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https://www.readbyqxmd.com/read/28735504/low-genetic-diversity-and-functional-constraint-of-mirna-genes-participating-pollen-pistil-interaction-in-rice
#1
Kun Wang, Xin Wang, Ming Li, Tao Shi, Pingfang Yang
In this study, we sequenced and analyzed the expression and evolution of rice miRNA genes participating pollen-pistil interaction that is crucial to rice yield. Pollen-pistil interaction is an essential reproductive process for all flowering plants. While microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNA levels in eukaryotic cells, there is little knowledge about which miRNAs involved in the early stages of pollen-pistil interaction in rice and how they evolve under this conserved process...
July 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28735409/silencing-of-stress-regulated-mirnas-in-plants-by-short-tandem-target-mimic-sttm-approach
#2
Sachin Teotia, Guiliang Tang
In plants, microRNAs (miRNAs) regulate more than hundred target genes comprising largely transcription factors that control growth and development as well as stress responses. However, the exact functions of miRNA families could not be deciphered because each miRNA family has multiple loci in the genome, thus are functionally redundant. Therefore, an ideal approach to study the function of a miRNA family is to silence the expression of all members simultaneously, which is a daunting task. However, this can be partly overcome by Target Mimic (TM) approach that can knockdown an entire miRNA family...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28731217/small-rnas-in-regulating-temperature-stress-response-in-plants
#3
Qing Liu, Shijuan Yan, Tifeng Yang, Shaohong Zhang, Yue-Qin Chen, Bin Liu
Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) have also been demonstrated as important players in plant temperature stress response. Using high-throughput sequencing, many small RNAs, especially miRNAs, have been identified to be triggered by cold or heat...
July 21, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28728593/high-throughput-sequencing-of-small-rnas-reveals-dynamic-micrornas-expression-of-lipid-metabolism-during-camellia-oleifera-and-c-meiocarpa-seed-natural-drying
#4
Jin-Ling Feng, Zhi-Jian Yang, Shi-Pin Chen, Yousry A El-Kassaby, Hui Chen
BACKGROUND: Camellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted...
July 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28723657/an-emerging-function-of-circrna-mirnas-mrna-axis-in-human-diseases
#5
REVIEW
Dawei Rong, Handong Sun, Zhouxiao Li, Shuheng Liu, Chaoxi Dong, Kai Fu, Weiwei Tang, Hongyong Cao
Circular RNAs (circRNAs), a novel class of long noncoding RNAs, are characterized by a covalently closed continuous loop without 5' or 3' polarities structure and have been widely found in thousands of lives including plants, animals and human beings. Utilizing the high-throughput RNA sequencing (RNA-seq) technology, recent findings have indicated thata great deal of circRNAs, which are endogenous, stable, widely expressed in mammalian cells, often exhibit cell type-specific, tissue-specific or developmental-stage-specific expression...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28717203/genome-wide-identification-and-characterization-of-circular-rnas-by-high-throughput-sequencing-in-soybean
#6
Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28713413/identification-of-conserved-and-novel-micrornas-in-blueberry
#7
Junyang Yue, Xiaohui Lu, Huan Zhang, Jiao Ge, Xueling Gao, Yongsheng Liu
MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711666/micrornas-associated-with-drought-response-in-the-pulse-crop-common-bean-phaseolus-vulgaris-l
#8
Jing Wu, Lanfen Wang, Shumin Wang
Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28711017/alginate-gelatin-scaffolds-incorporated-with-silibinin-loaded-chitosan-nanoparticles-for-bone-formation-in-vitro
#9
R S Leena, M Vairamani, N Selvamurugan
Silibinin is a plant derived flavonolignan known for its multiple biological properties, but its role in the promotion of bone formation has not yet been well studied. Moreover, the delivery of Silibinin is hindered by its complex hydrophobic nature, which limits its bioavailability. Hence, in this study, we fabricated a drug delivery system using chitosan nanoparticles loaded with Silibinin at different concentrations (20μM, 50μM, and 100μM). They were then incorporated into scaffolds containing Alginate and Gelatin (Alg/Gel) for the sustained and prolonged release of Silibinin...
