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https://www.readbyqxmd.com/read/28090264/drought-stress-induced-changes-of-micrornas-in-diploid-and-autotetraploid-paulownia-tomentosa
#1
Xibing Cao, Guoqiang Fan, Lin Cao, Minjie Deng, Zhenli Zhao, Suyan Niu, Zhe Wang, Yuanlong Wang
Drought stress adversely affects plant productivity. Growth and timber production of Paulownia trees are limited under drought stress. Changes in gene expression patterns and miRNA in different ploidy of Paulownia tomentosa have been investigated. However, the responses of P. tomentosa to drought stress at the microRNA (miRNA) level have not been reported so far. To identify miRNA candidates and their target genes involved in the drought stress response in diploid and tetraploid P. tomentosa, four small RNA and four degradome libraries from diploid and autotetraploid P...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28088028/role-of-small-rnas-in-epigenetic-reprogramming-during-plant-sexual-reproduction
#2
REVIEW
German Martinez, Claudia Köhler
Sexual reproduction, the formation of a new individual from specialized reproductive cells after fertilization, involves the precise orchestration of different developmental and genomic processes. These processes are to a large extent governed by small RNAs (sRNAs) that either belong to the class of micro RNAs (miRNAs) or small-interfering RNAs (siRNAs). The latter are derived from transposable elements (TEs) and involved in genome defense and transgenerational inheritance of heterochromatin identity, ensuring genome stability...
January 11, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28078489/identification-and-profiling-of-conserved-and-novel-micrornas-involved-in-oil-and-oleic-acid-production-during-embryogenesis-in-carya-cathayensis-sarg
#3
Zhengjia Wang, Ruiming Huang, Zhichao Sun, Tong Zhang, Jianqin Huang
MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs...
January 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#4
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28071760/origin-and-evolution-of-mir1444-genes-in-salicaceae
#5
Meizhen Wang, Caili Li, Shanfa Lu
miR1444s are functionally significant miRNAs targeting polyphenol oxidase (PPO) genes for cleavage. MIR1444 genes were reported only in Populus trichocarpa. Through the computational analysis of 215 RNA-seq data, four whole genome sequences of Salicaceae species and deep sequencing of six P. trichocarpa small RNA libraries, we investigated the origin and evolution history of MIR1444s. A total of 23 MIR1444s were identified. Populus and Idesia species contain two MIR1444 genes, while Salix includes only one...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28070736/genome-wide-analysis-of-mirnas-and-tasi-rnas-in-zea-mays-in-response-to-phosphate-deficiency
#6
Saurabh Gupta, Manju Kumari, Himansu Kumar, Pritish Kumar Varadwaj
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses...
January 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28068913/microrna-157-targeted-spl-genes-regulate-floral-organ-size-and-ovule-production-in-cotton
#7
Nian Liu, Lili Tu, Lichen Wang, Haiyan Hu, Jiao Xu, Xianlong Zhang
BACKGROUND: microRNAs (miRNAs) have been involved in regulation of diverse spectrum of plant development processes in many species. In cotton, few miRNAs have been well characterised in floral organ development. Floral organ, which should be finely tuned, is a crucial factor affecting the yield of cotton. Therefore, it is well worth revealing the function of miRNAs in regulation of floral organ development. Here, we report the role of miRNA156/157 in regulation of floral organ size in cotton...
January 10, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28068898/integrated-mrna-and-microrna-analysis-identifies-genes-and-small-mirna-molecules-associated-with-transcriptional-and-post-transcriptional-level-responses-to-both-drought-stress-and-re-watering-treatment-in-tobacco
#8
Qiansi Chen, Meng Li, Zhongchun Zhang, Weiwei Tie, Xia Chen, Lifeng Jin, Niu Zhai, Qingxia Zheng, Jianfeng Zhang, Ran Wang, Guoyun Xu, Hui Zhang, Pingping Liu, Huina Zhou
BACKGROUND: Drought stress is one of the most severe problem limited agricultural productivity worldwide. It has been reported that plants response to drought-stress by sophisticated mechanisms at both transcriptional and post-transcriptional levels. However, the precise molecular mechanisms governing the responses of tobacco leaves to drought stress and water status are not well understood. To identify genes and miRNAs involved in drought-stress responses in tobacco, we performed both mRNA and small RNA sequencing on tobacco leaf samples from the following three treatments: untreated-control (CL), drought stress (DL), and re-watering (WL)...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28064248/mir393-mediated-auxin-signaling-regulation-is-involved-in-root-elongation-inhibition-in-response-to-toxic-aluminum-stress-in-barley
#9
Bin Bai, Hongwu Bian, Zhanghui Zeng, Ning Hou, Bo Shi, Junhui Wang, Muyuan Zhu, Ning Han
High-throughput small RNA sequencing has identified several potential aluminum (Al)-responsive microRNAs (miRNAs); however, their regulatory role remains unknown. Here, we identified two miR393 family members in barley, and confirmed two target genes-HvTIR1 and HvAFB-through a modified form of 5'-RACE (rapid amplification of cDNA ends) as well as degradome data analysis. Furthermore, we investigated the biological function of the miR393/target module in root development and its Al stress response. The investigation showed that miR393 affected root growth and adventitious root number by altering auxin sensitivity...
