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miRNA target recognition identification

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https://www.readbyqxmd.com/read/27633456/the-mir-221-222-cluster-is-a-key-player-in-vascular-biology-via-the-fine-tuning-of-endothelial-cell-physiology
#1
Tanja Celic, Valérie Metzinger-Le Meuth, Isabelle Six Ziad A Massy, Laurent Metzinger
The discovery of small RNAs has shed new light on microRNA (mRNA) regulation and a range of biological processes. The recognition that miRNAs-221 and -222 are sensitive regulators in the endothelium may enable the identification of novel biomarkers and therapeutic targets. Given that endothelial dysfunction precedes the development of atherosclerosis and contributes to the development of cardiovascular damage, circulating miRNAs produced by endothelial cells (ECs) are putative biomarkers for a wide range of cardiovascular diseases...
September 14, 2016: Current Vascular Pharmacology
https://www.readbyqxmd.com/read/26980315/an-integrated-mirna-functional-screening-and-target-validation-method-for-organ-morphogenesis
#2
Ivan T Rebustini, Maryann Vlahos, Trevor Packer, Maria A Kukuruzinska, Richard L Maas
The relative ease of identifying microRNAs and their increasing recognition as important regulators of organogenesis motivate the development of methods to efficiently assess microRNA function during organ morphogenesis. In this context, embryonic organ explants provide a reliable and reproducible system that recapitulates some of the important early morphogenetic processes during organ development. Here we present a method to target microRNA function in explanted mouse embryonic organs. Our method combines the use of peptide-based nanoparticles to transfect specific microRNA inhibitors or activators into embryonic organ explants, with a microRNA pulldown assay that allows direct identification of microRNA targets...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26950183/tiny-giants-of-gene-regulation-experimental-strategies-for-microrna-functional-studies
#3
REVIEW
Bruno R Steinkraus, Markus Toegel, Tudor A Fulga
The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes...
May 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/26743510/improving-microrna-target-prediction-by-modeling-with-unambiguously-identified-microrna-target-pairs-from-clip-ligation-studies
#4
Xiaowei Wang
MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that are extensively involved in many physiological and disease processes. One major challenge in miRNA studies is the identification of genes targeted by miRNAs. Currently, most researchers rely on computational programs to initially identify target candidates for subsequent validation. Although considerable progress has been made in recent years for computational target prediction, there is still significant room for algorithmic improvement...
May 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26662994/computational-prediction-of-microrna-targets
#5
Alessandro Laganà
Computational prediction of microRNA (miRNA) targets is a fundamental step towards the characterization of miRNA function and the understanding of their role in disease. A single miRNA can regulate hundreds of different gene transcripts through partial sequence complementarity and a single gene may be regulated by several miRNAs acting cooperatively. The remarkable advances made in recent years have allowed the identification of key features for functional miRNA binding sites. A plethora of prediction tools are now available, but their accuracies remain rather poor, as miRNA target recognition has revealed itself to be a very complex and dynamic mechanism, still only partially understood...
2015: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/26463386/capture-and-identification-of-mirna-targets-by-biotin-pulldown-and-rna-seq
#6
Shen Mynn Tan, Judy Lieberman
MicroRNAs (miRNAs) are small noncoding RNAs that regulate the stability and expression of target RNAs in a sequence-dependent manner. Identifying miRNA-regulated genes is key to understanding miRNA function. Here, we describe an unbiased biochemical pulldown method to identify with high-specificity miRNA targets. Regulated transcripts are enriched in streptavidin-captured mRNAs that bind to a transfected biotinylated miRNA mimic. The method is relatively simple, does not involve cross-linking and can be performed with only a million cells...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26252447/expression-of-microrna%C3%A2-26b-and-identification-of-its-target-gene-epha2-in-pituitary-tissues-in-yanbian-cattle
#7
Bao Yuan, Wang-Yang Yu, Li-Sheng Dai, Yan Gao, Yu Ding, Xian-Feng Yu, Jian Chen, Jia-Bao Zhang
microRNAs (miRNAs/miRs) are a class of single‑stranded non‑coding RNA molecules of 19‑24 nucleotides (nt) in length. They are widely expressed in animals, plants, bacteria and viruses. Via specific mRNA complementary pairing of target genes, miRNAs are able to regulate the expression of mRNA levels or inhibit protein translation following transcription. miRNA expression has a time‑ and space specificity, and it is involved in cell proliferation and differentiation, apoptosis, development, tumor metastasis occurrence and other biological processes...
