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MicroRNA sequencing

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https://www.readbyqxmd.com/read/28445987/context-dependent-mir-204-and-mir-211-affect-the-biological-properties-of-amelanotic-and-melanotic-melanoma-cells
#1
Marianna Vitiello, Andrea Tuccoli, Romina D'Aurizio, Samanta Sarti, Laura Giannecchini, Simone Lubrano, Andrea Marranci, Monica Evangelista, Silvia Peppicelli, Chiara Ippolito, Ivana Barravecchia, Elena Guzzolino, Valentina Montagnani, Michael Gowen, Elisa Mercoledi, Alberto Mercatanti, Laura Comelli, Salvatore Gurrieri, Lawrence W Wu, Omotayo Ope, Keith Flaherty, Genevieve M Boland, Marc R Hammond, Lawrence Kwong, Mario Chiariello, Barbara Stecca, Gao Zhang, Alessandra Salvetti, Debora Angeloni, Letizia Pitto, Lido Calorini, Giovanna Chiorino, Marco Pellegrini, Meenhard Herlyn, Iman Osman, Laura Poliseno
Despite increasing amounts of experimental evidence depicting the involvement of non-coding RNAs in cancer, the study of BRAFV600E-regulated genes has thus far focused mainly on protein-coding ones. Here, we identify and study the microRNAs that BRAFV600E regulates through the ERK pathway.By performing small RNA sequencing on A375 melanoma cells and a vemurafenib-resistant clone that was taken as negative control, we discover miR-204 and miR-211 as the miRNAs most induced by vemurafenib. We also demonstrate that, although belonging to the same family, these two miRNAs have distinctive features...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445677/overexpression-of-the-cytokine-baff-and-autoimmunity-risk
#2
Maristella Steri, Valeria Orrù, M Laura Idda, Maristella Pitzalis, Mauro Pala, Ilenia Zara, Carlo Sidore, Valeria Faà, Matteo Floris, Manila Deiana, Isadora Asunis, Eleonora Porcu, Antonella Mulas, Maria G Piras, Monia Lobina, Sandra Lai, Mara Marongiu, Valentina Serra, Michele Marongiu, Gabriella Sole, Fabio Busonero, Andrea Maschio, Roberto Cusano, Gianmauro Cuccuru, Francesca Deidda, Fausto Poddie, Gabriele Farina, Mariano Dei, Francesca Virdis, Stefania Olla, Maria A Satta, Mario Pani, Alessandro Delitala, Eleonora Cocco, Jessica Frau, Giancarlo Coghe, Lorena Lorefice, Giuseppe Fenu, Paola Ferrigno, Maria Ban, Nadia Barizzone, Maurizio Leone, Franca R Guerini, Matteo Piga, Davide Firinu, Ingrid Kockum, Izaura Lima Bomfim, Tomas Olsson, Lars Alfredsson, Ana Suarez, Patricia E Carreira, Maria J Castillo-Palma, Joseph H Marcus, Mauro Congia, Andrea Angius, Maurizio Melis, Antonio Gonzalez, Marta E Alarcón Riquelme, Berta M da Silva, Maurizio Marchini, Maria G Danieli, Stefano Del Giacco, Alessandro Mathieu, Antonello Pani, Stephen B Montgomery, Giulio Rosati, Jan Hillert, Stephen Sawcer, Sandra D'Alfonso, John A Todd, John Novembre, Gonçalo R Abecasis, Michael B Whalen, Maria G Marrosu, Alessandra Meloni, Serena Sanna, Myriam Gorospe, David Schlessinger, Edoardo Fiorillo, Magdalena Zoledziewska, Francesco Cucca
Background Genomewide association studies of autoimmune diseases have mapped hundreds of susceptibility regions in the genome. However, only for a few association signals has the causal gene been identified, and for even fewer have the causal variant and underlying mechanism been defined. Coincident associations of DNA variants affecting both the risk of autoimmune disease and quantitative immune variables provide an informative route to explore disease mechanisms and drug-targetable pathways. Methods Using case-control samples from Sardinia, Italy, we performed a genomewide association study in multiple sclerosis followed by TNFSF13B locus-specific association testing in systemic lupus erythematosus (SLE)...
