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https://www.readbyqxmd.com/read/27910907/micrornas-modulate-adaption-to-multiple-abiotic-stresses-in-chlamydomonas-reinhardtii
#1
Xiang Gao, Fengge Zhang, Jinlu Hu, Wenkai Cai, Ge Shan, Dongsheng Dai, Kaiyao Huang, Gaohong Wang
MicroRNAs play an important role in abiotic stress responses in higher plants and animals, but their role in stress adaptation in algae remains unknown. In this study, the expression of identified and putative miRNAs in Chlamydomonas reinhardtii was assessed using quantitative polymerase chain reaction; some of the miRNAs (Cre-miR906-3p) were up-regulated, whereas others (Cre-miR910) were down-regulated when the species was subjected to multiple abiotic stresses. With degradome sequencing data, we also identified ATP4 (the d-subunit of ATP synthase) and NCR2 (NADPH: cytochrome P450 reductase) as one of the several targets of Cre-miR906-3p and Cre-miR910, respectively...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27845893/klk6-proteolysis-is-implicated-in-the-turnover-and-uptake-of-extracellular-alpha-synuclein-species
#2
Georgios Pampalakis, Vasia-Samantha Sykioti, Methodios Ximerakis, Ioanna Stefanakou-Kalakou, Ronald Melki, Kostas Vekrellis, Georgia Sotiropoulou
KLK6 is a serine protease highly expressed in the nervous system. In synucleinopathies, including Parkinson disease, the levels of KLK6 inversely correlate with α-synuclein in CSF. Recently, we suggested that recombinant KLK6 mediates the degradation of extracellular α-synuclein directly and via a proteolytic cascade that involves unidentified metalloproteinase(s). Here, we show that recombinant and naturally secreted KLK6 can readily cleave α-synuclein fibrils that have the potential for cell-to-cell propagation in "a prion-like mechanism"...
November 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27801427/developmental-changes-in-barley-microrna-expression-profiles-coupled-with-mirna-target-analysis
#3
Andrzej Pacak, Katarzyna Kruszka, Aleksandra Swida-Barteczka, Przemyslaw Nuc, Wojciech Karlowski, Artur Jarmolowski, Zofia Szweykowska-Kulinska
MicroRNAs are 19- to 24-nt-long single-stranded RNAs that are crucial regulators of gene expression which control plant development and response to environmental cues. We have analyzed microtranscriptomes of five barley developmental stages. Generally, during the barley development, miR168-3p and miR1432-5p levels increase while the 5'U-miR156-5p level decreases (with exception for the 2-week-old barley). We have identified two miR156-5p izomiRs (called 5'U-miR156-5p [20 nt] and 5'UU-miR156-5p [21 nt]), which were expressed differently during barley development...
November 2, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27760880/transcriptome-and-degradome-sequencing-reveals-dormancy-mechanisms-of-cunninghamia-lanceolata-seeds
#4
Dechang Cao, Huimin Xu, Yuanyuan Zhao, Xin Deng, Yongxiu Liu, Wim J J Soppe, Jinxing Lin
Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction...
December 2016: Plant Physiology
https://www.readbyqxmd.com/read/27754877/rna-degradome-studies-give-insights-into-ribosome-dynamics
#5
EDITORIAL
Gregory Bertoni
No abstract text is available yet for this article.
