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doRiNA: a database of RNA interactions in post-transcriptional regulation

Gerd Anders, Sebastian D. Mackowiak, Marvin Jens, Jonas Maaskola, Andreas Kuntzagk, Nikolaus Rajewsky, Markus Landthaler, Christoph Dieterich
2011 Nucleic Acids Research  
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA.  ...  We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators).  ...  ACKNOWLEDGEMENTS All authors wish to acknowledge fruitful discussions with members of the Berlin Institute for Medical Systems Biology.  ... 
doi:10.1093/nar/gkr1007 pmid:22086949 pmcid:PMC3245013 fatcat:lrnfop53cnc4thp2qjyweoh3z4

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

Kai Blin, Christoph Dieterich, Ricardo Wurmus, Nikolaus Rajewsky, Markus Landthaler, Altuna Akalin
2014 Nucleic Acids Research  
The expression of almost all genes in animals is subject to post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs (miRNAs).  ...  Especially, custom uploads is one of the key new features in doRiNA 2.0. To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API.  ...  ACKNOWLEDGEMENTS First of all, we would like to thank Dan Muntaneau for his support in setting up the web service for doRiNA 2.0.  ... 
doi:10.1093/nar/gku1180 pmid:25416797 pmcid:PMC4383974 fatcat:ak6sojlhofbujill3p4vltureu

A Brief Review of RNA-Protein Interaction Database Resources

Ying Yi, Yue Zhao, Yan Huang, Dong Wang
2017 Non-Coding RNA  
Here, we briefly review several widely used RNA-Protein interaction database resources developed in recent years to provide a guide of these databases.  ...  transcriptional and post-transcriptional regulatory network.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ncrna3010006 pmid:29657278 pmcid:PMC5832006 fatcat:sd3bw3sidvantame5nspva4flu

Distinct and Modular Organization of Protein Interacting Sites in Long Non-coding RNAs

Saakshi Jalali, Shrey Gandhi, Vinod Scaria
2018 Frontiers in Molecular Biosciences  
We also observe a positional preference of these RBPs across lncRNA and protein coding transcripts in addition to a significant co-occurrence of RBPs having similar functions, suggesting a modular organization  ...  The availability of genome-scale experimental datasets of RNA binding proteins (RBP) motivated us to understand the role of lncRNAs in terms of its interactions with these proteins.  ...  subclasses hence potentially contribute to a novel layer of regulatory interactions mediated through protein-RNA interactions in ncRNA transcripts.  ... 
doi:10.3389/fmolb.2018.00027 pmid:29670884 pmcid:PMC5893854 fatcat:k6ong7j6wbfzlko4fdovc4fyya

Computational Methods for CLIP-Seq Data Processing

Paula H. Reyes-Herrera, Elisa Ficarra
2014 Bioinformatics and Biology Insights  
RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level.  ...  One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action.  ...  It is worth noting that doRiNA gives a post-transcriptional regulation view from the target or the regulator (miRNAs or RBP) point of view.  ... 
doi:10.4137/bbi.s16803 pmid:25336930 pmcid:PMC4196881 fatcat:4ofmyacdlfh2tmzu5bt3j2yovi

Bcl11b is essential for licensing Th2 differentiation during helminth infection and allergic asthma

Kyle J. Lorentsen, Jonathan J. Cho, Xiaoping Luo, Ashley N. Zuniga, Joseph F. Urban, Liang Zhou, Raad Gharaibeh, Christian Jobin, Michael P. Kladde, Dorina Avram
2018 Nature Communications  
Acknowledgements We gratefully acknowledge all the colleagues of the Center for Epigenetics at UF for insightful discussions on mechanisms of transcriptional regulation. We thank Dr.  ...  Support: NIH grants R01AI067846, R21AI112492, and UF Gatorade Trust and UF Cancer Center to Dorina Avram, T32AI007110 to K.J.L. and A.N.Z., R01DK105562 to L.Z., and USDA/ARS 8042-32000-104-00D to J.F.U  ...  The Th2 LCR RHS V enhances Il4 transcription through interactions with the Il4 promoter, with GATA3 playing a central role in this process 10 .  ... 
doi:10.1038/s41467-018-04111-0 pmid:29700302 pmcid:PMC5920086 fatcat:q3ssnok3cjehfpibrwbnugwhgq