October 2015: Molecular Medicine Reports
https://www.readbyqxmd.com/read/26086375/na%C3%A3-ve-bayes-classifier-predicts-functional-microrna-target-interactions-in-colorectal-cancer
#8
Raheleh Amirkhah, Ali Farazmand, Shailendra K Gupta, Hamed Ahmadi, Olaf Wolkenhauer, Ulf Schmitz
Alterations in the expression of miRNAs have been extensively characterized in several cancers, including human colorectal cancer (CRC). Recent publications provide evidence for tissue-specific miRNA target recognition. Several computational methods have been developed to predict miRNA targets; however, all of these methods assume a general pattern underlying these interactions and therefore tolerate reduced prediction accuracy and a significant number of false predictions. The motivation underlying the presented work was to unravel the relationship between miRNAs and their target mRNAs in CRC...
August 2015: Molecular BioSystems
https://www.readbyqxmd.com/read/25972521/atmirnet-a-web-based-resource-for-reconstructing-regulatory-networks-of-arabidopsis-micrornas
#9
Chia-Hung Chien, Yi-Fan Chiang-Hsieh, Yi-An Chen, Chi-Nga Chow, Nai-Yun Wu, Ping-Fu Hou, Wen-Chi Chang
Compared with animal microRNAs (miRNAs), our limited knowledge of how miRNAs involve in significant biological processes in plants is still unclear. AtmiRNET is a novel resource geared toward plant scientists for reconstructing regulatory networks of Arabidopsis miRNAs. By means of highlighted miRNA studies in target recognition, functional enrichment of target genes, promoter identification and detection of cis- and trans-elements, AtmiRNET allows users to explore mechanisms of transcriptional regulation and miRNA functions in Arabidopsis thaliana, which are rarely investigated so far...
2015: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/25813044/submirine-assessing-variants-in-microrna-targets-using-clinical-genomic-data-sets
#10
Evan K Maxwell, Joshua D Campbell, Avrum Spira, Andreas D Baxevanis
MicroRNAs (miRNAs) regulate gene expression by binding to partially complementary sequences on target mRNA transcripts, thereby causing their degradation, deadenylation, or inhibiting their translation. Genomic variants can alter miRNA regulation by modifying miRNA target sites, and multiple human disease phenotypes have been linked to such miRNA target site variants (miR-TSVs). However, systematic genome-wide identification of functional miR-TSVs is difficult due to high false positive rates; functional miRNA recognition sequences can be as short as six nucleotides, with the human genome encoding thousands of miRNAs...
April 30, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25612681/micrornas-and-targeted-therapies-in-non-small-cell-lung-cancer-minireview
#11
REVIEW
Carmelo Tibaldi, Armida D'Incecco, Alessandro Lagana
The discovery of driver oncogene alterations in non-small cell lung cancer (NSCLC), such as EGFR, EML4-ALK, MET and RAS, as well as the identification of their specific targeted inhibitors have led to new opportunities for treatment of this tumor. Drug resistance, intrinsic or acquired, represents the major cause of failure of novel biological agents. MicroRNAs (miRNAs) are a family of small non-coding RNAs that can silence their cognate target genes by specifically binding mRNAs or inhibiting their translation...
2015: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/25472924/micrornaome-of-porcine-conceptuses-and-trophoblasts-expression-profile-of-micrornas-and-their-potential-to-regulate-genes-crucial-for-establishment-of-pregnancy
#12
Kamil Krawczynski, Joanna Najmula, Stefan Bauersachs, Monika M Kaczmarek
Tightly coordinated, reciprocal embryo-maternal interactions affect gene expression during early pregnancy. Recently, microRNAs (miRNAs) have emerged as new players in the fine tuning of embryo development and implantation in mammals via posttranscriptional gene regulation mechanisms. Here, we integrated transcriptomic and computational approaches to profile miRNAs and miRNA synthesis and transport-related genes at different developmental stages of porcine conceptuses and trophoblast during early pregnancy in the pig...
January 2015: Biology of Reproduction
https://www.readbyqxmd.com/read/25424593/emerging-strategies-for-rna-interference-rnai-applications-in-insects
#13
REVIEW
Raja Sekhar Nandety, Yen-Wen Kuo, Shahideh Nouri, Bryce W Falk
RNA interference (RNAi) in insects is a gene regulatory process that also plays a vital role in the maintenance and in the regulation of host defenses against invading viruses. Small RNAs determine the specificity of the RNAi through precise recognition of their targets. These small RNAs in insects comprise small interfering RNAs (siRNAs), micro RNAs (miRNAs) and Piwi interacting RNAs (piRNAs) of various lengths. In this review, we have explored different forms of the RNAi inducers that are presently in use, and their applications for an effective and efficient fundamental and practical RNAi research with insects...
