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https://www.readbyqxmd.com/read/27910907/micrornas-modulate-adaption-to-multiple-abiotic-stresses-in-chlamydomonas-reinhardtii
#1
Xiang Gao, Fengge Zhang, Jinlu Hu, Wenkai Cai, Ge Shan, Dongsheng Dai, Kaiyao Huang, Gaohong Wang
MicroRNAs play an important role in abiotic stress responses in higher plants and animals, but their role in stress adaptation in algae remains unknown. In this study, the expression of identified and putative miRNAs in Chlamydomonas reinhardtii was assessed using quantitative polymerase chain reaction; some of the miRNAs (Cre-miR906-3p) were up-regulated, whereas others (Cre-miR910) were down-regulated when the species was subjected to multiple abiotic stresses. With degradome sequencing data, we also identified ATP4 (the d-subunit of ATP synthase) and NCR2 (NADPH: cytochrome P450 reductase) as one of the several targets of Cre-miR906-3p and Cre-miR910, respectively...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910040/generation-of-efficient-mirna-inhibitors-using-tough-decoy-constructs
#2
Jimeen Yoo, Roger J Hajjar, Dongtak Jeong
Over the last decade a previously unappreciated mechanism of gene regulation has been uncovered that is mediated by a large class of small noncoding RNAs known as microRNAs (miRNAs), and this mechanism is utilized by organisms ranging from plants to humans. MiRNAs are important downregulators of gene expression and are seen to be dysregulated in disease development. Thus inhibition of aberrantly upregulated miRNAs as a therapeutic approach has become a promising field.Many models of miRNA inhibitors currently exist, with decoy models being the most successful in current research...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909970/over-expression-of-mir158-causes-pollen-abortion-in-brassica-campestris-ssp-chinensis
#3
Zhiming Ma, Jianxia Jiang, Ziwei Hu, Tianqi Lyu, Yang Yang, Jingjing Jiang, Jiashu Cao
We identified and cloned the two precursors of miR158 and its target gene in Brassica campestris ssp. chinensis, which both had high relative expression in the inflorescences. Further study revealed that over-expression of miR158 caused reduced pollen varbility, which was caused by the degradation of pollen contents from the binucleate microspore stage. These results first suggest the role of miR158 in pollen development of Brassica campestris ssp. chinensis. MicroRNAs (miRNAs) play crucial roles in many important growth and development processes both in plants and animals by regulating the expression of their target genes via mRNA cleavage or translational repression...
December 1, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27909445/identification-and-profiling-of-micrornas-expressed-in-elongating-cotton-fibers-using-small-rna-deep-sequencing
#4
Yanmei Wang, Yan Ding, Jin-Yuan Liu
Plant microRNAs (miRNAs) have been shown to play essential roles in the regulation of gene expression. In this study, small RNA deep sequencing was applied to explore novel miRNAs expressed in elongating cotton fibers. A total of 46 novel and 96 known miRNAs, primarily derived from the corresponding specific loci in genome of Gossypium arboreum, were identified. 64 miRNAs were shown to be differentially expressed during the fiber elongation process; 16 were predicted to be novel miRNAs while the remaining 48 belong to known miRNA families...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27907902/active-5-splice-sites-regulate-the-biogenesis-efficiency-of-arabidopsis-micrornas-derived-from-intron-containing-genes
#5
Katarzyna Knop, Agata Stepien, Maria Barciszewska-Pacak, Michal Taube, Dawid Bielewicz, Michal Michalak, Jan W Borst, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5' splice sites (5'ss') have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27900550/biogenesis-of-diverse-plant-phasirnas-involves-an-mirna-trigger-and-dicer-processing
#6
Reina Komiya
It has been almost 30 years since RNA interference (RNAi) was shown to silence genes via double-stranded RNAs (dsRNAs) in Caenorhabditis elegans (Fire et al. 1998). 20-30-nucleotide (nt) small non-coding RNAs are a key element of the RNAi machinery. Recently, phased small interfering RNAs (phasiRNAs), small RNAs that are generated from a long RNA precursor at intervals of 21 to 26-nt, have been identified in plants and animals. In Drosophila, phasiRNAs are generated by the endonuclease, Zucchini (Zuc), in germlines...
