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https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#1
EDITORIAL
Hikmet Budak, Baohong Zhang
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms...
February 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28219335/stress-responsive-pathways-and-small-rna-changes-distinguish-variable-developmental-phenotypes-caused-by-msh1-loss
#2
Mon-Ray Shao, Sunil Kumar Kenchanmane Raju, John D Laurie, Robersy Sanchez, Sally A Mackenzie
BACKGROUND: Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge...
February 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28217707/microrna-regulation-of-human-pancreatic-cancer-stem-cells
#3
REVIEW
Yi-Fan Xu, Bethany N Hannafon, Wei-Qun Ding
microRNAs (miRNAs) are a group of small non-coding RNAs that function primarily in the post transcriptional regulation of gene expression in plants and animals. Deregulation of miRNA expression in cancer cells, including pancreatic cancer cells, is well documented, and the involvement of miRNAs in orchestrating tumor genesis and cancer progression has been recognized. This review focuses on recent reports demonstrating that miRNAs are involved in regulation of pancreatic cancer stem cells (CSCs). A number of miRNA species have been identified to be involved in regulating pancreatic CSCs, including miR-21, miR-34, miR-1246, miR-221, the miR-17-92 cluster, the miR-200 and let-7 families...
2017: Stem Cell Investigation
https://www.readbyqxmd.com/read/28215140/position-based-nucleotide-analysis-of-mir168-family-in-higher-plants-and-its-targets-in-mammalian-transcripts
#4
Mohammed Javed, Manish Solanki, Anshika Sinha, Lata Israni Shukla
The conserved miR168 family is evaluated for position based nucleotide preference in higher plants. The mature miRNA sequences include miR168-5p and miR168-3p, were obtained from miRBase (v21, June 2014) for 15 families (28 plants) containing a-c subfamilies. The preferred position based nucleotide sequences were obtained for miR168-5p and miR168-3p using Data Analysis in Molecular Biology and Evolution (DAMBE). miR168-5p shows same nucleotides at positions 1-6, 8-9, 11-12, 15-17 and 19. Also, miR168-3p is present in 3 families (10 plants) shows the same nucleotide at position 1-11, 13-15 and 17-21...
February 15, 2017: MicroRNA
https://www.readbyqxmd.com/read/28207805/unraveling-the-microrna-of-caragana-korshinskii-along-a-precipitation-gradient-on-the-loess-plateau-china-using-high-throughput-sequencing
#5
Pengbo Ning, Yulu Zhou, Lifang Gao, Yingying Sun, Wenfei Zhou, Furong Liu, Zhenye Yao, Lifang Xie, Junhui Wang, Chunmei Gong
Drought remains one of the main factors that negatively affect plant growth and development. Caragana korshinskii is widely distributed on the Loess Plateau, China, where it mediates soil and water loss and helps prevent desertification. However, little is known about the stress response mechanisms of C. korshinskii in water-starved environments. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several types of biotic and abiotic stress. Here, we describe the miRNAs of wild C...
2017: PloS One
https://www.readbyqxmd.com/read/28204845/mirnas-target-databases-developmental-methods-and-target-identification-techniques-with-functional-annotations
#6
REVIEW
Nagendra Kumar Singh
PURPOSE: microRNA (miRNA) regulates diverse biological mechanisms and metabolisms in plants and animals. Thus, the discoveries of miRNA has revolutionized the life sciences and medical research.The miRNA represses and cleaves the targeted mRNA by binding perfect or near perfect or imperfect complementary base pairs by RNA-induced silencing complex (RISC) formation during biogenesis process. One miRNA interacts with one or more mRNA genes and vice versa, hence takes part in causing various diseases...
