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miRNA target recognition identification

Max Hübner, Pedro A F Galante, Simone Kreth, Ludwig Christian Hinske
MiRNAs control gene expression via recognition of specific sequences in the 3' untranslated region of target genes, leading to mRNA degradation and consequently translational repression. The regulatory impact of miRNAs does not only depend on their expression levels, but also on their targets' mRNA configuration. Via alternative polyadenylation mRNA isoforms are created that may or may not contain the respective miRNA target sequence, turning the regulatory between these two on or off. In the following article, we describe our protocol on how to combine a bioinformatics evaluation of a potential miRNA-target gene interaction using the public web framework miRIAD with 5' rapid amplification of cDNA ends (5'-RACE) in order to explore differential gene regulation by miRNAs through alternative polyadenylation...
2018: Methods in Molecular Biology
Bing Han, Jie Chao, Honghong Yao
The emerging recognition of the functional roles of circular RNAs (circRNAs) has given rise to a new perspective regarding our understanding of cellular physiology and disease pathogenesis. Unlike linear RNAs, circRNAs are covalently closed continuous loops that act as gene regulators in mammals, and their sequence composition determines the mode of circRNA biogenesis. The availability and integrated use of advanced genome analysis platforms have allowed the identification of a large number of these molecules...
February 14, 2018: Pharmacology & Therapeutics
Isabella Pentimone, Ricardo Lebrón, Michael Hackenberg, Laura C Rosso, Mariantonietta Colagiero, Franco Nigro, Aurelio Ciancio
The molecular mechanisms active during the endophytic phase of the fungus Pochonia chlamydosporia are still poorly understood. In particular, few data are available on the links between the endophyte and the root response, as modulated by noncoding small RNAs. In this study, we describe the microRNAs (miRNAs) that are differentially expressed (DE) in the roots of tomato, colonized by P. chlamydosporia. A genome-wide NGS expression profiling of small RNAs in roots, either colonized or not by the fungus, showed 26 miRNAs upregulated in inoculated roots...
November 5, 2017: Applied Microbiology and Biotechnology
Yiming Zhang, Ran Kang, Wenrong Liu, Yalan Yang, Ruofan Ding, Qingqing Huang, Junhua Meng, Lili Xiong, Zhiyun Guo
Recent studies have indicated that long non-coding RNAs (lncRNAs) and mRNA function as competing endogenous RNAs (ceRNAs) that compete to bind to shared microRNA (miRNA) recognition elements (MREs) to perform specific biological functions during tumorigenesis. The tumor suppressor p53 is a master regulator of cancer-related biological processes by acting as a transcription factor to regulate target genes including miRNA and lncRNA. However, the mechanism in human hepatocellular carcinoma and whether p53-mediated RNA targets could form ceRNA network remain unclear...
2017: International Journal of Biological Sciences
Kourosh Zarringhalam, Yvonne Tay, Prajna Kulkarni, Assaf C Bester, Pier Paolo Pandolfi, Rahul V Kulkarni
Regulation by microRNAs (miRNAs) and modulation of miRNA activity are critical components of diverse cellular processes. Recent research has shown that miRNA-based regulation of the tumor suppressor gene PTEN can be modulated by the expression of other miRNA targets acting as competing endogenous RNAs (ceRNAs). However, the key sequence-based features enabling a transcript to act as an effective ceRNA are not well understood and a quantitative model associating statistical significance to such features is currently lacking...
August 10, 2017: Scientific Reports
Jing Wang, Liushuai Hua, Junfeng Chen, Jiaqing Zhang, Xianxiao Bai, Binwen Gao, Congjun Li, Zhihai Shi, Weidong Sheng, Yuan Gao, Baosong Xing
BACKGROUND: Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular systems and metabolic features. RESULTS: We identified lncRNAs in subcutaneous adipose tissue by deep RNA-sequencing using the intact and castrated Huainan male pigs...
July 19, 2017: BMC Genomics
Noam Perry, Marina Volin, Hila Toledano
Regulation of gene expression governs all aspects of the lifespan of the organism, such as embryonic development, stem cell differentiation, reproduction and aging. Among the most important regulators of these extremely complex processes are microRNAs (miRNAs), small non-coding RNAs that repress gene expression by binding to primary sequences on the mRNA of their target. Theoretically, the mere existence of a miRNA recognition sequence on a given mRNA is sufficient to generate a functional response. Since these short sequences are abundant, one miRNA can potentially bind to multiple targets, thus generating endless possible biological outcomes...
2017: International Journal of Developmental Biology
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
Matthew G Costales, Christopher L Haga, Sai Pradeep Velagapudi, Jessica L Childs-Disney, Donald G Phinney, Matthew D Disney
A hypoxic state is critical to the metastatic and invasive characteristics of cancer. Numerous pathways play critical roles in cancer maintenance, many of which include noncoding RNAs such as microRNA (miR)-210 that regulates hypoxia inducible factors (HIFs). Herein, we describe the identification of a small molecule named Targapremir-210 that binds to the Dicer site of the miR-210 hairpin precursor. This interaction inhibits production of the mature miRNA, derepresses glycerol-3-phosphate dehydrogenase 1-like enzyme (GPD1L), a hypoxia-associated protein negatively regulated by miR-210, decreases HIF-1α, and triggers apoptosis of triple negative breast cancer cells only under hypoxic conditions...
February 27, 2017: Journal of the American Chemical Society
Chiara De Santi, Sebastian Vencken, Jonathon Blake, Bettina Haase, Vladimir Benes, Federica Gemignani, Stefano Landi, Catherine M Greene
MicroRNAs (miRNAs) are small non-coding RNAs that regulate mRNA expression mainly by silencing target transcripts via binding to miRNA recognition elements (MREs) in the 3'untranslated region (3'UTR). The identification of bona fide targets is challenging for researchers working on the functional aspect of miRNAs. Recently, we developed a method (miR-CATCH) based on biotinylated DNA antisense oligonucleotides that capture the mRNA of interest and facilitates the characterisation of miRNAs::mRNA interactions in a physiological cellular context...
2017: PloS One
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...
2017: Current Vascular Pharmacology
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...
March 16, 2016: Scientific Reports
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
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
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
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
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
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
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
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
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