April 27, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28444748/identification-of-coagulation-gene-3-utr-variants-that-are-potentially-regulated-by-micrornas
#3
Carla Y Vossen, Astrid van Hylckama Vlieg, Raúl Teruel-Montoya, Salam Salloum-Asfar, Hugoline de Haan, Javier Corral, Pieter Reitsma, Bobby P C Koeleman, Constantino Martínez
MicroRNAs have been recognized as critical regulators of gene expression and might affect the risk of venous thrombosis. We aimed to identify 3' untranslated region (UTR) variants in coagulation genes that influence coagulation factor levels and venous thrombosis risk. The 3'UTR of coagulation genes were sequenced in subjects with extremely high or low plasma levels of these factors in two case-control studies. In total, 28 variants were identified. Five single nucleotide polymorphisms (SNPs) were predominantly present in one extreme level group (F2 rs1799963, F8 rs1050705 and F11 rs4253429, rs4253430 and rs1062547)...
April 26, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28444238/high-purity-circular-rna-isolation-method-rpad-reveals-vast-collection-of-intronic-circrnas
#4
Amaresh C Panda, Supriyo De, Ioannis Grammatikakis, Rachel Munk, Xiaoling Yang, Yulan Piao, Dawood B Dudekula, Kotb Abdelmohsen, Myriam Gorospe
High-throughput RNA sequencing methods coupled with specialized bioinformatic analyses have recently uncovered tens of thousands of unique circular (circ)RNAs, but their complete sequences, genes of origin and functions are largely unknown. Given that circRNAs lack free ends and are thus relatively stable, their association with microRNAs (miRNAs) and RNA-binding proteins (RBPs) can influence gene expression programs. While exoribonuclease treatment is widely used to degrade linear RNAs and enrich circRNAs in RNA samples, it does not efficiently eliminate all linear RNAs...
April 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28443119/parsing-the-regulatory-network-between-small-rnas-and-target-genes-in-ethylene-pathway-in-tomato
#5
Yunxiang Wang, Qing Wang, Lipu Gao, Benzhong Zhu, Zheng Ju, Yunbo Luo, Jinhua Zuo
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28443105/identification-of-microrna-targets-of-capsicum-spp-using-mirtrans-a-trans-omics-approach
#6
Lu Zhang, Cheng Qin, Junpu Mei, Xiaocui Chen, Zhiming Wu, Xirong Luo, Jiaowen Cheng, Xiangqun Tang, Kailin Hu, Shuai C Li
The microRNA (miRNA) can regulate the transcripts that are involved in eukaryotic cell proliferation, differentiation, and metabolism. Especially for plants, our understanding of miRNA targets, is still limited. Early attempts of prediction on sequence alignments have been plagued by enormous false positives. It is helpful to improve target prediction specificity by incorporating the other data sources such as the dependency between miRNA and transcript expression or even cleaved transcripts by miRNA regulations, which are referred to as trans-omics data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442363/the-global-expression-profiling-in-esophageal-squamous-cell-carcinoma
#7
Fuqiang Dai, Longyong Mei, Shenglan Meng, Zheng Ma, Wei Guo, Jinghai Zhou, Jingge Zhang
Esophageal squamous cell carcinoma (ESCC) is the dominant subtype of esophageal cancer worldwide. This study aimed to explore the aberrant global expression profiling and construct regulatory network in ESCC for understanding tumorigenesis of ESCC. The expression pattern of long non-coding RNA (lncRNA), microRNA (miRNA) and mRNA was measured by RNA-sequencing in ESCC. Differentially expressed lncRNAs/miRNAs/mRNAs (DELs/DEMs/DEMIs) were identified in ESCC. DEMIs-DEMs network was constructed; hsa-miR-424-5p and hsa-miR-450b-5p were the hub miRNAs in the network, which negatively regulated 19 and 17 DEMs...