November 29, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27899663/large-scale-analysis-of-microrna-expression-epi-transcriptomic-features-and-biogenesis
#7
Dimitrios M Vitsios, Matthew P Davis, Stijn van Dongen, Anton J Enright
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898768/transcriptome-and-small-rnaome-dynamics-during-a-resistant-and-susceptible-interaction-between-cucumber-and-downy-mildew
#8
Alyssa Burkhardt, Brad Day
Cucumber ( L.) downy mildew, caused by the obligate oomycete pathogen (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible ('Vlaspik') cucumber during a time course of infection using Illumina sequencing...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895664/application-of-genomic-technologies-to-the-breeding-of-trees
#9
REVIEW
Maria L Badenes, Angel Fernández I Martí, Gabino Ríos, María J Rubio-Cabetas
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895202/the-lbd12-1-transcription-factor-suppresses-apical-meristem-size-by-repressing-argonaute-10-expression
#10
Weiwei Ma, Fuqing Wu, Peike Sheng, Xiaole Wang, Zhe Zhang, Kunneng Zhou, Huan Zhang, Jinlong Hu, Qibing Lin, Zhijun Cheng, Jiulin Wang, Shanshan Zhu, Xin Zhang, Xiuping Guo, Haiyang Wang, Chuanyin Wu, Jianmin Wan
The shoot apical meristem (SAM) consists of a population of multipotent cells that generate all aerial structures and regenerates itself. SAM maintenance and lateral organ development are regulated by several complex signaling pathways, in which the Argonaute gene mediated pathway plays a key role. One Argonaute gene, AGO10, functions as a miRNA locker that attenuates miR165/166 activity and positively regulates shoot apical meristem development, but little is known about when and how AGO10 is regulated at the transcriptional level...
November 28, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27886593/the-evolution-of-micrornas-in-plants
#11
REVIEW
Jie Cui, Chenjiang You, Xuemei Chen
MicroRNAs (miRNAs) are a central player in post-transcriptional regulation of gene expression and are involved in numerous biological processes in eukaryotes. Knowledge of the origins and divergence of miRNAs paves the way for a better understanding of the complexity of the regulatory networks that they participate in. The biogenesis, degradation, and regulatory activities of miRNAs are relatively better understood, but the evolutionary history of miRNAs still needs more exploration. Inverted duplication of target genes, random hairpin sequences and small transposable elements constitute three main models that explain the origination of miRNA genes (MIR)...
November 22, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27885505/pre-microrna-processing-activity-in-nuclear-extracts-from-arabidopsis-suspension-cells
#12
Manabu Yoshikawa
MicroRNAs (miRNAs) play important roles in a variety of biological phenomena, such as development and responses to abiotic and biotic stresses, by regulating complementary target transcripts. Primary MIRNA transcripts (pri-miRNAs) are processed into miRNA/miRNA* duplexes via pre-miRNA intermediates by DICER family proteins. In plants miRNA/miRNA* duplexes are produced from pri-miRNAs exclusively by a complex containing DICER-LIKE1 (DCL1), Hyponastic leaves1 (HYL1) and SERREATE (SE) in the nucleus. Pri-miRNA or pre-miRNA processing activity has been detected using recombinant DCL1, HYL1 and SE proteins expressed in insect cells and immunopurified DCL1-HYL1-SE-containing complexes that transiently co-overexpressed in Nicotiana benthamiana...
November 24, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27879674/transcriptome-analysis-of-mrna-and-mirna-in-somatic-embryos-of-larix-leptolepis-subjected-to-hydrogen-treatment
#13
Yali Liu, Suying Han, Xiangming Ding, Xinmin Li, Lifeng Zhang, Wanfeng Li, Haiyan Xu, Zhexin Li, Liwang Qi
Hydrogen is a therapeutic antioxidant that has been used extensively in clinical trials. It also acts as a bioactive molecule that can alleviate abiotic stress in plants. However, the biological effects of hydrogen in somatic embryos and the underlying molecular basis remain largely unknown. In this study, the morphological and physiological influence of exogenous H₂ treatment during somatic embryogenesis was characterized in Larix leptolepis Gordon. The results showed that exposure to hydrogen increased the proportions of active pro-embryogenic cells and normal somatic embryos...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27878651/messages-on-small-rna-duplexes-in-plants
#14
Taichiro Iki
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs...
