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https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#1
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28424721/mirna-and-degradome-sequencing-reveal-mirna-and-their-target-genes-that-may-mediate-shoot-growth-in-spur-type-mutant-yanfu-6
#2
Chunhui Song, Dong Zhang, Liwei Zheng, Jie Zhang, Baojuan Zhang, Wenwen Luo, Youmei Li, Guangfang Li, Juanjuan Ma, Mingyu Han
The spur-type growth habit in apple trees is characterized by short internodes, increased number of fruiting spurs, and compact growth that promotes flowering and facilitates management practices, such as pruning. The molecular mechanisms responsible for regulating spur-type growth have not been elucidated. In the present study, miRNAs and the expression of their potential target genes were evaluated in shoot tips of "Nagafu 2" (CF) and spur-type bud mutation "Yanfu 6" (YF). A total of 700 mature miRNAs were identified, including 202 known apple miRNAs and 498 potential novel miRNA candidates...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421097/development-of-incompletely-fused-carpels-in-maize-ovary-revealed-by-mirna-target-gene-and-phytohormone-analysis
#3
Hongping Li, Ting Peng, Qun Wang, Yufeng Wu, Jianfeng Chang, Moubiao Zhang, Guiliang Tang, Chaohai Li
Although the molecular basis of carpel fusion in maize ovary development remains largely unknown, increasing evidence suggests a critical role of microRNAs (miRNAs). In this study, a combination of miRNA sequencing, degradome and physiological analyses was used to characterize carpel fusion development in maize ovaries showing incompletely (IFC) and completely fused carpels (CFC). A total of 162 known miRNAs distributed across 33 families were identified, of which 20 were differentially expressed. In addition, 53 miRNA candidates were identified, of which 10 were differentially expressed in the IFC and CFC ovaries...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28395198/propagation-and-some-physiological-effects-of-citrus-bark-cracking-viroid-and-apple-fruit-crinkle-viroid-in-multiple-infected-hop-humulus-lupulus-l
#4
J Matoušek, K Siglová, J Jakše, S Radišek, Joseph R J Brass, T Tsushima, T Guček, G S Duraisamy, T Sano, G Steger
The hop metabolome important for the brewing industry and for medical purposes is endangered worldwide due to multiple viroid infections affecting hop physiology. Combinatorial biolistic hop inoculation with Citrus bark cracking viroid (CBCVd), Apple fruit crinkle viroid (AFCVd), Hop latent viroid, and Hop stunt viroid (HSVd) showed a low CBCVd compatibility with HSVd, while all other viroid combinations were highly compatible. Unlike to other viroids, single CBCVd propagation showed a significant excess of (-) over (+) strands in hop, tomato, and Nicotiana benthamiana, but not in citruses...
March 27, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28377111/genome-wide-identification-of-micrornas-involved-in-fatty-acid-and-lipid-metabolism-of-brassica-napus-by-small-rna-and-degradome-sequencing
#5
Zhiwei Wang, Yan Qiao, Jingjing Zhang, Wenhui Shi, Jinwen Zhang
Rapeseed (Brassica napus) is an important cash crop considered as the third largest oil crop worldwide. Rapeseed oil contains various saturation or unsaturation fatty acids, these fatty acids, whose could incorporation with TAG form into lipids stored in seeds play various roles in the metabolic activity. The different fatty acids in B. napus seeds determine oil quality, define if the oil is edible or must be used as industrial material. miRNAs are kind of non-coding sRNAs that could regulate gene expressions through post-transcriptional modification to their target transcripts playing important roles in plant metabolic activities...
April 1, 2017: Gene
https://www.readbyqxmd.com/read/28338719/the-legume-mir1514a-modulates-a-nac-transcription-factor-transcript-to-trigger-phasirna-formation-in-response-to-drought
#6
Guadalupe Sosa-Valencia, Miguel Palomar, Alejandra A Covarrubias, José L Reyes
Recent studies have identified microRNAs as post-transcriptional regulators involved in stress responses. miR1514a is a legume microRNA that is induced in response to drought stress in Phaseolus vulgaris (common bean) and shows differential accumulation levels in roots during water deficit in two cultivars with different drought tolerance phenotypes. A recent degradome analysis revealed that miR1514a targets the transcripts of two NAC transcription factors (TFs), Phvul.010g121000 and Phvul.010g120700. Furthermore, expression studies and small RNA-seq data indicate that only Phvul...
