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https://www.readbyqxmd.com/read/29027423/-research-progress-of-relationship-between-continuous-cropping-obstacles-and-micrornas-in-rehmannia-glutinosa
#1
REVIEW
Xiao-Feng Cao, Yan-Hui Yang, Fa-Jie Feng, Ming-Jie Li, Li Gu, Feng-Qing Wang, Xin-Jian Chen, Zhong-Yi Zhang
The efficacy of Rehmannia glutinosa which as a large quantity of traditional Chinese medicine is significant. However, the land must be given up after one season of R. glutinosa cultivation or replanted after a period of 8-10 years because of the severe continuous cropping obstacles. MicroRNAs is a class of endogenous non-coding small RNAs, which participate in regulation of physiological activities by target mRNA cleavage or translational repression in plants. In recent years,studies on the role of miRNAs in plants have made significant progresses,especially in medicinal plants.MiRNAs from some different medicinal plant species have been identified with regulatory effects.When plants are exposed to environmental stress, miRNAs act on stress-related genes and initiate stress-resistance mechanisms in the body against adverse factors...
March 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29023006/expression-profile-of-stress-responsive-arabidopsis-thaliana-mirnas-and-their-target-genes-in-response-to-inoculation-with-pectobacterium-carotovorum-subsp-carotovorum
#2
A T Djami-Tchatchou, K Ntushelo
BACKGROUND: Pectobacterium carotovorum subsp. carotovorum (Pcc) is a soft rot bacterium which upon entry into the plant macerates plant tissues by producing plant cell wall degrading enzymes. It has a wide host range which includes carrot, potato, tomato, leafy greens, squash and other cucurbits, onion, green peppers and cassava. During plant-microbe interactions, one of the ways of plant response to pathogen infection is through the small RNA silencing mechanism. Under pathogen attack the plant utilizes microRNAs to regulate gene expression by means of mediating gene silencing at transcriptional and post-transcriptional level...
2017: Pakistan Journal of Biological Sciences: PJBS
https://www.readbyqxmd.com/read/29021802/genome-wide-identification-of-circular-rnas-in-arabidopsis-thaliana
#3
Gang Chen, Jiawen Cui, Li Wang, Yingfang Zhu, Zhaogeng Lu, Biao Jin
Circular RNAs (circRNAs) are a family of transcripts with covalently closed circular structures and still largely unknown functions. Large numbers of circRNAs have been found in various biological processes in humans and animals, but fewer circRNAs have been identified in plants. We performed a genome-wide analysis of circRNAs in Arabidopsis thaliana via deep sequencing. We constructed 14 strand-specific libraries from 13 samples of plants from four developmental stages, four stress treatments, and five organs and a mixed sample across the lifespan...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29021799/improved-quantitative-plant-proteomics-via-the-combination-of-targeted-and-untargeted-data-acquisition
#4
Gene Hart-Smith, Rodrigo S Reis, Peter M Waterhouse, Marc R Wilkins
Quantitative proteomics strategies - which are playing important roles in the expanding field of plant molecular systems biology - are traditionally designated as either hypothesis driven or non-hypothesis driven. Many of these strategies aim to select individual peptide ions for tandem mass spectrometry (MS/MS), and to do this mixed hypothesis driven and non-hypothesis driven approaches are theoretically simple to implement. In-depth investigations into the efficacies of such approaches have, however, yet to be described...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29017967/non-coding-rnas-and-their-roles-in-stress-response-in-plants
#5
REVIEW
Jingjing Wang, Xianwen Meng, Oxana B Dobrovolskaya, Yuriy L Orlov, Ming Chen
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance...
October 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29017848/suppression-of-cotton-leaf-curl-disease-symptoms-in-gossypium-hirsutum-through-overexpression-of-host-encoded-mirnas
#6
Mohd Akmal, Mirza S Baig, Jawaid A Khan
Cotton leaf curl disease (CLCuD), a major factor resulting in the enormous yield losses in cotton crop, is caused by a distinct monopartite begomovirus in association with Cotton leaf curl Multan betasatellite (CLCuMB). Micro(mi)RNAs are known to regulate gene expression in eukaryotes, including antiviral defense in plants. In a previous study, we had computationally identified a set of cotton miRNAs, which were shown to have potential targets in the genomes of Cotton leaf curl Multan virus (CLCuMuV) and CLCuMB at multiple loci...