February 15, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28203233/exo-mirexplorer-a-comprehensive-resource-for-exploring-and-comparatively-analyzing-exogenous-micrornas
#7
Ling-Ling Zheng, Kai-Wen Deng, An-Cheng Deng, Jie Wu, Jian-Hua Yang, Zhao-Rong Lun, Liang-Hu Qu
MicroRNAs (miRNAs) are small regulatory RNAs that play important roles in animals, plants, and viruses. Deep-sequencing technology has been widely adopted in miRNA investigations. However, it is still a big mysterious why nearly all sequencing data contain miRNA sequences from exogenous species, called exo-miRNAs. In this study, we developed a novel platform, exo-miRExplorer, for mining and identifying exo-miRNAs from high-throughput small RNA sequencing experiments which originated from tissues and cell lines of multiple organisms...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28202045/identification-of-micrornas-and-their-response-to-the-stress-of-plant-allelochemicals-in-aphis-gossypii-hemiptera-aphididae
#8
Kang-Sheng Ma, Fen Li, Ying Liu, Ping-Zhuo Liang, Xue-Wei Chen, Xi-Wu Gao
BACKGROUND: MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. RESULTS: We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals...
February 16, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28197719/regulatory-crosstalk-between-micrornas-and-hormone-signalling-cascades-controls-the-variation-on-seed-dormancy-phenotype-at-arabidopsis-thaliana-seed-set
#9
Yang Liu, Yousry A El-Kassaby
We employed an Illumina sequencing approach to identify candidate microRNA cohorts that may greatly contribute to seed dormancy modulation and to construct a microRNA-gene regulatory network in hormone signalling cascades. MicroRNAs (miRNAs) are important signalling molecules and regulate many developmental programs of plants. Some miRNAs have been integrated into gene regulatory networks (GRNs) and coordinate developmental plasticity, but few study systematically investigated how phenotypical variations are regulated through differential expression of miRNA tags in GRNs during seed set...
February 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28187422/differential-expression-of-hyperhydricity-responsive-peach-mirnas
#10
Ebru Diler, Turgay Unver, Gökhan Karakülah
Hyperhydricity is a syndrome that causes morpho-physiological malformations in tissue culture plantlets. Micro-RNAs (miRNA) are small non-coding RNAs that play important regulatory roles in plant development, stress response, and adaptation to environmental conditions. In this study, differential expression analysis indicated that miRNAs play an underlying role in the responses to the hyperhydricity syndrome in peach Prunus persica (L.) leaves. 24 known and three novel potential miRNAs were characterized in hyperhydric and non-hyperhydric transcriptome libraries...
December 31, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28182967/the-suppression-of-tomato-defence-response-genes-upon-potato-cyst-nematode-infection-indicates-a-key-regulatory-role-of-mirnas
#11
Magdalena Święcicka, Waldemar Skowron, Piotr Cieszyński, Joanna Dąbrowska-Bronk, Mateusz Matuszkiewicz, Marcin Filipecki, Marek Daniel Koter
Potato cyst nematode Globodera rostochiensis is an obligate parasite of solanaceous plants, triggering metabolic and morphological changes in roots which may result in substantial crop yield losses. Previously, we used the cDNA-AFLP to study the transcriptional dynamics in nematode infected tomato roots. Now, we present the rescreening of already published, upregulated transcript-derived fragment dataset using the most current tomato transcriptome sequences. Our reanalysis allowed to add 54 novel genes to 135, already found as upregulated in tomato roots upon G...
January 30, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28174587/integrating-small-rna-sequencing-with-qtl-mapping-for-identification-of-mirnas-and-their-target-genes-associated-with-heat-tolerance-at-the-flowering-stage-in-rice
#12
Qing Liu, Tifeng Yang, Ting Yu, Shaohong Zhang, Xingxue Mao, Junliang Zhao, Xiaofei Wang, Jingfang Dong, Bin Liu
Although, microRNAs (miRNAs) have been reported to be associated with heat tolerance at the seedling stage in rice, their involvement in heat tolerance at the flowering stage is still unknown. In this study, small RNA profiling was conducted in a heat-tolerant variety Gan-Xiang-Nuo (GXN) and a heat-sensitive variety Hua-Jing-Xian-74 (HJX), respectively. Totally, 102 miRNAs were differentially expressed (DE) under heat stress. Compared to HJX, GXN had more DE miRNAs and its DE miRNAs changed earlier under heat stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28167951/micrornas-are-intensively-regulated-during-induction-of-somatic-embryogenesis-in-arabidopsis
#13
Katarzyna Szyrajew, Dawid Bielewicz, Jakub Dolata, Anna M Wójcik, Katarzyna Nowak, Aleksandra Szczygieł-Sommer, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Małgorzata D Gaj
Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28150142/genome-wide-exploration-of-metal-tolerance-protein-mtp-genes-in-common-wheat-triticum-aestivum-insights-into-metal-homeostasis-and-biofortification
#14
Recep Vatansever, Ertugrul Filiz, Seckin Eroglu
Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized...
