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miRNA plant

Anastasia K Atabekova, Anna V Pankratenko, Svetlana S Makarova, Ekaterina A Lazareva, Robert A Owens, Andrey G Solovyev, Sergey Y Morozov
Human B-cell receptor-associated protein BAP31 (HsBAP31) is the endoplasmic reticulum-resident protein involved in protein sorting and transport as well as pro-apoptotic signaling. Plant orthologs of HsBAP31 termed 'plant BAP-like proteins' (PBL proteins) have thus far remained unstudied. Recently, the PBL protein from Nicotiana tabacum (NtPBL) was identified as an interactor of Nt-4/1, a plant protein known to interact with plant virus movement proteins and affect the long-distance transport of potato spindle tuber viroid (PSTVd) via the phloem...
October 19, 2016: Biochimie
Aleksandra Swida-Barteczka, Katarzyna Kruszka, Aleksandra Grabowska, Andrzej Pacak, Artur Jarmolowski, Marzena Kurowska, Iwona Szarejko, Zofia Szweykowska-Kulinska
MicroRNAs are short molecules of 21-24 nt in length. They are present in all eukaryotic organisms and regulate gene expression by guiding posttranscriptional silencing of mRNAs. In plants, they are key players in signal transduction, growth and development, and in response to abiotic and biotic stresses. Barley (Hordeum vulgare) is an economically important monocotyledonous crop plant. Drought is the world's main cause of loss in cereal production. We have constructed a high-throughput Real-Time RT-qPCR platform for parallel determination of 159 barley primary microRNAs' levels...
October 21, 2016: Acta Biochimica Polonica
Masayuki Tsuzuki, Yuichiro Watanabe
Small RNAs are key molecules in RNA silencing pathways that exert the sequence-specific regulation of gene expression and chromatin modifications in many eukaryotes. In plants, endogenous small RNAs, including microRNAs (miRNAs), trans-acting short interfering RNAs (tasiRNAs), and heterochromatic siRNAs (hc-siRNAs), play an important role in switching or orchestrating biological processes during the development and at the onset of stress responses. These endogenous and exogenous small RNAs are mainly 20-24 nucleotides in length...
2017: Methods in Molecular Biology
Erika Varkonyi-Gasic
Plant microRNAs (miRNAs) play important roles in the posttranscriptional regulation of protein-coding genes, and they are essential for a normal development and survival. Mature miRNAs are cleaved from larger precursor RNAs and are typically 21-22 nt long.The small size, the lack of a common feature like a poly(A) tail, 3' end-modifications, and presence of a precursor-all these factors affect the detection and hinder the quantification of miRNAs. The stem-loop qRT-PCR method described here is designed to detect and quantify mature miRNAs in a fast, specific, accurate, and reliable manner...
2017: Methods in Molecular Biology
Sara Hernández-Castellano, Geovanny I Nic-Can, Clelia De-la-Peña
Among the epigenetic mechanisms studied with a greater interest in the last decade are the microRNAs (miRNAs). These small noncoding RNA sequences that are approximately 17-22 nucleotides in length play an essential role in many biological processes of various organisms, including plants. The analysis of spatiotemporal expression of miRNAs provides a better understanding of the role of these small molecules in plant development, cell differentiation, and other processes; but such analysis is also an important method for the validation of biological functions...
2017: Methods in Molecular Biology
Rongsheng Zhu, Zhanguo Zhang, Yang Li, Zhenbang Hu, Dawei Xin, Zhaoming Qi, Qingshan Chen
Previous studies have confirmed that there are many differences between animal and plant microRNAs (miRNAs), and that numerical features based on sequence and structure can be used to predict the function of individual miRNAs. However, there is little research regarding numerical differences between animal and plant miRNAs, and whether a single numerical feature or combination of features could be used to distinguish animal and plant miRNAs or not. Therefore, in current study we aimed to discover numerical features that could be used to accomplish this...