October 7, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29016889/argonaute10-inhibits-in-vitro-shoot-regeneration-via-repression-of-mir165-166-in-arabidopsis-thaliana
#7
Tao Xue, Xuehuan Dai, Ruipu Wang, Junzhu Wang, Zhenhua Liu, Fengning Xiang
Many plant cells retain their totipotency when cultured in vitro. The regulation of shoot regeneration from in vitro culture involves a number of gene products, but the nature of the associated post-transcriptional events remains largely unknown. Here, the post transcriptional regulator ARGONAUTE10 (AGO10), a protein which is specifically expressed in the explant during the period when pro-SAMs are forming, has been known to inhibit shoot regeneration. In in vitro cultured explants of the loss-of-function mutant ago10, a much larger than normal number of shoot apical meristems was formed, and in these, the stem-cell marker genes WUS, CLV3 and STM were all strongly expressed...
August 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28990488/the-microrna-mir773-is-involved-in-the-arabidopsis-immune-response-to-fungal-pathogens
#8
Raquel Salvador-Guirao, Patricia Baldrich, Detlef Weigel, Ignacio Rubio-Somoza, Blanca San Segundo
MicroRNAs (miRNAs) are 21-24 nucleotide short non-coding RNAs that trigger gene silencing in eukaryotes. In plants, miRNAs play a crucial role in a wide range of developmental processes and adaptive responses to abiotic and biotic stresses. In this work, we investigated the role of miR773 in modulating resistance to infection by fungal pathogens in Arabidopsis thaliana. Interference with miR773 activity by target mimics (in MIM773 plants) and concomitant up-regulation of the miR773 target gene METHYLTRANSFERASE 2 (MET2) increased resistance to infection by necrotrophic (Plectosphaerrella cucumerina) and hemibiotrophic (Fusarium oxysporum, Colletototrichum higginianum) fungal pathogens...
October 9, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28986912/plant-gene-regulation-using-multiplex-crispr-dcas9-artificial-transcription-factors
#9
Levi G Lowder, Aimee Malzahn, Yiping Qi
Besides genome editing, the CRISPR-Cas9-based platform provides a new way of engineering artificial transcription factors (ATFs). Multiplex of guide RNA (gRNA) expression cassettes holds a great promise for many useful applications of CRISPR-Cas9. In this chapter, we provide a detailed protocol for building advanced multiplexed CRISPR-dCas9-Activator/repressor T-DNA vectors for carrying out transcriptional activation or repression experiments in plants. We specifically describe the assembly of multiplex T-DNA vectors that can express multiple gRNAs to activate a silenced gene, or to repress two independent miRNA genes simultaneously in Arabidopsis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28986803/knockdown-of-rice-microrna166-by-short-tandem-target-mimic-sttm
#10
Sachin Teotia, Dabing Zhang, Guiliang Tang
Small RNAs, including microRNAs (miRNAs), are abundant in plants and play key roles in controlling plant development and physiology. miRNAs regulate the expression of the target genes involved in key plant processes. Due to functional redundancy among miRNA family members in plants, an ideal approach to silence the expression of all members simultaneously, for their functional characterization, is desirable. Target mimic (TM) was the first approach to achieve this goal. Short tandem target mimic (STTM) is a potent approach complementing TM for silencing miRNAs in plants...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984673/toward-biological-subtyping-of-papillary-renal-cell-carcinoma-with-clinical-implications-through-histologic-immunohistochemical-and-molecular-analysis
#11
Rola M Saleeb, Fadi Brimo, Mina Farag, Alexis Rompré-Brodeur, Fabio Rotondo, Vidya Beharry, Samantha Wala, Pamela Plant, Michelle R Downes, Kenneth Pace, Andrew Evans, Georg Bjarnason, John M S Bartlett, George M Yousef