April 22, 2017: Genomics
https://www.readbyqxmd.com/read/28441774/brain-derived-neurotrophic-factor-mediated-perfluorooctane-sulfonate-induced-neurotoxicity-via-epigenetics-regulation-in-sk-n-sh-cells
#8
Xin-Xin Guo, Qing-Zhi He, Wu Li, Ding-Xin Long, Xiao-Yuan Pan, Cong Chen, Huai-Cai Zeng
Perfluorooctane sulfonate (PFOS), a new kind of persistent organic pollutant, is widely distributed in the environment and exists in various organisms, where it is also a neurotoxic compound. However, the potential mechanism of its neurotoxicity is still unclear. To examine the role of epigenetics in the neurotoxicity induced by PFOS, SK-N-SH cells were treated with different concentrations of PFOS or control medium (0.1% DMSO) for 48 h. The mRNA levels of DNA methyltransferases (DNMTs) and Brain-derived neurotrophic factor (BDNF), microRNA-16, microRNA-22, and microRNA-30a-5p were detected by Quantitative PCR (QPCR)...
April 24, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28441666/a-microrna-124-polymorphism-is-associated-with-fracture-healing-via-modulating-bmp6-expression
#9
Lin Zou, Guichun Zhang, Lifeng Liu, Chen Chen, Xuecheng Cao, Jinfang Cai
BACKGROUND: miR-124-3p has been reported to be involved in the pathogenesis of many diseases by modulating a variety of signaling pathways. In this study, we aimed to understand the impact of miR-124-3p expression level on the fracture healing in the patients of metaphyseal fracture of distal tibia, who received minimal invasive percutaneous plate osteosynthesis. METHODS: We firstly collected 195 patients of metaphyseal fracture of distal tibia, and the genotype of rs531564 was determined: GG (n=124) and GC+CC (n=71)...
April 20, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28441533/a-global-view-of-rna-protein-interactions-identifies-post-transcriptional-regulators-of-root-hair-cell-fate
#10
Shawn W Foley, Sager J Gosai, Dongxue Wang, Nur Selamoglu, Amelia C Sollitti, Tino Köster, Alexander Steffen, Eric Lyons, Fevzi Daldal, Benjamin A Garcia, Dorothee Staiger, Roger B Deal, Brian D Gregory
The Arabidopsis thaliana root epidermis is comprised of two cell types, hair and nonhair cells, which differentiate from the same precursor. Although the transcriptional programs regulating these events are well studied, post-transcriptional factors functioning in this cell fate decision are mostly unknown. Here, we globally identify RNA-protein interactions and RNA secondary structure in hair and nonhair cell nuclei. This analysis reveals distinct structural and protein binding patterns across both transcriptomes, allowing identification of differential RNA binding protein (RBP) recognition sites...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28440395/microrna-mediated-inflammatory-responses-induced-by-cryptococcus-neoformans-are-dependent-on-the-nf-%C3%AE%C2%BAb-pathway-in-human-monocytes
#11
Hong Chen, Yi Jin, Huan Chen, Ningxin Liao, Yan Wang, Jianghan Chen
Cryptococcosis is a significant invasive fungal infection with noteworthy morbidity and mortality that is usually caused by either Cryptococcus neoformans (C. neoformans) or Cryptococcus gattii (C. gattii). Epidemiological studies have indicated that C. neoformans are more often reported in immunocompromised and immunocompetent patients. It has been well established that the cytokine profile of the host markedly affects the outcome of cryptococcal disease, and the negative regulators of microRNAs(miRs or miRNAs) are critically important for immunomodulation...
