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Arm switching miRNA

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https://www.readbyqxmd.com/read/27367785/catalytic-hairpin-assembly-actuated-dna-nanotweezer-for-logic-gate-building-and-sensitive-enzyme-free-biosensing-of-micrornas
#1
Dandan Li, Wei Cheng, Yujian Li, YongJie Xu, Xinmin Li, Yibing Yin, Huangxian Ju, Shijia Ding
A target-switched DNA nanotweezer is designed for AND logic gate operation and enzyme-free detection of microRNAs (miRNAs) by catalytic hairpin assembly (CHA) and proximity-dependent DNAzyme formation. The double crossover motif-based nanotweezer consists of an arched structure as the set strand for target inputs and two split G-rich DNAs at the termini of two arms for signal output. Upon a CHA, a small amount of binary target inputs can switch numerous open nanotweezers to a closed state, which leads to the formation of proximity-dependent DNAzyme in the presence of hemin to produce a highly sensitive biosensing system...
August 2, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/26592715/microrna-expression-is-altered-in-lateral-septum-across-reproductive-stages
#2
M C Saul, C Zhao, T M Driessen, B E Eisinger, S C Gammie
MicroRNAs (miRNAs) inhibit RNA targets and may contribute to postpartum central nervous system (CNS) gene expression changes, although this has never been tested. In the present study, we directly evaluated miRNA levels using RNA sequencing during reproduction in female mice in the lateral septum (LS). We found the reliable and robust changes of miRNAs away from the virgin stage at the three other stages, namely pregnant, day 1 postpartum, and day 8 postpartum. For a given miRNA that was significantly different from the virgin condition in more than one group, the direction of change was always the same...
January 15, 2016: Neuroscience
https://www.readbyqxmd.com/read/26514826/dengue-virus-infection-alters-post-transcriptional-modification-of-micrornas-in-the-mosquito-vector-aedes-aegypti
#3
Kayvan Etebari, Solomon Osei-Amo, Simon Phillip Blomberg, Sassan Asgari
Recent discoveries regarding the importance of isomiRs have increased our understanding of the regulatory complexities of the miRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infected Aedes aegypti mosquitoes with the major human pathogen dengue virus (DENV). We found that several specific isomiRs were significantly altered in their abundance patterns in response to DENV infection potentially affecting their target repertoire...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26434581/mirpro-a-novel-standalone-program-for-differential-expression-and-variation-analysis-of-mirnas
#4
Jieming Shi, Min Dong, Lei Li, Lin Liu, Agustin Luz-Madrigal, Panagiotis A Tsonis, Katia Del Rio-Tsonis, Chun Liang
Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and "arm switching" are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called "mirPRo" to quantify known miRNAs and predict novel miRNAs...
October 5, 2015: Scientific Reports
https://www.readbyqxmd.com/read/26166713/differential-and-coherent-processing-patterns-from-small-rnas
#5
Sachin Pundhir, Jan Gorodkin
Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm switching across different tissues is a well-known example of what we define as differential processing. Here, short RNAs from the nine cell lines of the ENCODE project, irrespective of their annotation status, were analyzed for genomic loci representing differential or coherent processing. We observed differential processing predominantly in RNAs annotated as miRNA, snoRNA or tRNA...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26075215/evolutionary-and-expression-analysis-of-mir-5p-and-mir-3p-at-the-mirnas-isomirs-levels
#6
Li Guo, Jiafeng Yu, Hao Yu, Yang Zhao, Shujie Chen, Changqing Xu, Feng Chen
We mainly discussed miR-#-5p and miR-#-3p under three aspects: (1) primary evolutionary analysis of human miRNAs; (2) evolutionary analysis of miRNAs from different arms across the typical 10 vertebrates; (3) expression pattern analysis of miRNAs at the miRNA/isomiR levels using public small RNA sequencing datasets. We found that no bias can be detected between the numbers of 5p-miRNA and 3p-miRNA, while miRNAs from miR-#-5p and miR-#-3p show variable nucleotide compositions. IsomiR expression profiles from the two arms are always stable, but isomiR expressions in diseased samples are prone to show larger degree of dispersion...
2015: BioMed Research International
https://www.readbyqxmd.com/read/26028588/variability-of-mirna-expression-during-the-differentiation-of-human-embryonic-stem-cells-into-retinal-pigment-epithelial-cells
#7
Zhidong Yuan, Suping Ding, Mingli Yan, Xiao Zhu, Lili Liu, Shuhua Tan, Yuanchang Jin, Yuandong Sun, Yufeng Li, Ting Huang
Embryonic stem cells (ESCs) and induced pluripotent stem cells can be induced to differentiate into retinal pigment epithelium (RPE). MiRNAs have been characterized and found playing important roles in the differentiation process of ESCs, but their length and sequence heterogeneity (isomiRs), and their non-canonical forms of miRNAs are underestimated or ignored. In this report, we found some non-canonical miRNAs (dominant isomiRs) in all differentiation stages, and 27 statistically significant editing sites were identified in 24 different miRNAs...