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27752116/small-rna-mediated-responses-to-low-and-high-temperature-stresses-in-cotton
#6
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
https://www.readbyqxmd.com/read/27743419/the-evolution-of-plant-micrornas-insights-from-a-basal-eudicot-sacred-lotus
#7
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
https://www.readbyqxmd.com/read/27742800/global-analysis-of-truncated-rna-ends-reveals-new-insights-into-ribosome-stalling-in-plants
#8
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
https://www.readbyqxmd.com/read/27739413/identification-and-functional-analysis-of-micrornas-involved-in-the-anther-development-in-cotton-genic-male-sterile-line-yu98-8a
#9
Xiaojie Yang, Yuanming Zhao, Deyi Xie, Yao Sun, Xunlu Zhu, Nardana Esmaeili, Zuoren Yang, Ye Wang, Guo Yin, Shuping Lv, Lihong Nie, Zhongjie Tang, Fu'an Zhao, Wu Li, Neelam Mishra, Li Sun, Wei Zhu, Weiping Fang
Hybrid vigor contributes in a large way to the yield and quality of cotton (Gossypium hirsutum) fiber. Although microRNAs play essential regulatory roles in flower induction and development, it is still unclear if microRNAs are involved in male sterility, as the regulatory molecular mechanisms of male sterility in cotton need to be better defined. In this study, two independent small RNA libraries were constructed and sequenced from the young buds collected from the sporogenous cell formation to the meiosis stage of the male sterile line Yu98-8A and the near-isogenic line...
October 7, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27724902/identification-and-differential-regulation-of-micrornas-in-response-to-methyl-jasmonate-treatment-in-lycoris-aurea-by-deep-sequencing
#10
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
https://www.readbyqxmd.com/read/27708662/comparative-analysis-of-mirnas-and-their-target-transcripts-between-a-spontaneous-late-ripening-sweet-orange-mutant-and-its-wild-type-using-small-rna-and-degradome-sequencing
#11
Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Fruit ripening in citrus is not well-understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their target genes in a spontaneous late-ripening mutant, "Fengwan" sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ("Fengjie 72-1," WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27708557/plasma-degradome-affected-by-variable-storage-of-human-blood
#12
Maria Kaisar, Leon F A van Dullemen, Marie-Laëtitia Thézénas, M Zeeshan Akhtar, Honglei Huang, Sandrine Rendel, Philip D Charles, Roman Fischer, Rutger J Ploeg, Benedikt M Kessler
BACKGROUND: The successful application of-omics technologies in the discovery of novel biomarkers and targets of therapeutic interventions is facilitated by large collections of well curated clinical samples stored in bio banks. Mining the plasma proteome holds promise to improve our understanding of disease mechanisms and may represent a source of biomarkers. However, a major confounding factor for defining disease-specific proteomic signatures in plasma is the variation in handling and processing of clinical samples leading to protein degradation...
2016: Clinical Proteomics
https://www.readbyqxmd.com/read/27699487/uncovering-leaf-rust-responsive-mirnas-in-wheat-triticum-aestivum-l-using-high-throughput-sequencing-and-prediction-of-their-targets-through-degradome-analysis
#13
Dhananjay Kumar, Summi Dutta, Dharmendra Singh, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay
Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression...
October 3, 2016: Planta
https://www.readbyqxmd.com/read/27698373/identification-of-drought-responsive-micrornas-and-their-targets-in-ammopiptanthus-mongolicus-by-using-high-throughput-sequencing
#14
Fei Gao, Ning Wang, Huayun Li, Jisheng Liu, Chenxi Fu, Zihua Xiao, Chunxiang Wei, Xiaoduo Lu, Jinchao Feng, Yijun Zhou
MicroRNAs (miRNAs) regulate target gene expression to modulate plant growth, development, and biotic and abiotic stress response at the post-transcriptional level. Ammopiptanthus mongolicus, an ecologically important desert plant, is increasingly used as a model for studying stress tolerance in plants. The miRNA-mediated gene regulatory network might remarkably contribute to the high stress tolerance of A. mongolicus. However, a genome-wide identification of miRNAs and their targets is still lacking in A. mongolicus...
October 4, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27695059/genome-wide-identification-of-mirnas-and-their-targets-involved-in-the-developing-internodes-under-maize-ears-by-responding-to-hormone-signaling
#15
Zhan Zhao, Yadong Xue, Huili Yang, Huimin Li, Gaoyang Sun, Xiaofeng Zhao, Dong Ding, Jihua Tang
Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, 'Xun928' and 'Xun9058', which had significantly different internode lengths...