October 7, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28315251/fpps-fast-profiling-of-protease-specificity
#7
Matej Vizovišek, Robert Vidmar, Marko Fonović
Profiling of protease specificity is crucial for characterization of these important enzymes that play numerous roles in health and disease. In the past, several proteomic methods have been developed that enable profiling of protease specificities. Although able to identify thousands of protease cleavage events, these degradomics approaches are often time consuming and methodologically challenging, which limits their application to specialized proteomic groups or the laboratories that initially introduced them...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315250/multiplexed-protease-specificity-profiling-using-isobaric-labeling
#8
Joanna Tucher, Andreas Tholey
The determination of a protease's cleavage site specificity is one of the major goals in degradomics. In the last years, the use of proteome-derived peptide libraries and liquid chromatography-mass spectrometry (LC-MS) in a proteomic identification of protease cleavage sites (PICS) experiment became popular for that purpose.In this chapter, we offer a step-by-step protocol for the execution of a quantitative proteomic identification of protease cleavage sites (Q-PICS) experiment, which enables the relative quantification of proteolytic events by isobaric labeling, e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28315249/determining-protease-substrates-within-a-complex-protein-background-using-the-protein-topography-and-migration-analysis-platform-protomap
#9
R A Fuhrman-Luck, L M Silva, M L Hastie, J J Gorman, J A Clements
The PROtein TOpography and Migration Analysis Platform (PROTOMAP) approach is a degradomics technique used to determine protease substrates within complex protein backgrounds. The method involves protein separation according to protein relative mobility, using sodium dodecyl sulfate polyacrylamide gel electrophoresis. Gel lanes are then sliced into horizontal sections, and in-gel trypsin digestion performed for each gel slice. Extracted peptides and corresponding proteins are identified using liquid chromatography-tandem mass spectrometry and bioinformatics...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28304398/characterization-of-the-polyphenol-oxidase-gene-family-reveals-a-novel-microrna-involved-in-posttranscriptional-regulation-of-ppos-in-salvia-miltiorrhiza
#10
Caili Li, Dongqiao Li, Jiang Li, Fenjuan Shao, Shanfa Lu
Salvia miltiorrhiza is a well-known material of traditional Chinese medicine. Understanding the regulatory mechanisms of phenolic acid biosynthesis and metabolism are important for S. miltiorrhiza quality improvement. We report here that S. miltiorrhiza contains 19 polyphenol oxidases (PPOs), forming the largest PPO gene family in plant species to our knowledge. Analysis of gene structures and sequence features revealed the conservation and divergence of SmPPOs. SmPPOs were differentially expressed in plant tissues and eight of them were predominantly expressed in phloem and xylem, indicating that some SmPPOs are functionally redundant, whereas the others are associated with different physiological processes...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253861/small-rna-profiling-and-degradome-analysis-reveal-regulation-of-microrna-in-peanut-embryogenesis-and-early-pod-development
#11
Chao Gao, Pengfei Wang, Shuzhen Zhao, Chuanzhi Zhao, Han Xia, Lei Hou, Zheng Ju, Ye Zhang, Changsheng Li, Xingjun Wang
BACKGROUND: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored...
March 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28241738/response-of-micrornas-to-cold-treatment-in-the-young-spikes-of-common-wheat
#12
Guoqi Song, Rongzhi Zhang, Shujuan Zhang, Yulian Li, Jie Gao, Xiaodong Han, Mingli Chen, Jiao Wang, Wei Li, Genying Li
BACKGROUND: MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood. RESULTS: We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28228536/a-viral-satellite-dna-vector-tylccnv-for-functional-analysis-of-mirnas-and-sirnas-in-plants
#13
Zheng Ju, Dongyan Cao, Chao Gao, Jinhua Zuo, Baiqiang Zhai, Shan Li, Hongliang Zhu, Daqi Fu, Yunbo Luo, Benzhong Zhu
With experimental and bioinformatical methods, numerous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), have been found in plants, and they play vital roles in various biological regulation processes. However, most of these small RNAs remain to be functionally characterized. Until now, only several viral vectors were developed to overexpress miRNAs with limited application in plants. In this study, we report a new small RNA overexpression system via viral satellite DNA associated with Tomato yellow leaf curl China virus (TYLCCNV) vector, which could highly overexpress not only artificial and endogenous miRNAs but also endogenous siRNAs in Nicotiana benthamiana First, we constructed basic TYLCCNV-amiRPDS(319L) vector with widely used AtMIR319a backbone, but the expected photobleaching phenotype was very weak...
April 2017: Plant Physiology
https://www.readbyqxmd.com/read/28225779/combined-small-rna-and-degradome-sequencing-reveals-complex-microrna-regulation-of-catechin-biosynthesis-in-tea-camellia-sinensis
#14
Ping Sun, Chunzhen Cheng, Yuling Lin, Qiufang Zhu, Jinke Lin, Zhongxiong Lai
MicroRNAs are endogenous non-coding small RNAs playing crucial regulatory roles in plants. Tea, a globally popular non-alcoholic drink, is rich in health-enhancing catechins. In this study, 69 conserved and 47 novel miRNAs targeting 644 genes were identified by high-throughout sequencing. Predicted target genes of miRNAs were mainly involved in plant growth, signal transduction, morphogenesis and defense. To further identify targets of tea miRNAs, degradome sequencing and RNA ligase-mediated rapid amplification of 5'cDNA ends (RLM-RACE) were applied...