September 15, 2015: Gene
https://www.readbyqxmd.com/read/25692236/comprehensive-analysis-of-human-small-rna-sequencing-data-provides-insights-into-expression-profiles-and-mirna-editing
#8
Jing Gong, Yuliang Wu, Xiantong Zhang, Yifang Liao, Vusumuzi Leroy Sibanda, Wei Liu, An-Yuan Guo
MicroRNAs (miRNAs) play key regulatory roles in various biological processes and diseases. A comprehensive analysis of large scale small RNA sequencing data (smRNA-seq) will be very helpful to explore tissue or disease specific miRNA markers and uncover miRNA variants. Here, we systematically analyzed 410 human smRNA-seq datasets, which samples are from 24 tissue/disease/cell lines. We tested the mapping strategies and found that it was necessary to make multiple-round mappings with different mismatch parameters...
2014: RNA Biology
https://www.readbyqxmd.com/read/25420875/micrornas-of-two-medically-important-mosquito-species-aedes-aegypti-and-anopheles-stephensi
#9
W Hu, F Criscione, S Liang, Z Tu
MicroRNAs (miRNAs) are endogenous, single-stranded small RNAs that have important regulatory functions at the post-transcriptional level. In the present study, we characterize miRNAs in two divergent mosquito species, Aedes aegypti and Anopheles stephensi, through deep sequencing of small RNAs spanning all developmental stages. We discovered eight novel miRNAs in Ae. aegypti and 20 novel miRNAs in An. stephensi, which enabled the first systematic analysis of miRNA evolution in mosquitos. We traced the phylogenetic history of all miRNAs in both species and report a rate of 0...
April 2015: Insect Molecular Biology
https://www.readbyqxmd.com/read/25398902/ym500v2-a-small-rna-sequencing-smrna-seq-database-for-human-cancer-mirnome-research
#10
Wei-Chung Cheng, I-Fang Chung, Cheng-Fong Tsai, Tse-Shun Huang, Chen-Yang Chen, Shao-Chuan Wang, Ting-Yu Chang, Hsing-Jen Sun, Jeffrey Yung-Chuan Chao, Cheng-Chung Cheng, Cheng-Wen Wu, Hsei-Wei Wang
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2...
January 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25292026/evolution-of-the-mir-155-family-and-possible-targets-in-cancers-and-the-immune-system
#11
Guang-Bing Xie, Wei-Jia Liu, Zhi-Jun Pan, Tian-Yin Cheng, Chao Luo
The mir-155 family is not only involved in a diversity of cancers, but also as a regulator of the immune system. However, the evolutionary history of this family is still unclear. The present study indicates that mir-155 evolved independently with lineage-specific gain of miRNAs. In addition, arm switching has occurred in the mir-155 family, and alternative splicing could produce two different lengths of ancestral sequences, implying the alternative splicing can also drive evolution for intragenic miRNAs. Here we screened validated target genes and immunity- related proteins, followed by analyzation of the mir-155 family function by high-throughput methods like the gene ontology (GO) and Kyoto Eneyclopedin of Genes and Genemes (KEGG) pathway enrichment analysis...
2014: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/24997592/transcriptome-wide-analysis-of-microrna-expression-in-the-malaria-mosquito-anopheles-gambiae
#12
Inna Biryukova, Tao Ye, Elena Levashina
BACKGROUND: microRNAs (miRNAs) are a highly abundant class of small noncoding regulatory RNAs that post-transcriptionally regulate gene expression in multicellular organisms. miRNAs are involved in a wide range of biological and physiological processes, including the regulation of host immune responses to microbial infections. Small-scale studies of miRNA expression in the malaria mosquito Anopheles gambiae have been reported, however no comprehensive analysis of miRNAs has been performed so far...
2014: BMC Genomics
https://www.readbyqxmd.com/read/24120620/selected-isomir-expression-profiles-via-arm-switching
#13
Li Guo, Hui Zhang, Yang Zhao, Sheng Yang, Feng Chen
A mature miRNA may be generated from 5p or 3p arm of a hairpin precursor. The selection may be flexible via "arm switching". However, accumulating evidences suggest that both arms of many pre-miRNAs can yield mature functional miRNAs. Herein, we attempted to compare the isomiR expression profiles between the two arms through analyzing in-house and published small RNA deep sequencing datasets. Although many miR-#-5p and miR-#-3p have been reported as functional miRNAs, fewer miRNA pairs (11 and 6 pairs are collected in tumor and normal cells, respectively) are simultaneously identified as abundant miRNA species...