2016: PloS One
Todd P Michael, Douglas Bryant, Ryan Gutierrez, Nikolai Borisjuk, Philomena Chu, Hanzhong Zhang, Jing Xia, Junfei Zhou, Hai Peng, Moaine El Baidouri, Boudewijn Ten Hallers, Alex R Hastie, Tiffany Liang, Kenneth Acosta, Sarah Gilbert, Connor McEntee, Scott A Jackson, Todd C Mockler, Weixiong Zhang, Eric Lam
Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158 Mbp Spirodela genome sequence has not been resolved to chromosomes and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features...
October 18, 2016: Plant Journal: for Cell and Molecular Biology
Qiongshan Wang, Nian Liu, Xiyan Yang, Lili Tu, Xianlong Zhang
MicroRNAs (miRNAs) are one class of endogenous non-coding RNAs modulating the expression of target genes involved in plant development and stress tolerance, by degrading mRNA or repressing translation. In this study, small RNA and mRNA degradome sequencing were used to identify low- and high-temperature stress-responsive miRNAs and their targets in cotton (Gossypium hirsutum). Cotton seedlings were treated under different temperature conditions (4, 12, 25, 35, and 42 °C) and then the effects were investigated...
October 18, 2016: Scientific Reports
Weifang Wu, Qin Deng, Pibiao Shi, Jinghua Yang, Zhongyuan Hu, Mingfang Zhang
Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy...
2016: PloS One
Julia Bally, Glen J McIntyre, Rachel L Doran, Karen Lee, Alicia Perez, Hyungtaek Jung, Fatima Naim, Ignacio M Larrinua, Kenneth E Narva, Peter M Waterhouse
Expressing double-stranded RNA (dsRNA) in transgenic plants to silence essential genes within herbivorous pests is referred to as trans-kingdom RNA interference (TK-RNAi) and has emerged as a promising strategy for crop protection. However, the dicing of dsRNA into siRNAs by the plant's intrinsic RNAi machinery may reduce this pesticidal activity. Therefore, genetic constructs, encoding ∼200 nt duplex-stemmed-hairpin (hp) RNAs, targeting the acetylcholinesterase gene of the cotton bollworm, Helicoverpa armigera, were integrated into either the nuclear or the chloroplast genome of Nicotiana benthamiana...
2016: Frontiers in Plant Science
Tao Shi, Kun Wang, Pingfang Yang
microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Cheng-Yu Hou, Wen-Chi Lee, Hsiao-Chun Chou, Ai-Ping Chen, Shu-Jen Chou, Ho-Ming Chen
High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied to analyze and validate cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome other than miRNA targets is currently largely uncharacterized, and this limits the application of RNA degradome studies. We conducted a global analysis of 5'-truncated mRNA ends that mapped to coding sequences (CDSs) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max)...
October 14, 2016: Plant Cell
Vijay Gahlaut, Vandana Jaiswal, Anuj Kumar, Pushpendra Kumar Gupta
TFs involved in drought tolerance in plants may be utilized in future for developing drought tolerant cultivars of wheat and some other crops. Plants have developed a fairly complex stress response system to deal with drought and other abiotic stresses. These response systems often make use of transcription factors (TFs); a gene encoding a specific TF together with -its target genes constitute a regulon, and take part in signal transduction to activate/silence genes involved in response to drought. Since, five specific families of TFs (out of >80 known families of TFs) have gained widespread attention on account of their significant role in drought tolerance in plants, TFs and regulons belonging to these five multi-gene families (AP2/EREBP, bZIP, MYB/MYC, NAC and WRKY) have been described and their role in improving drought tolerance discussed in this brief review...