Papillary renal cell carcinoma (PRCC) has 2 histologic subtypes. Almost half of the cases fail to meet all morphologic criteria for either type, hence are characterized as PRCC not otherwise specified (NOS). There are yet no markers to resolve the PRCC NOS category. Accurate classification can better guide the management of these patients. In our previous PRCC study we identified markers that can distinguish between the subtypes. A PRCC patient cohort of 108 cases was selected for the current study. A panel of potentially distinguishing markers was chosen from our previous genomic analysis, and assessed by immunohistochemistry...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28984054/rna-uridylation-a-key-posttranscriptional-modification-shaping-the-coding-and-noncoding-transcriptome
#12
REVIEW
Caroline De Almeida, Hélène Scheer, Hélène Zuber, Dominique Gagliardi
RNA uridylation is a potent and widespread posttranscriptional regulator of gene expression. RNA uridylation has been detected in a range of eukaryotes including trypanosomes, animals, plants, and fungi, but with the noticeable exception of budding yeast. Virtually all classes of eukaryotic RNAs can be uridylated and uridylation can also tag viral RNAs. The untemplated addition of a few uridines at the 3' end of a transcript can have a decisive impact on RNA's fate. In rare instances, uridylation is an intrinsic step in the maturation of noncoding RNAs like for the U6 spliceosomal RNA or mitochondrial guide RNAs in trypanosomes...
October 5, 2017: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28981840/the-sirna-suppressor-rtl1-is-redox-regulated-through-glutathionylation-of-a-conserved-cysteine-in-the-double-stranded-rna-binding-domain
#13
Cyril Charbonnel, Adnan K Niazi, Emilie Elvira-Matelot, Elzbieta Nowak, Matthias Zytnicki, Anne de Bures, Edouard Jobet, Alisson Opsomer, Nahid Shamandi, Marcin Nowotny, Christine Carapito, Jean-Philippe Reichheld, Hervé Vaucheret, Julio Sáez-Vásquez
RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage...
September 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28979248/microrna-mediated-gene-silencing-in-plant-defense-and-viral-counter-defense
#14
REVIEW
Sheng-Rui Liu, Jing-Jing Zhou, Chun-Gen Hu, Chao-Ling Wei, Jin-Zhi Zhang
MicroRNAs (miRNAs) are non-coding RNAs of approximately 20-24 nucleotides in length that serve as central regulators of eukaryotic gene expression by targeting mRNAs for cleavage or translational repression. In plants, miRNAs are associated with numerous regulatory pathways in growth and development processes, and defensive responses in plant-pathogen interactions. Recently, significant progress has been made in understanding miRNA-mediated gene silencing and how viruses counter this defense mechanism. Here, we summarize the current knowledge and recent advances in understanding the roles of miRNAs involved in the plant defense against viruses and viral counter-defense...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28979170/epigenetic-regulation-of-gene-expression-induced-by-butyrate-in-colorectal-cancer-involvement-of-microrna
#15
REVIEW
Karen S Bishop, Huawen Xu, Gareth Marlow
Colorectal cancer (CRC) is the third most common cause of cancer mortality globally. Development of CRC is closely associated with lifestyle, and diet may modulate risk. A Western-style diet is characterised by a high intake of red meat but low consumption of fruit, vegetables, and whole cereals. Such a diet is associated with CRC risks. It has been demonstrated that butyrate, produced by the fermentation of dietary plant fibre, can alter both genetic and epigenetic expressions. MicroRNAs (miRNAs) are small non-coding RNAs that are commonly present in both normal and tumour cells...