Tuning the engine

Erik Dassi, Alessandro Quattrone
2012 RNA Biology  
In the last years post-transcriptional regulation (PTR) of gene expression has been increasingly recognized to be a powerful and general determinant of the quantitative changes in proteomes, and therefore  ...  A number of dedicated resources and tools, including databases and predictive algorithms, have been proposed as bioinformatics aids for the study of this fundamental layer of gene expression regulation  ...  UTRdb/UTRsite, 12 AURA 13 and doRiNA 31 hold RBPrelated data as the two resources described above, but they differ in still keeping a broader perspective on post-transcriptional regulation.  ... 
doi:10.4161/rna.22035 pmid:22995832 pmcid:PMC3583852 fatcat:xnemykfmrbg2fn2ulhzllzq4w4

eIF6 over-expression increases the motility and invasiveness of cancer cells by modulating the expression of a critical subset of membrane-bound proteins

Michela Pinzaglia, Claudia Montaldo, Dorina Polinari, Mattei Simone, Anna La Teana, Marco Tripodi, Carmine Mancone, Paola Londei, Dario Benelli
2015 BMC Cancer  
role as an effector of enhanced migratory phenotype induced upon eIF6 over-expression; (iii) the variations in abundance observed for cdc42 protein occur at a post-transcriptional level; (iv) the increased  ...  We show that a number of membrane-associated proteins indeed vary in abundance upon eIF6 over-expression, and that the up-regulated proteins can be located within a functional network controlling cell  ...  This work was supported by grants to PL from the Istituto Pasteur-Fondazione Cenci Bolognetti project "Detecting and characterizing specialized ribosomes translating specific classes of mRNAs in Archaea  ... 
doi:10.1186/s12885-015-1106-3 pmid:25886394 pmcid:PMC4381359 fatcat:n7eryi3ae5hfzjacanv6xndula

Cis-acting elements in its 3′ UTR mediate post-transcriptional regulation of KRAS

Minlee Kim, Nicole Kogan, Frank J. Slack
2016 OncoTarget  
Multiple RNA-binding proteins and non-coding RNAs, such as microRNAs (miRNAs), are involved in post-transcriptional gene regulation through recognition motifs in the 3′ untranslated region (UTR) of their  ...  However, 3′ UTR-dependent regulation of KRAS expression has not been explored in detail.  ...  Both classes of trans-regulatory factors can play a pleiotropic role in post-transcriptional gene regulation.  ... 
doi:10.18632/oncotarget.7599 pmid:26930719 pmcid:PMC4914247 fatcat:37zt33rn4zfoji4tehbnc4r7m4

Advances in the Techniques for the Prediction of microRNA Targets

Hao Zheng, Rongguo Fu, Jin-Tao Wang, Qinyou Liu, Haibin Chen, Shi-Wen Jiang
2013 International Journal of Molecular Sciences  
MicroRNAs (miRNAs) are small, non-coding, endogenous RNA molecules that play important roles in a variety of normal and diseased biological processes by post-transcriptionally regulating the expression  ...  They can bind to target messenger RNA (mRNA) transcripts of protein-coding genes and negatively control their translation or cause mRNA degradation. miRNAs have been found to actively regulate a variety  ...  CLIPZ provides a database and analysis environment for experimentally determined binding sites of RNA-binding proteins [43] .  ... 
doi:10.3390/ijms14048179 pmid:23591837 pmcid:PMC3645737 fatcat:px7t4zox75hc7eo77e3urdpjeq

Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data

Fernando Carazo, Marian Gimeno, Juan A. Ferrer-Bonsoms, Angel Rubio
2019 BMC Genomics  
Splicing factors and other RNA-binding proteins (RBPs) play a key role in the regulation of splicing. The specific binding sites of an RBP can be measured using CLIP experiments.  ...  For this, we systematically collect, integrate and analyze more than 900 CLIP experiments stored in four CLIP databases: POSTAR2, CLIPdb, DoRiNA and StarBase.  ...  RNA-binding proteins (RBPs) bind to single-or double-stranded RNA and conduct post-transcriptional modifications of pre-mRNA (alternative splicing, mRNA stabilization, mRNA location, polyadenylation, translation  ... 
doi:10.1186/s12864-019-5900-1 pmid:31238884 pmcid:PMC6592009 fatcat:hg2zbav6ifa55grg55awjdziqe

CLIPdb: a CLIP-seq database for protein-RNA interactions

Yu-Cheng T Yang, Chao Di, Boqin Hu, Meifeng Zhou, Yifang Liu, Nanxi Song, Yang Li, Jumpei Umetsu, Zhi Lu
2015 BMC Genomics  
RNA-binding proteins (RBPs) play essential roles in gene expression regulation through their interactions with RNA transcripts, including coding, canonical non-coding and long non-coding RNAs.  ...  Description: Here, we constructed a database, CLIPdb, to describe RBP-RNA interactions based on 395 publicly available CLIP-seq data sets for 111 RBPs from four organisms: human, mouse, worm and yeast.  ...  We also thank Peipei Yin and Yuchuan Wang for their help in data collection.  ... 
doi:10.1186/s12864-015-1273-2 pmid:25652745 pmcid:PMC4326514 fatcat:m3peu5gjojbohjj5tuzxcfpz4y

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott (+8 others)
2017 Nucleic Acids Research  
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNAbased regulation is not taken into account.  ...  Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction  ...  Moreover, the authors acknowledge the support of many upstream developers that helped us to integrate their tools into the RNA workbench and accepted patches.  ... 
doi:10.1093/nar/gkx409 pmid:28582575 pmcid:PMC5570170 fatcat:qhl5knnpazd3noomvloekfefsy

Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs

Alexandra Weyrich, Marie Jeschek, Katharina T. Schrapers, Dorina Lenz, Tzu Hung Chung, Kathrin Ruebensam, Sermin Yasar, Markus Schneemann, Sylvia Ortmann, Katarina Jewgenow, Jörns Fickel
2020 Postprints der Universität Potsdam: Mathematisch-Naturwissenschaftliche Reihe  
Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.  ...  Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift').  ...  Acknowledgements We thank Prof Trillmich and Dr Anja Guenther from the University of Bielefeld for the provision of C. aperea and the staff of the IZW-field research station for their support.  ... 
doi:10.25932/publishup-46003 fatcat:yctdguq4xbaixcc7oywxftmt5q

Do Molecular Profiles of Primary Versus Metastatic Radioiodine Refractory Differentiated Thyroid Cancer Differ?

Cristiane J. Gomes-Lima, Leila Shobab, Di Wu, Dorina Ylli, Athanasios Bikas, Matthew McCoy, Rebecca Feldman, Wen Lee, Sarika N. Rao, Kirk Jensen, Vasily Vasko, Luiz Claudio Castro (+3 others)
2021 Frontiers in Endocrinology  
The molecular profiling of paired tumors was performed with a panel of 592 genes for Next Generation Sequencing, RNA-sequencing, and immunohistochemistry.  ...  The present study compared the molecular profile of paired tumor specimens (primary tumor/metastatic sites) from patients with radioiodine refractory DTC in order to gain insight into a possible basis  ...  of Interacting Genes/Proteins) (21) .  ... 
doi:10.3389/fendo.2021.623182 pmid:33716974 pmcid:PMC7949910 fatcat:5rjjyfsk7nhybolensc73p3b54
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