October 13, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Lorenzo Giusti, Erica Mica, Edoardo Bertolini, Anna Maria De Leonardis, Primetta Faccioli, Luigi Cattivelli, Cristina Crosatti
Plant stress response is a complex molecular process based on transcriptional and posttranscriptional regulation of many stress-related genes. microRNAs are the best-studied class of small RNAs known to play key regulatory roles in plant response to stress, besides being involved in plant development and organogenesis. We analyzed the leaf miRNAome of two durum wheat cultivars (Cappelli and Ofanto) characterized by a contrasting water use efficiency, exposed to heat stress, and mild and severe drought stress...
October 12, 2016: Functional & Integrative Genomics
Bin Dong, Haibin Wang, Aiping Song, Tao Liu, Yun Chen, Weimin Fang, Sumei Chen, Fadi Chen, Zhiyong Guan, Jiafu Jiang
Many plant species are autopolyploid, a condition frequently associated with improvements in both vegetative and reproductive vigor. The possible contribution of miRNAs to this improvement was investigated by characterizing the miRNA content of a diploid and an autotetraploid form of Chrysanthemum nankingense. 162 and 161 known miRNA sequences were identified in 2x and 4x library. The length of 22 and 25 nt was predominant in diploid. However, 21 and 24 nt showed dominance in autotetraploid. It seems likely that autopolyploidization have had an immediate effect the distribution of miRNAs...
2016: Frontiers in Plant Science
Jannatul Ferdous, Ryan Whitford, Martin Nguyen, Chris Brien, Peter Langridge, Penny J Tricker
Drought is one of the major abiotic stresses reducing crop yield. Since the discovery of plant microRNAs (miRNAs), considerable progress has been made in clarifying their role in plant responses to abiotic stresses, including drought. miR827 was previously reported to confer drought tolerance in transgenic Arabidopsis. We examined barley (Hordeum vulgare L. 'Golden Promise') plants over-expressing miR827 for plant performance under drought. Transgenic plants constitutively expressing CaMV-35S::Ath-miR827 and drought-inducible Zm-Rab17::Hv-miR827 were phenotyped by non-destructive imaging for growth and whole plant water use efficiency (WUEwp)...
October 11, 2016: Functional & Integrative Genomics
Soumitra Paul, Dipak Gayen, Swapan K Datta, Karabi Datta
The present study highlights the molecular regulation of iron transport in soyFER1-overexpressing transgenic rice. Accumulation of iron in three different seed developmental stages, milk, dough, and mature, has been examined. The transgenic seeds of the milk stage showed significant augmentation of iron and zinc levels compared with wild-type seeds, and similar results were observed throughout the dough and mature stages. To investigate the regulation of iron transport, the role of miRNAs was studied in roots of transgenic rice...
October 2016: Journal of Experimental Botany
Nathalie Boissot, Alexandra Schoeny, Flavie Vanlerberghe-Masutti
We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster...
2016: Frontiers in Plant Science
Sheng Xu, Yumei Jiang, Ning Wang, Bing Xia, Yilong Jiang, Xiaodan Li, Zhengzhi Zhang, Yikui Li, Ren Wang
BACKGROUND: Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer's disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing...
October 10, 2016: BMC Genomics
Zhaoxia Li, Xinrui Zhang, Xiuxia Liu, Yajie Zhao, Baomei Wang, Juren Zhang
Maize is a globally important crop, and a low phosphate (LP) supply frequently limits maize yields in many areas. microRNAs (miRNAs) play important roles in plant development and environmental adaptation. In this study, spatio-temporal miRNA transcript profiling and some of the target genes in the roots and leaves of the maize inbred line Q319 were analyzed in response to LP. Complex small RNA populations were detected after LP culture, and they displayed different patterns in the roots and leaves. Differentially expressed miRNAs can be grouped into 'early' miRNAs, which respond rapidly and are often non-specific to phosphate deficiency, and 'late' miRNAs, which alter the morphology, physiology or metabolism of plants upon prolonged phosphate deficiency...
November 2016: Plant Science: An International Journal of Experimental Plant Biology
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