the serious folia disease of lily, which reduces production because of the high susceptibility of most cultivated species. However, the miRNAs related to Botrytis infection of lily, and the miRNA-mediated gene regulatory networks providing resistance to B. elliptica in lily remain largely unexplored. To systematically dissect B. elliptica-responsive miRNAs and their target genes, three small RNA libraries were constructed from the leaves of Lilium regale, a promising Chinese wild Lilium species, which had been subjected to mock B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28560642/identification-and-characterization-of-micrornas-and-their-targets-in-high-altitude-stress-adaptive-plant-maca-lepidium-meyenii-walp
#20
Sujay Paul
MicroRNAs (miRNAs) are endogenous, short (~21-nucleotide), non-coding RNA molecules that play pivotal roles in plant growth, development, and stress response signaling. In this study using recently published draft genome sequence of a high-altitude plant maca (Lepidium meyenii Walp) and applying genome-wide computational-based approaches, a total of 62 potentially conserved miRNAs belonging to 28 families were identified and four (lme-miR160a, lme-miR164c, lme-miR 166a, and lme-miR 319a) of them further validated by RT-PCR...
June 2017: 3 Biotech
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