January 1, 2014: Gene
https://www.readbyqxmd.com/read/23905055/posttranscriptional-gene-regulation-novel-pathways-for-glucocorticoids-anti-inflammatory-action
#14
Cristiana Stellato
Posttranscriptional gene regulation (PTR) is a fundamental biological process that integrates with the master transcriptional control of gene expression, in ways that only in the last decade have been increasingly understood [1, 2]. While epigenetic and transcriptional events shape cell response qualitatively, deciding the pattern of gene expression to 'switch on or off' in response to endogenous or environmental triggers, the key task of PTR is to act as a 'rheostat' and rapidly adapt the cellular response by providing the appropriate amplitude and timing to the protein expression patterns [3, 4]...
May 2012: Translational Medicine @ UniSa
https://www.readbyqxmd.com/read/23407421/micrornaome-of-spodoptera-frugiperda-cells-sf9-and-its-alteration-following-baculovirus-infection
#15
Mohammad Mehrabadi, Mazhar Hussain, Sassan Asgari
MicroRNAs (miRNAs) as small non-coding RNAs play important roles in many biological processes such as development, cell signalling and immune response. Studies also suggest that miRNAs are important in host-virus interactions where the host limits virus infection by differentially expressing miRNAs that target essential viral genes. Here, we identified conserved and new miRNAs from Spodoptera frugiperda cells (Sf9) using a combination of deep sequencing and bioinformatics as well as experimental approaches...
June 2013: Journal of General Virology
https://www.readbyqxmd.com/read/23203880/ym500-a-small-rna-sequencing-smrna-seq-database-for-microrna-research
#16
Wei-Chung Cheng, I-Fang Chung, Tse-Shun Huang, Shih-Ting Chang, Hsing-Jen Sun, Cheng-Fong Tsai, Muh-Lii Liang, Tai-Tong Wong, Hsei-Wei Wang
MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 (http://ngs.ym.edu.tw/ym500/), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources...
January 2013: Nucleic Acids Research
https://www.readbyqxmd.com/read/22943187/a-comparative-study-of-small-rnas-in-toxoplasma-gondii-of-distinct-genotypes
#17
COMPARATIVE STUDY
Jielin Wang, Xiaolei Liu, Boyin Jia, Huijun Lu, Shuai Peng, Xianyu Piao, Nan Hou, Pengfei Cai, Jigang Yin, Ning Jiang, Qijun Chen
BACKGROUND: Toxoplasma gondii is an intracellular parasite with a significant impact on human health. Inside the mammalian and avian hosts, the parasite can undergo rapid development or remain inactive in the cysts. The mechanism that regulates parasite proliferation has not been fully understood. Small noncoding RNAs (sncRNA) such as microRNAs (miRNAs) are endogenous regulatory factors that can modulate cell differentiation and development. It is anticipated that hundreds of miRNAs regulate the expression of thousands of genes in a single organism...
2012: Parasites & Vectors
https://www.readbyqxmd.com/read/21212805/microrna-evolution-by-arm-switching
#18
Sam Griffiths-Jones, Jerome H L Hui, Antonio Marco, Matthew Ronshaugen
MicroRNAs (miRNAs) modulate transcript stability and translation. Functional mature miRNAs are processed from one or both arms of the hairpin precursor. The miR-100/10 family has undergone three independent evolutionary events that have switched the arm from which the functional miRNA is processed. The dominant miR-10 sequences in the insects Drosophila melanogaster and Tribolium castaneum are processed from opposite arms. However, the duplex produced by Dicer cleavage has an identical sequence in fly and beetle...
February 2011: EMBO Reports
https://www.readbyqxmd.com/read/20817720/functional-shifts-in-insect-microrna-evolution
#19
Antonio Marco, Jerome H L Hui, Matthew Ronshaugen, Sam Griffiths-Jones
MicroRNAs (miRNAs) are short endogenous RNA molecules that regulate gene expression at the posttranscriptional level and have been shown to play critical roles during animal development. The identification and comparison of miRNAs in metazoan species are therefore paramount for our understanding of the evolution of body plans. We have characterized 203 miRNAs from the red flour beetle Tribolium castaneum by deep sequencing of small RNA libraries. We can conclude, from a single study, that the Tribolium miRNA set is at least 15% larger than that in the model insect Drosophila melanogaster (despite tens of high-throughput sequencing experiments in the latter)...
2010: Genome Biology and Evolution
https://www.readbyqxmd.com/read/19755563/repertoire-and-evolution-of-mirna-genes-in-four-divergent-nematode-species
#20
Elzo de Wit, Sam E V Linsen, Edwin Cuppen, Eugene Berezikov
miRNAs are approximately 22-nt RNA molecules that play important roles in post-transcriptional regulation. We have performed small RNA sequencing in the nematodes Caenorhabditis elegans, C. briggsae, C. remanei, and Pristionchus pacificus, which have diverged up to 400 million years ago, to establish the repertoire and evolutionary dynamics of miRNAs in these species. In addition to previously known miRNA genes from C. elegans and C. briggsae we demonstrate expression of many of their homologs in C. remanei and P...
November 2009: Genome Research
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