July 12, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28705193/spatial-regulation-of-monolignol-biosynthesis-and-laccase-genes-control-developmental-and-stress-related-lignin-in-flax
#10
Julien Le Roy, Anne-Sophie Blervacq, Anne Créach, Brigitte Huss, Simon Hawkins, Godfrey Neutelings
BACKGROUND: Bast fibres are characterized by very thick secondary cell walls containing high amounts of cellulose and low lignin contents in contrast to the heavily lignified cell walls typically found in the xylem tissues. To improve the quality of the fiber-based products in the future, a thorough understanding of the main cell wall polymer biosynthetic pathways is required. In this study we have carried out a characterization of the genes involved in lignin biosynthesis in flax along with some of their regulation mechanisms...
July 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28698160/investigating-the-regulatory-roles-of-the-micrornas-and-the-argonaute-1-enriched-small-rnas-in-plant-metabolism
#11
Jingping Qin, Zhonghai Tang, Xiaoxia Ma, Yijun Meng
The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was performed for microRNAs (miRNAs) and Argonaute 1 (AGO1)-enriched sRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)...
July 8, 2017: Gene
https://www.readbyqxmd.com/read/28695996/downregulation-of-genes-coding-for-core-rnai-components-and-disease-resistance-proteins-via-corresponding-micrornas-might-be-correlated-with-successful-smv-infection-in-soybean
#12
Duran Bao, Oyunchuluun Ganbaatar, Xiuqi Cui, Ruonan Yu, Wenhua Bao, Bryce W Falk, Hada Wuriyanghan
Plants protect themselves from virus infections by several different defense mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode NBS-LRR family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including regulation of host defenses. SMV (Soybean mosaic virus) is the most common virus in soybean and here we identified dozens of SMV-responsive miRNAs by microarray analysis in a SMV-susceptible soybean line...
July 11, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28694799/a-tiny-rna-that-packs-a-big-punch-the-critical-role-of-a-viral-mir-155-ortholog-in-lymphomagenesis-in-marek-s-disease
#13
REVIEW
Guoqing Zhuang, Aijun Sun, Man Teng, Jun Luo
MicroRNAs (miRNAs) are small non-coding RNAs that have been identified in animals, plants, and viruses. These small RNAs play important roles in post-transcriptional regulation of various cellular processes, including development, differentiation, and all aspects of cancer biology. Rapid-onset T-cell lymphoma of chickens, namely Marek's disease (MD), induced by Gallid alphaherpesvirus 2 (GaHV2), could provide an ideal natural animal model for herpesvirus-related cancer research. GaHV2 encodes 26 mature miRNAs derived from 14 precursors assembled in three distinct gene clusters in the viral genome...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28687775/integrated-analysis-of-tobacco-mirna-and-mrna-expression-profiles-under-pvy-infection-provids-insight-into-tobacco-pvy-interactions
#14
Yushuang Guo, Meng-Ao Jia, Yumei Yang, Linlin Zhan, Xiaofei Cheng, Jianyu Cai, Jie Zhang, Jie Yang, Tao Liu, Qiang Fu, Jiehong Zhao, Imran Haider Shamsi
Potato virus Y (PVY) is a globally and economically important pathogen of potato, tobacco, tomato and other staple crops and caused significant yield losses and reductions in quality.To explore the molecular PVY-host interactions, we analysed changes in the miRNA and mRNA profiles of tobacco in response to PVY infection. A total of 81 differentially expressed miRNAs belonging to 29 families and 8133 mRNAs were identified. The Gene Ontology (GO) enrichment analyses showed that genes encoding the DNA/RNA binding, catalytic activity and signalling molecules were all significantly enriched...
July 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28680433/allelic-interactions-among-pto-mir475b-and-its-four-target-genes-potentially-affect-growth-and-wood-properties-in-populus
#15
Liang Xiao, Mingyang Quan, Qingzhang Du, Jinhui Chen, Jianbo Xie, Deqiang Zhang
MicroRNAs (miRNAs) play crucial roles in plant growth and development, but few studies have illuminated the allelic interactions among miRNAs and their targets in perennial plants. Here, we combined analysis of expression patterns and single-nucleotide polymorphism (SNP)-based association studies to explore the interactions between Pto-MIR475b and its four target genes (Pto-PPR1, Pto-PPR2, Pto-PPR3, and Pto-PPR4) in 435 unrelated individuals of Populus tomentosa. Expression patterns showed a significant negative correlation (r = -0...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28676446/identification-and-expression-profiling-of-oryza-sativa-nucleotidyl-transferase-protein-ntp-genes-under-various-stress-conditions
#16
Haiqi Yang, Jianbo Song, Luming Yue, Xiaowei Mo, Jun Song, Beixin Mo
Nucleotidyl transferase proteins (NTPs) modify the 3' ends of mature small RNAs, leading to their stabilization or degradation. The first two plant NTPs, HESO1 and URT1, were identified in Arabidopsis. These two NTPs act cooperatively to uridylate the 3' terminal nucleotide of specific miRNAs, leading to their degradation and thereby affecting the expression of genes regulated by these miRNAs. Little is known about NTPs in other plants. Here, we performed a comprehensive analysis of 13 putative NTP genes in Oryza sativa, a major crop in global food production...