January 7, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28062594/survey-of-800-datasets-from-human-tissue-and-body-fluid-reveals-xenomirs-are-likely-artifacts
#10
Wenjing Kang, Claus Heiner Bang-Bertelsen, Anja Holm, Anna Houben, Anne Holt Müller, Thomas Thymann, Flemming Pociot, Xavier Estivill, Marc Riemer Friedländer
miRNAs are small 22 nucleotide RNAs that can post-transcriptionally regulate gene expression. It has been proposed that dietary plant miRNAs can enter the human bloodstream and regulate host transcripts, however these findings have been widely disputed. We here conduct the first comprehensive meta-study in the field, surveying the presence and abundances of cross-species miRNAs (xenomiRs) in 824 sequencing datasets from various human tissues and body fluids. We find that xenomiRs are commonly present in tissues (17%) and body fluids (69%), however the abundances are low, comprising 0...
January 6, 2017: RNA
https://www.readbyqxmd.com/read/28060406/a-simple-protoplast-based-method-for-screening-potent-artificial-mirna-for-maximal-gene-silencing-in-arabidopsis
#11
Nannan Zhang, Dandan Zhang, Jian-Feng Li
The unpredictability of in planta silencing efficiency of artificial micro RNAs (amiRNAs) has greatly limited the application of the amiRNA technology in basic and applied plant research. This unit describes a simple and robust method called the epitope-tagged protein-based amiRNA (ETPamir) screen for identifying the most effective amiRNA for silencing a particular Arabidopsis gene. After selecting three to four amiRNA candidates designed by the WMD3 web server for the target gene, the silencing efficiencies of the amiRNA candidates can be compared by co-expressing individual amiRNAs with the target mRNA encoding an epitope-tagged target protein in Arabidopsis mesophyll protoplasts...
January 5, 2017: Current Protocols in Molecular Biology
https://www.readbyqxmd.com/read/28059073/ros-accumulation-and-antiviral-defence-control-by-microrna528-in-rice
#12
Jianguo Wu, Rongxin Yang, Zhirui Yang, Shengze Yao, Shanshan Zhao, Yu Wang, Pingchuan Li, Xianwei Song, Lian Jin, Tong Zhou, Ying Lan, Lianhui Xie, Xueping Zhou, Chengcai Chu, Yijun Qi, Xiaofeng Cao, Yi Li
MicroRNAs (miRNAs) are key regulators of plant-pathogen interactions. Modulating miRNA function has emerged as a new strategy to produce virus resistance traits(1-5). However, the miRNAs involved in antiviral defence and the underlying mechanisms remain largely elusive. We previously demonstrated that sequestration by Argonaute (AGO) proteins plays an important role in regulating miRNA function in antiviral defence pathways(6). Here we reveal that cleavage-defective AGO18 complexes sequester microRNA528 (miR528) upon viral infection...
January 6, 2017: Nature Plants
https://www.readbyqxmd.com/read/28054378/microrna-annotation-of-plant-genomes-do-it-right-or-not-at-all
#13
Richard S Taylor, James E Tarver, Alireza Foroozani, Philip C J Donoghue
MicroRNAs are non-coding regulators of gene expression and key factors in development, disease, and targets for bioengineering. Consequently, microRNAs have become essential elements of already burgeoning draft plant genome descriptions where their annotation is often particularly poor, contributing unduly to the corruption of public databases. Using the Citrus sinensis as an example, we highlight and review common failings of miRNAome annotations. Understanding and exploiting the role of miRNAs in plant biology will be stymied unless the research community acts decisively to improve the accuracy of miRNAome annotations...