2016: PloS One
https://www.readbyqxmd.com/read/27601030/irhom2-regulates-csf1r-cell-surface-expression-and-non-steady-state-myelopoiesis-in-mice
#16
Xiaoping Qing, Lindsay D Rogers, Arthur Mortha, Yonit Lavin, Patricia Redecha, Priya D Issuree, Thorsten Maretzky, Miriam Merad, David R McIlwain, Tak W Mak, Christopher M Overall, Carl P Blobel, Jane E Salmon
CSF1R (colony stimulating factor 1 receptor) is the main receptor for CSF1 and has crucial roles in regulating myelopoeisis. CSF1R can be proteolytically released from the cell surface by ADAM17 (A disintegrin and metalloprotease 17). Here, we identified CSF1R as a major substrate of ADAM17 in an unbiased degradomics screen. We explored the impact of CSF1R shedding by ADAM17 and its upstream regulator, inactive rhomboid protein 2 (iRhom2, gene name Rhbdf2), on homeostatic development of mouse myeloid cells...
September 7, 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/27595790/srnaome-and-degradome-sequencing-analysis-reveals-specific-regulation-of-srna-in-response-to-chilling-injury-in-tomato-fruit
#17
Jinhua Zuo, Qing Wang, Cong Han, Zheng Ju, Dongyan Cao, Benzhong Zhu, Yunbo Luo, Lipu Gao
Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository...
September 6, 2016: Physiologia Plantarum
https://www.readbyqxmd.com/read/27576135/mass-spectrometry-based-proteomics-revealed-glypican-1-as-a-novel-adam17-substrate
#18
Rebeca Kawahara, Daniela Campos Granato, Sami Yokoo, Romênia Ramos Domingues, Daniel Maragno Trindade, Adriana Franco Paes Leme
: ADAM17 (a disintegrin and metalloproteinase 17) is a plasma membrane metalloprotease involved in proteolytic release of the extracellular domain of many cell surface molecules, a process known as ectodomain shedding. Through this process, ADAM17 is implicated in several aspects of tumor growth and metastasis in a broad range of tumors, including head and neck squamous cell carcinomas (HNSCC). In this study, mass spectrometry-based proteomics approaches revealed glypican-1 (GPC1) as a new substrate for ADAM17, and its shedding was confirmed to be metalloprotease-dependent, induced by a pleiotropic agent (PMA) and physiologic ligand (EGF), and inhibited by marimastat...
August 27, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27565736/small-rna-and-degradome-profiling-reveals-mirna-regulation-in-the-seed-germination-of-ancient-eudicot-nelumbo-nucifera
#19
Jihong Hu, Jing Jin, Qian Qian, Keke Huang, Yi Ding
BACKGROUND: MicroRNAs (miRNAs) play important roles in plant growth and development. MiRNAs and their targets have been widely studied in model plants, but limited knowledge is available concerning this small RNA population and their targets in sacred lotus (Nelumbo nucifera Gaertn.). RESULTS: In this study, a total of 145 known miRNAs belonging to 47 families and 78 novel miRNAs were identified during seed germination using high-throughput small RNA sequencing...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27506907/high-throughput-sequencing-and-degradome-analysis-reveal-altered-expression-of-mirnas-and-their-targets-in-a-male-sterile-cybrid-pummelo-citrus-grandis
#20
Yan-Ni Fang, Bei-Bei Zheng, Lun Wang, Wei Yang, Xiao-Meng Wu, Qiang Xu, Wen-Wu Guo
BACKGROUND: G1 + HBP is a male sterile cybrid line with nuclear genome from Hirado Buntan pummelo (C. grandis Osbeck) (HBP) and mitochondrial genome from "Guoqing No.1" (G1, Satsuma mandarin), which provides a good opportunity to study male sterility and nuclear-cytoplasmic cross talk in citrus. High-throughput sRNA and degradome sequencing were applied to identify miRNAs and their targets in G1 + HBP and its fertile type HBP during reproductive development. RESULTS: A total of 184 known miRNAs, 22 novel miRNAs and 86 target genes were identified...
2016: BMC Genomics
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