February 1, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
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
#15
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/28144248/osa-mir169-negatively-regulates-rice-immunity-against-the-blast-fungus-magnaporthe-oryzae
#16
Yan Li, Sheng-Li Zhao, Jin-Lu Li, Xiao-Hong Hu, He Wang, Xiao-Long Cao, Yong-Ju Xu, Zhi-Xue Zhao, Zhi-Yuan Xiao, Nan Yang, Jing Fan, Fu Huang, Wen-Ming Wang
miR169 is a conserved microRNA (miRNA) family involved in plant development and stress-induced responses. However, how miR169 functions in rice immunity remains unclear. Here, we show that miR169 acts as a negative regulator in rice immunity against the blast fungus Magnaporthe oryzae by repressing the expression of nuclear factor Y-A (NF-YA) genes. The accumulation of miR169 was significantly increased in a susceptible accession but slightly fluctuated in a resistant accession upon M. oryzae infection. Consistently, the transgenic lines overexpressing miR169a became hyper-susceptible to different M...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28143404/conservation-and-diversification-of-the-mir166-family-in-soybean-and-potential-roles-of-newly-identified-mir166s
#17
Xuyan Li, Xin Xie, Ji Li, Yuhai Cui, Yanming Hou, Lulu Zhai, Xiao Wang, Yanli Fu, Ranran Liu, Shaomin Bian
BACKGROUND: microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood...
February 1, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28122266/identification-and-characterization-of-novel-micrornas-for-fruit-development-and-quality-in-hot-pepper-capsicum-annuum-l
#18
Zhoubin Liu, Yuping Zhang, Lijun Ou, Linyu Kang, Yuhua Liu, Junheng Lv, Ge Wei, Bozhi Yang, Sha Yang, Wenchao Chen, Xiongze Dai, Xuefeng Li, Shudong Zhou, Zhuqing Zhang, Yanqing Ma, Xuexiao Zou
MicroRNAs (miRNAs) are non-coding small RNAs which play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are involved in fruit development in model plants. However, the miRNAs related to fruit development and quality in hot pepper (Capsicum annuum L.) remains unknown. In this study, small RNA populations from different fruit ripening stages and different varieties were compared using next-generation sequencing technology. Totally, 59 known miRNAs and 310 novel miRNAs were identified from four libraries using miRDeep2 software...
January 22, 2017: Gene
https://www.readbyqxmd.com/read/28115301/functions-of-microrna-in-seed-development-dormancy-and-germination-processes
#19
Wei Jun, Lu Xiujun, Zhang Xiaolin, Mei Mei, Huang Xiaoli
In plants, microRNAs (miRNAs) are a class of non-coding small RNAs that play important roles in various biological processes, such as seed development, dormancy and germination. In these stages, seeds are regulated by various extrinsic environmental factors and intrinsic hormones. Different species of seeds have distinct development and dormancy characteristics. Recent investigations have identified more and more miRNAs to regulate seed morphogenesis, material metabolism and stress response capacities through hormonal signal transduction, antioxidant effects and transcription factors, etc...
January 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28107426/identification-of-micrornas-in-response-to-drought-in-common-wild-rice-oryza-rufipogon-griff-shoots-and-roots
#20
Jing-Wen Zhang, Yan Long, Man-de Xue, Xing-Guo Xiao, Xin-Wu Pei
BACKGROUND: Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. RESULTS: In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where 'R' indicates the root tissue and 'L' indicates the shoot tissue...
2017: PloS One
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