April 12, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28439841/label-free-direct-detection-of-mirnas-with-poly-silicon-nanowire-biosensors
#12
Jing He, Jianjun Zhu, Bin Jiang, Yulan Zhao
The diagnostic and prognostic value of microRNAs (miRNAs) in diseases becomes promising. Owing to fast response and high sensitivity, silicon nanowire (SiNW) biosensor has been considered a potential tool for miRNAs detection. Here, we describe a booming method to detect miRNAs with poly-silicon nanowire biosensors. Standard and real miRNA samples are applied in this study. The results show a limitation of 1 fM in the detection of standard miRNA sample with our poly-nanowire devices. Meanwhile, one-base mismatched sequence could be distinguished...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439840/micrornas-regulatory-networks-and-comorbidities-decoding-complex-systems
#13
Francesco Russo, Kirstine Belling, Anders Boeck Jensen, Flavia Scoyni, Søren Brunak, Marco Pellegrini
MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of messenger RNAs (mRNAs). Each miRNA targets a specific set of mRNAs. Upon binding the miRNA inhibits mRNA translation or facilitate mRNA degradation. miRNAs are frequently deregulated in several pathologies including cancer and cardiovascular diseases. Since miRNAs have a crucial role in fine-tuning the expression of their targets, they have been proposed as biomarkers of disease progression and prognostication.In this chapter we discuss different approaches for computational predictions of miRNA targets based on sequence complementarity and integration of expression data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439836/prediction-of-mirna-mrna-interactions-using-mirgate
#14
Eduardo Andrés-León, Gonzalo Gómez-López, David G Pisano
miRGate ( http://mirgate.bioinfo.cnio.es /) is a freely available database that contains predicted and experimentally validated microRNA-messenger RNA (miRNA-mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3'-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439834/an-assessment-of-the-next-generation-of-animal-mirna-target-prediction-algorithms
#15
Thomas Bradley, Simon Moxon
The advent of genome-wide next-generation sequencing technologies has revolutionized the genomic and transcriptomic fields. New technologies also present an opportunity for greater discovery and understanding of post-transcriptional processes, in particular, translational inhibition of transcripts by miRBP (microRNA-RNA binding protein) complexes. Not only have novel methodologies been developed for the direct sequencing of RBP-bound RNA, but a new class of miRNA (microRNA) target prediction algorithms trained on this data has emerged...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439832/computational-and-experimental-identification-of-tissue-specific-microrna-targets
#16
Raheleh Amirkhah, Hojjat Naderi Meshkin, Ali Farazmand, John E J Rasko, Ulf Schmitz
In this chapter we discuss computational methods for the prediction of microRNA (miRNA) targets. More specifically, we consider machine learning-based approaches and explain why these methods have been relatively unsuccessful in reducing the number of false positive predictions. Further we suggest approaches designed to improve their performance by considering tissue-specific target regulation. We argue that the miRNA targetome differs depending on the tissue type and introduce a novel algorithm that predicts miRNA targets specifically for colorectal cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439831/predicting-functional-microrna-mrna-interactions
#17
Zixing Wang, Yin Liu
MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439827/droplet-microfluidic-device-fabrication-and-use-for-isothermal-amplification-and-detection-of-microrna
#18
Maria Chiara Giuffrida, Roberta D'Agata, Giuseppe Spoto
Droplet microfluidics combined with the isothermal circular strand displacement polymerization (ICSDP) represents a powerful new technique to detect both single-stranded DNA and microRNA sequences. The method here described helps in overcoming some drawbacks of the lately introduced droplet polymerase chain reaction (PCR) amplification when implemented in microfluidic devices. The method also allows the detection of nanoliter droplets of nucleic acids sequences solutions, with a particular attention to microRNA sequences that are detected at the picomolar level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439824/genome-wide-comparison-of-next-generation-sequencing-and-qpcr-platforms-for-microrna-profiling-in-serum
#19
Thorarinn Blondal, Maurizia Rossana Brunetto, Daniela Cavallone, Martin Mikkelsen, Michael Thorsen, Yuan Mang, Hazel Pinheiro, Ferruccio Bonino, Peter Mouritzen
This study compares next-generation sequencing (NGS) technologies that have been optimized specifically for biofluid samples, with more established qPCR-based methods for profiling microRNAs in biofluids. The same patient serum samples were analyzed by NGS and qPCR, and differences in the serum microRNA profile between HBV and HCV infected patients were investigated. While there was overall good agreement between NGS and qPCR, there were some differences between the platforms, highlighting the importance of validation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439823/high-throughput-rt-qpcr-for-the-analysis-of-circulating-micrornas
#20
Geok Wee Tan, Lu Ping Tan
Reverse transcription followed by real-time or quantitative polymerase chain reaction (RT-qPCR) is the gold standard for validation of results from transcriptomic profiling studies such as microarray and RNA sequencing. The current need for most studies, especially biomarker studies, is to evaluate the expression levels or fold changes of many transcripts in a large number of samples. With conventional low to medium throughput qPCR platforms, many qPCR plates would have to be run and a significant amount of RNA input per sample will be required to complete the experiments...
2017: Methods in Molecular Biology
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