Read by QxMD icon Read

miRNA target recognition identification

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
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
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
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
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
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
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
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
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"