November 23, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27878142/microrna-biogenesis-epigenetic-modifications-as-another-layer-of-complexity-in-the-microrna-expression-regulation
#15
Susheel Sagar Bhat, Artur Jarmolowski, Zofia Szweykowska-Kulińska
Since their discovery, microRNAs have led to a huge shift in our understanding of the regulation of key biological processes. The discovery of epigenetic modifications that affect microRNA expression has added another layer of complexity to the already tightly controlled regulatory machinery. Modifications like uridylation, adenylation and RNA editing have been shown to have variable effects on miRNA biogenesis and action. Methylation of the N6 adenosine has been studied extensively in mRNA. Presence of the N6-methyl-adenosine (m(6)A) mark and its critical importance in miRNA biogenesis in animals adds to our understanding of the regulatory mechanisms, while its effect on miRNA biogenesis in plants is yet to be understood...
November 22, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27877179/genome-wide-identification-of-micrornas-and-their-targets-in-the-leaves-and-fruits-of-eucommia-ulmoides-using-high-throughput-sequencing
#16
Lin Wang, Hongyan Du, Ta-Na Wuyun
MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27874310/ancient-microrna-families-that-regulate-transcription-factors-are-preferentially-preserved-during-plant-radiation
#17
Tao Shi, Kun Wang, Pingfang Yang
Essential genes are usually less likely to be lost during evolution, whereas dispensable genes are lost more frequently. Integrating sacred lotus and other plant microRNA (miRNA) data, we found different ancient miRNA families that arose before eudicot radiation exhibit different evolutionary trajectories. Those ancient miRNA families with higher copy and target numbers, and older age are more likely to be retained in plant descendants and more conserved in (hairpin-structured) miRNA gene sequences. Interestingly, a large portion of the well conserved miRNA families in plant lineages can target transcription factors (TFs)...
November 22, 2016: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/27871001/identification-of-mirna-from-bouteloua-gracilis-a-drought-tolerant-grass-by-deep-sequencing-and-their-in-silico-analysis
#18
Perla Lucía Ordóñez-Baquera, Everardo González-Rodríguez, Gerardo Armando Aguado-Santacruz, Quintín Rascón-Cruz, Ana Conesa, Verónica Moreno-Brito, Raquel Echavarria, Joel Dominguez-Viveros
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate signal transduction, development, metabolism, and stress responses in plants through post-transcriptional degradation and/or translational repression of target mRNAs. Several studies have addressed the role of miRNAs in model plant species, but miRNA expression and function in economically important forage crops, such as Bouteloua gracilis (Poaceae), a high-quality and drought-resistant grass distributed in semiarid regions of the United States and northern Mexico remain unknown...
November 9, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27870853/intron-lariat-rna-inhibits-microrna-biogenesis-by-sequestering-the-dicing-complex-in-arabidopsis
#19
Ziwei Li, Shengpeng Wang, Jinping Cheng, Chuanbin Su, Songxiao Zhong, Qi Liu, Yuda Fang, Yao Yu, Hong Lv, Yun Zheng, Binglian Zheng
Lariat RNAs formed as by-products of splicing are quickly degraded by the RNA debranching enzyme 1 (DBR1), leading to their turnover. Null dbr1 mutants in both animals and plants are embryo lethal, but the mechanism underlying the lethality remains unclear. Here we characterized a weak mutant allele of DBR1 in Arabidopsis, dbr1-2, and showed that a global increase in lariat RNAs was unexpectedly accompanied by a genome-wide reduction in miRNA accumulation. The dbr1-2 mutation had no effects on expression of miRNA biogenesis genes or primary miRNAs (pri-miRNAs), but the association of pri-miRNAs with the DCL1/HYL1 dicing complex was impaired...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27870849/phosphorylation-of-cbp20-links-microrna-to-root-growth-in-the-ethylene-response
#20
Fan Zhang, Likai Wang, Jae Yun Lim, Taewook Kim, Youngjae Pyo, Sibum Sung, Chanseok Shin, Hong Qiao
Ethylene is one of the most important hormones for plant developmental processes and stress responses. However, the phosphorylation regulation in the ethylene signaling pathway is largely unknown. Here we report the phosphorylation of cap binding protein 20 (CBP20) at Ser245 is regulated by ethylene, and the phosphorylation is involved in root growth. The constitutive phosphorylation mimic form of CBP20 (CBP20S245E or CBP20S245D), while not the constitutive de-phosphorylation form of CBP20 (CBP20S245A) is able to rescue the root ethylene responsive phenotype of cbp20...
November 2016: PLoS Genetics
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