2017: PloS One
https://www.readbyqxmd.com/read/28203245/small-rnas-derived-from-the-t-dna-of-agrobacterium-rhizogenes-in-hairy-roots-of-phaseolus-vulgaris
#15
Pablo Peláez, Alejandrina Hernández-López, Georgina Estrada-Navarrete, Federico Sanchez
Agrobacterium rhizogenes is a pathogenic bacteria that causes hairy root disease by transferring bacterial DNA into the plant genome. It is an essential tool for industry and research due to its capacity to produce genetically modified roots and whole organisms. Here, we identified and characterized small RNAs generated from the transfer DNA (T-DNA) of A. rhizogenes in hairy roots of common bean (Phaseolus vulgaris). Distinct abundant A. rhizogenes T-DNA-derived small RNAs (ArT-sRNAs) belonging to several oncogenes were detected in hairy roots using high-throughput sequencing...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28179412/sharpening-host-defenses-during-infection-proteases-cut-to-the-chase
#16
REVIEW
Natalie C Marshall, B Brett Finlay, Christopher M Overall
The human immune system consists of an intricate network of tightly controlled pathways, where proteases are essential instigators and executioners at multiple levels. Invading microbial pathogens also encode proteases that have evolved to manipulate and dysregulate host proteins, including host proteases during the course of disease. The identification of pathogen proteases as well as their substrates and mechanisms of action have empowered significant developments in therapeutics for infectious diseases. Yet for many pathogens, there remains a great deal to be discovered...
April 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28149304/identification-of-submergence-responsive-micrornas-and-their-targets-reveals-complex-mirna-mediated-regulatory-networks-in-lotus-nelumbo-nucifera-gaertn
#17
Qijiang Jin, Yingchun Xu, Neil Mattson, Xin Li, Bei Wang, Xiao Zhang, Hongwei Jiang, Xiaojing Liu, Yanjie Wang, Dongrui Yao
MicroRNAs (miRNAs) are endogenous non-coding RNAs with important regulatory functions in plant development and stress responses. However, their population abundance in lotus (Nelumbo nucifera Gaertn) has so far been poorly described, particularly in response to stresses. In this work, submergence-related miRNAs and their target genes were systematically identified, compared, and validated at the transcriptome-wide level using high-throughput sequencing data of small RNA, Mrna, and the degradome. A total of 128 known and 20 novel miRNAs were differentially expressed upon submergence...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28146558/genome-wide-exonic-small-interference-rna-mediated-gene-silencing-regulates-sexual-reproduction-in-the-homothallic-fungus-fusarium-graminearum
#18
Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Various ascomycete fungi possess sex-specific molecular mechanisms, such as repeat-induced point mutations, meiotic silencing by unpaired DNA, and unusual adenosine-to-inosine RNA editing, for genome defense or gene regulation. Using a combined analysis of functional genetics and deep sequencing of small noncoding RNA (sRNA), mRNA, and the degradome, we found that the sex-specifically induced exonic small interference RNA (ex-siRNA)-mediated RNA interference (RNAi) mechanism has an important role in fine-tuning the transcriptome during ascospore formation in the head blight fungus Fusarium graminearum...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28112201/novel-bioinformatics-based-approach-for-proteomic-biomarkers-prediction-of-calpain-2-caspase-3-protease-fragmentation-application-to-%C3%AE-ii-spectrin-protein
#19
Atlal El-Assaad, Zaher Dawy, Georges Nemer, Firas Kobeissy
The crucial biological role of proteases has been visible with the development of degradomics discipline involved in the determination of the proteases/substrates resulting in breakdown-products (BDPs) that can be utilized as putative biomarkers associated with different biological-clinical significance. In the field of cancer biology, matrix metalloproteinases (MMPs) have shown to result in MMPs-generated protein BDPs that are indicative of malignant growth in cancer, while in the field of neural injury, calpain-2 and caspase-3 proteases generate BDPs fragments that are indicative of different neural cell death mechanisms in different injury scenarios...
January 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28109429/body-fluid-degradomics-and-characterization-of-basic-n-terminome
#20
F Sabino, O Hermes, U Auf dem Keller
Rapid improvements in instrumentation and data analysis make mass spectrometry-based proteomics the method of choice for global characterization of proteomes and discovery of protein-based biomarkers. On the contrary to tissue biopsies, body fluids-e.g., blood, wound fluid, urine, and saliva-are noninvasive and easy to collect and process. However, they are very complex and present high dynamic ranges of protein concentrations, rendering direct shotgun proteomics analysis as inefficient for identification of low-abundance proteins in these specimens...
2017: Methods in Enzymology
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