2017: Genetics & Epigenetics
https://www.readbyqxmd.com/read/28977024/rice-stripe-virus-ns3-protein-regulates-primary-mirna-processing-through-association-with-the-mirna-biogenesis-factor-osdrb1-and-facilitates-virus-infection-in-rice
#16
Lijia Zheng, Chao Zhang, Chaonan Shi, Yu Wang, Tong Zhou, Feng Sun, Hong Wang, Shanshan Zhao, Qingqing Qin, Rui Qiao, Zuomei Ding, Chunhong Wei, Lianhui Xie, Jianguo Wu, Yi Li
MicroRNAs (miRNAs) are small regulatory RNAs processed from primary miRNA transcripts, and plant miRNAs play important roles in plant growth, development, and response to infection by microbes. Microbial infections broadly alter miRNA biogenesis, but the underlying mechanisms remain poorly understood. In this study, we report that the Rice stripe virus (RSV)-encoded nonstructural protein 3 (NS3) interacts with OsDRB1, an indispensable component of the rice (Oryza sativa) miRNA-processing complex. Moreover, the NS3-OsDRB1 interaction occurs at the sites required for OsDRB1 self-interaction, which is essential for miRNA biogenesis...
October 4, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28971772/herbs-for-effective-treatment-of-diabetes-mellitus-medicinal-chemistry-and-future-therapeutic-options
#17
Farida Hussan, Mohamad Fairuz Yahaya, Seong Lin Teoh, Srijit Das
The incidence of diabetes mellitus (DM) has increased globally. Various complications such as blindness, nephropathy leading to renal failure, neuropathy, foot ulceration, amputation, and disturbance in autonomic nervous system have been reported. Although, allopathy treatment still remains the treatment of choice, there is a need to look at the easy availability, patient compliance and cheaper cost of the drugs used in day-day practice. In this regard, complementary and alternative medicine has a greater role to play...
September 27, 2017: Mini Reviews in Medicinal Chemistry
https://www.readbyqxmd.com/read/28970560/endogenous-mirna-in-the-green-alga-chlamydomonas-regulates-gene-expression-through-cds-targeting
#18
Betty Y-W Chung, Michael J Deery, Arnoud J Groen, Julie Howard, David C Baulcombe
MicroRNAs (miRNAs) are 21-24-nucleotide RNAs present in many eukaryotes that regulate gene expression as part of the RNA-induced silencing complex. The sequence identity of the miRNA provides the specificity to guide the silencing effector Argonaute (AGO) protein to target mRNAs via a base-pairing process (1) . The AGO complex promotes translation repression and/or accelerated decay of this target mRNA (2) . There is overwhelming evidence both in vivo and in vitro that translation repression plays a major role (3-7) ...
October 2, 2017: Nature Plants
https://www.readbyqxmd.com/read/28970509/integrating-transcriptome-and-microrna-analysis-identifies-genes-and-micrornas-for-aho-induced-systemic-acquired-resistance-in-n-tabacum
#19
Yongdui Chen, Jiahong Dong, Jeffrey L Bennetzen, Micai Zhong, Jun Yang, Jie Zhang, Shunlin Li, Xiaojiang Hao, Zhongkai Zhang, Xuewen Wang
3-Acetonyl-3-hydroxyoxindole (AHO) induces systemic acquired resistance (SAR) in Nicotiana. However, the underlying molecular mechanism is not well understood. To understand the molecular regulation during SAR induction, we examined mRNA levels, microRNA (miRNA) expression, and their regulatory mechanisms in control and AHO-treated tobacco leaves. Using RNA-seq analysis, we identified 1,445 significantly differentially expressed genes (DEGs) at least 2 folds with AHO treatment. The DEGs significantly enriched in six metabolism pathways including phenylpropanoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis for protective cuticle and wax...
October 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28964896/genome-wide-identification-of-cotton-gossypium-hirsutum-encoded-microrna-targets-against-cotton-leaf-curl-burewala-virus
#20
Shweta, Yusuf Akhter, Jawaid Ahmad Khan
Cotton leaf curl Burewala virus (CLCuBV, genus Begomovirus) causes devastating cotton leaf curl disease. Among various known virus controlling strategies, siRNA-mediated one has shown potential to protect host crop plants. Micro(mi) RNAs, are the endogenous small RNAs and play a key role in plant development and stress resistance. In the present study we have identified cotton (Gossypium hirsutum)-encoded miRNAs targeting the CLCuBV. Based on threshold free energy and maximum complementarity scores of host miRNA-viral mRNA target pairs, a number of potential miRNAs were annotated...
September 27, 2017: Gene
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