July 1, 2017: Gene
https://www.readbyqxmd.com/read/28674744/ectopic-expression-of-csd1-and-csd2-targeting-genes-of-mir398-in-grapevine-is-associated-with-oxidative-stress-tolerance
#17
XiangPeng Leng, Peipei Wang, Xudong Zhu, Xiaopeng Li, Ting Zheng, Lingfei Shangguan, Jinggui Fang
MicroRNAs (miRNAs) are endogenous small RNAs of -21 nucleotides that play an important role in diverse plant physiological processes at the post-transcriptional level by directing mRNA cleavage or translational inhibition. Previous studies have indicated that down-regulation of miR398 in response to oxidative stress allows up-regulation of the two target genes, cytosolic CSD1 and chloroplastic CSD2 (copper/zinc superoxide dismutase), resulting in protecting the plants to tolerate oxidative stress. In this study, we provide evidence that grapevine miR398 (Vv-miR398), by regulating the expression of its target genes, VvCSD1 and VvCSD2, mediates responses of grapevine to copper (Cu) stress which have been magnified due to increase in Cu-containing pesticide application...
July 3, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28672765/discovery-and-annotation-of-plant-endogenous-target-mimicry-sequences-from-public-transcriptome-libraries-a-case-study-of-prunus-persica
#18
Gökhan Karakülah
Novel transcript discovery through RNA sequencing has substantially improved our understanding of the transcriptome dynamics of biological systems. Endogenous target mimicry (eTM) transcripts, a novel class of regulatory molecules, bind to their target microRNAs (miRNAs) by base pairing and block their biological activity. The objective of this study was to provide a computational analysis framework for the prediction of putative eTM sequences in plants, and as an example, to discover previously un-annotated eTMs in Prunus persica (peach) transcriptome...
June 28, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28670834/temporal-and-spatial-transcriptomic-and-microrna-dynamics-of-cam-photosynthesis-in-pineapple
#19
Ching Man Wai, Robert VanBuren, Jisen Zhang, Lixian Huang, Wenjing Miao, Patrick P Edger, Won C Yim, Henry D Priest, Blake C Meyers, Todd Mockler, J Andrew C Smith, John C Cushman, Ray Ming
The altered carbon assimilation pathway of crassulacean acid metabolism (CAM) photosynthesis results in up to 80% higher water-use efficiency than C3 photosynthesis plants making it a potentially useful pathway for engineering crop plants with improved drought tolerance. Here we surveyed detailed temporal (diel time course) and spatial (across a leaf gradient) gene and microRNA (miRNA) expression patterns in the obligate CAM plant pineapple (Ananas comosus (L.) Merr.). The high-resolution transcriptome atlas allowed us to distinguish between CAM-related and non-CAM gene copies...
July 3, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28668702/differential-expression-of-novel-micrornas-in-response-to-the-infection-of-a-tmv-mutant-with-an-internal-poly-a-tract-in-n-benthamiana
#20
Song Guo, Ya-Chih Hsueh, Greg Tucker-Kellogg, Sek-Man Wong
We first constructed small RNA libraries of TMV- and TMV-43A-infected N. benthamiana for high throughput sequencing. A total number of 181 novel microRNAs (miRNAs) were identified through an improved miRNAs analysis pipeline. We were able to identify consistent miRNA expression changes induced in TMV and TMV-43A-infected plants, as well as differences associated with the UPD substitution in the TMV-43A viral genome. Virally induced miRNAs are associated with distinct processes and functions of predicted mRNA targets, including relation to host target defense...
June 28, 2017: Virus Research
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