2015: Bioengineered
https://www.readbyqxmd.com/read/25326327/global-identification-of-target-recognition-and-cleavage-by-the-microprocessor-in-human-es-cells
#14
Youngmo Seong, Do-Hwan Lim, Augustine Kim, Jae Hong Seo, Young Sik Lee, Hoseok Song, Young-Soo Kwon
The Microprocessor plays an essential role in canonical miRNA biogenesis by facilitating cleavage of stem-loop structures in primary transcripts to yield pre-miRNAs. Although miRNA biogenesis has been extensively studied through biochemical and molecular genetic approaches, it has yet to be addressed to what extent the current miRNA biogenesis models hold true in intact cells. To address the issues of in vivo recognition and cleavage by the Microprocessor, we investigate RNAs that are associated with DGCR8 and Drosha by using immunoprecipitation coupled with next-generation sequencing...
November 10, 2014: Nucleic Acids Research
https://www.readbyqxmd.com/read/25242049/the-functional-scope-of-plant-microrna-mediated-silencing
#15
REVIEW
Junyan Li, Marlene Reichel, Yanjiao Li, Anthony A Millar
Deep sequencing has identified a complex set of plant miRNAs that potentially regulates many target genes of high complementarity. Furthermore, the discovery that many plant miRNAs work through a translational repression mechanism, along with the identification of noncanonical targets, has encouraged bioinformatic searches with less stringent parameters, identifying an even wider range of potential targets. Together, these findings suggest that any given plant miRNA family may regulate a highly diverse set of mRNAs...
December 2014: Trends in Plant Science
https://www.readbyqxmd.com/read/25240886/identification-and-validation-of-mirna-target-sites-within-nontraditional-mirna-targets
#16
Scott T Younger, David R Corey
miRNAs are endogenous small RNAs that regulate gene expression through recognition of complementary RNA sequences. While miRNAs have generally been understood to repress gene expression posttranscriptionally through recognition of 3'-untranslated regions (3'-UTRs) of mRNA transcripts, they have the potential to target additional classes of RNAs. Understanding the expanding pool of potential miRNA targets has been hindered by the lack of tools for predicting target sites within these RNAs. Here, the principles for developing computational algorithms for identifying putative miRNA target sites outside of mRNA are discussed...
2015: Methods in Molecular Biology
https://www.readbyqxmd.com/read/25201113/identification-of-mirnas-and-their-targets-in-c-elegans
#17
REVIEW
Sarah Azoubel Lima, Amy E Pasquinelli
MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional regulation of specific target genes. Since their discovery in Caenorhabditis elegans, they have been associated with the control of virtually all biological processes and are known to play major roles in development and cellular homeostasis. Yet the biological roles of most miRNAs remain to be fully known. Furthermore, the precise rules by which miRNAs recognize their targets and mediate gene silencing are still unclear. Systematic identification of miRNAs and of the RNAs they regulate is essential to close these knowledge gaps...
2014: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/25131211/sequencing-of-captive-target-transcripts-identifies-the-network-of-regulated-genes-and-functions-of-primate-specific-mir-522
#18
Shen Mynn Tan, Rory Kirchner, Jingmin Jin, Oliver Hofmann, Larry McReynolds, Winston Hide, Judy Lieberman
Identifying microRNA (miRNA)-regulated genes is key to understanding miRNA function. However, many miRNA recognition elements (MREs) do not follow canonical "seed" base-pairing rules, making identification of bona fide targets challenging. Here, we apply an unbiased sequencing-based systems approach to characterize miR-522, a member of the oncogenic primate-specific chromosome 19 miRNA cluster, highly expressed in poorly differentiated cancers. To identify miRNA targets, we sequenced full-length transcripts captured by a biotinylated miRNA mimic...
August 21, 2014: Cell Reports
https://www.readbyqxmd.com/read/24717361/macros-in-microrna-target-identification-a-comparative-analysis-of-in-silico-in-vitro-and-in-vivo-approaches-to-microrna-target-identification
#19
REVIEW
Shikha Tarang, Michael D Weston
MicroRNAs (miRNAs) are short RNA molecules that modulate post-transcriptional gene expression by partial or incomplete base-pairing to the complementary sequences on their target genes. Sequence-based miRNA target gene recognition enables the utilization of computational methods, which are highly informative in identifying a subset of putative miRNA targets from the genome. Subsequently, single miRNA-target gene binding is evaluated experimentally by in vitro assays to validate and quantify the transcriptional or post-transcriptional effects of miRNA-target gene interaction...
2014: RNA Biology
https://www.readbyqxmd.com/read/24645599/-microrna-target-predicition-based-on-svm-and-the-optimized-feature-set
#20
Baowen Wang, Xiaoyang Qi, Changwu Wang, Wenyuan Liu, Yali Si
MicroRNA (miRNA) is a family of endogenous single-stranded RNA about 22 nucleotides in length. Through targeting 3' UTR of message RNA (mRNA), they play important roles in post-transcriptional regulatory functions. For further research of miRNA function, the identification of more miRNA positive targets is needed urgently. Aiming at the high-dimensional small sample data sets in miRNA target prediction, an algorithm of eliminating redundant features is proposed based on v-SVM in this paper, and classification and features selection are also fused...
December 2013: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
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