January 5, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28054059/a-three-way-junction-structure-based-isothermal-exponential-amplification-strategy-for-sensitive-detection-of-3-terminal-2-o-methylated-plant-microrna
#14
Xiangdong Wang, Hui Wang, Chenghui Liu, Honghong Wang, Zhengping Li
Plant microRNAs (miRNAs) differ from animal miRNAs in that they are 2'-O-methylated at the 3' end nucleotide which limits the ability of plant miRNAs to serve as primers for polymerization reactions. Herein, we have rationally designed a three-way junction structure-based isothermal exponential amplification reaction (3WJ-EXPAR) which is well-suited for sensitive detection of 3'-terminal 2'-O-methylated miRNAs.
January 5, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28053168/ccnet-database-of-co-expression-networks-with-functional-modules-for-diploid-and-polyploid-gossypium
#15
Qi You, Wenying Xu, Kang Zhang, Liwei Zhang, Xin Yi, Dongxia Yao, Chunchao Wang, Xueyan Zhang, Xinhua Zhao, Nicholas J Provart, Fuguang Li, Zhen Su
Plant genera with both diploid and polyploid species are a common evolutionary occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great model system for heterosis research. Here, we have integrated genome sequences and transcriptome data of Gossypium species to construct co-expression networks and identified functional modules from different cotton species, including 1155 and 1884 modules in G. arboreum and G. hirsutum, respectively. We overlayed the gene expression results onto the co-expression network...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28053167/pcerbase-a-database-of-plant-competing-endogenous-rna
#16
Chunhui Yuan, Xianwen Meng, Xue Li, Nicola Illing, Robert A Ingle, Jingjing Wang, Ming Chen
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28041928/positive-gene-regulation-by-a-natural-protective-mirna-enables-arbuscular-mycorrhizal-symbiosis
#17
Jean-Malo Couzigou, Dominique Lauressergues, Olivier André, Caroline Gutjahr, Bruno Guillotin, Guillaume Bécard, Jean-Philippe Combier
Arbuscular mycorrhizal (AM) symbiosis associates most plants with fungi of the phylum Glomeromycota. The fungus penetrates into roots and forms within cortical cell branched structures called arbuscules for nutrient exchange. We discovered that miR171b has a mismatched cleavage site and is unable to downregulate the miR171 family target gene, LOM1 (LOST MERISTEMS 1). This mismatched cleavage site is conserved among plants that establish AM symbiosis, but not in non-mycotrophic plants. Unlike other members of the miR171 family, miR171b stimulates AM symbiosis and is expressed specifically in root cells that contain arbuscules...
January 11, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28032247/a-systemic-identification-approach-for-primary-transcription-start-site-of-arabidopsis-mirnas-from-multidimensional-omics-data
#18
Qi You, Hengyu Yan, Yue Liu, Xin Yi, Kang Zhang, Wenying Xu, Zhen Su
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts...
December 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28031235/htp-nutraceutical-screening-for-histone-deacetylase-inhibitors-and-effects-of-hdacis-on-tumor-suppressing-mirnas-by-trichostatin-a-and-grapeseed-vitis-vinifera-in-hela-cells
#19
Elizabeth A Mazzio, Karam F A Soliman
BACKGROUND/AIM: Aggressive tumor malignancies are a consequence of delayed diagnosis, epigenetic/phenotype changes and chemo-radiation resistance. Histone deacetylases (HDACs) are a major epigenetic regulator of transcriptional repression, which are highly overexpressed in advanced malignancy. While original chemotherapy drugs were modeled after phytochemicals elucidated by botanical screenings, HDAC inhibitors (HDACi) such as apicidin, trichostatin A (TSA) and butyrate were discovered as products of fungus and microbes, in particular, gut microbiota...
January 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28025711/differential-expression-of-mirnas-and-associated-gene-targets-in-grapevine-leafroll-associated-virus-3-infected-plants
#20
Rachelle Bester, Johan T Burger, Hans J Maree
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (sRNA) that play an essential role in the regulation of target mRNAs expressed during plant development and in response to stress. MicroRNA expression profiling has helped to identify miRNAs that regulate a range of processes, including the plant's defence response to pathogens. In this study, differential miRNA expression in own-rooted Vitis vinifera cv. Cabernet Sauvignon plants infected with grapevine leafroll-associated virus 3 was investigated with microarrays and next-generation sequencing (NGS) of sRNA and mRNA...
December 26, 2016: Archives of Virology
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