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Differential Repression of Alternative Transcripts: A Screen for miRNA Targets

Matthieu Legendre, William Ritchie, Fabrice Lopez, Daniel Gautheret
2006 PLoS Computational Biology  
Citation: Legendre M, Ritchie W, Lopez F, Gautheret D (2006) Differential repression of alternative transcripts: A screen for miRNA targets. PLoS Comput Biol 2(5): e43.  ...  This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.  ...  Samuel Granjeaud for their critical reading of the manuscript. Author contributions. ML, WR, and DG conceived and designed the experiments. ML, WR, and FL performed the experiments.  ... 
doi:10.1371/journal.pcbi.0020043 pmid:16699595 pmcid:PMC1458965 fatcat:u3of6wzi3bhobo4nim22s6zj44

Differential repression of alternative transcripts: a screen for miRNA targets

matthieu legendre, Willam Ritchie, Fabrice Lopez, Daniel Gautheret
2005 PLoS Computational Biology  
Citation: Legendre M, Ritchie W, Lopez F, Gautheret D (2006) Differential repression of alternative transcripts: A screen for miRNA targets. PLoS Comput Biol 2(5): e43.  ...  This analysis can help identify target-miRNA couples that went undetected in previous screens, but it may also reveal targets for other types of regulatory factors.  ...  Samuel Granjeaud for their critical reading of the manuscript. Author contributions. ML, WR, and DG conceived and designed the experiments. ML, WR, and FL performed the experiments.  ... 
doi:10.1371/journal.pcbi.0020043.eor fatcat:6bggtsetgvbipojhv6zqwmzjwm

Transcriptional corepressors in cancer

Petros D. Grivas, Athanasios G. Papavassiliou
2012 Cancer  
The normal cell transcriptional process entails a high degree of combinatorial effects and time-dependent "flexibility" to translate cellular signaling into differential gene expression levels.  ...  Alterations of the expression level and/or function of transcriptional corepressors have been reported in a wide range of human cancers; thus, corepressors may present rational therapeutic targets as well  ...  factor CoREST forms a complex with REST to repress target-gene transcription and acts as a docking platform for the assemblage of HDAC1/HDAC2, BRCA2-associated factor 35 (BRAF35), BRAF35-HDAC complex  ... 
doi:10.1002/cncr.27908 pmid:23224952 fatcat:cnn4ajxvv5ggloip7w34drt4fi

Regulation of a TrkB Alternative Transcript by microRNAs

Jenny Wong
2014 Dementia and Geriatric Cognitive Disorders Extra  
In this study, the focus was placed on TrkB-Shc, a neuronspecific transcript, to determine if microRNAs (miRNAs) play a role in TrkB-Shc regulation.  ...  In this study, the focus was placed on TrkB-Shc, a neuron-specific transcript, to determine if microRNAs (miRNAs) play a role in TrkB-Shc regulation.  ...  Disclosure Statement There are no conflicts of interest and financial disclosures.  ... 
doi:10.1159/000365917 pmid:25337079 pmcid:PMC4202609 fatcat:vj32yyfvxne35e4j27ljnpelwm

Transcriptional and Post-Transcriptional Mechanisms of the Development of Neocortical Lamination

Tatiana Popovitchenko, Mladen-Roko Rasin
2017 Frontiers in Neuroanatomy  
Indeed, recent screens have uncovered post-transcriptional mechanisms as being integral regulatory mechanisms to neocortical development.  ...  Transcription factors are dynamic proteins because of the cohort of downstream factors that they regulate.  ...  While we sought to provide a general review of laminar mechanisms, we extend our apology to those who we do not cite due to space limitations.  ... 
doi:10.3389/fnana.2017.00102 pmid:29170632 pmcid:PMC5684109 fatcat:xivh7ukbbvdlpjnesmn37gzela

Transcriptional control of cancer metastasis

Brian Ell, Yibin Kang
2013 Trends in Cell Biology  
We focus here on recent research advances in transcriptional control of metastasis and highlight the therapeutic potential of targeting such transcriptional regulatory networks.  ...  Transcriptional regulation is an essential component of tumor progression and metastasis.  ...  Research in our laboratory is supported by grants from the National Institutes of Health (R01CA134519 and R01CA141062), Department of Defense (BC123187), Komen for the Cure, the Brewster Foundation and  ... 
doi:10.1016/j.tcb.2013.06.001 pmid:23838335 pmcid:PMC3815486 fatcat:rjdxrh3hcng57kc3toehabjfiy

Beyond Transcription: Fine-Tuning of Circadian Timekeeping by Post-Transcriptional Regulation

Julieta Lisa Mateos, Maria José de Leone, Jeanette Torchio, Marlene Reichel, Dorothee Staiger
2018 Genes  
The clockwork of this molecular timer is made up of clock proteins that regulate transcription of their own genes with a 24 h rhythm.  ...  On top of the transcriptional regulation by the clock, circadian rhythms in mRNAs rely in large parts on post-transcriptional regulation, including alternative pre-mRNA splicing, mRNA degradation, and  ...  Acknowledgments: The open access was supported by the open access fund of Bielefeld University. Conflicts of Interest: The authors declare that they have no competing interests.  ... 
doi:10.3390/genes9120616 fatcat:qlfnukjygjc3fhka6z6fimupoe

Transcriptional, post-transcriptional and epigenetic control of porcine oocyte maturation and embryogenesis

R.S. Prather, J.W. Ross, Isom S Clay, J.A. Green
2020 Bioscientifica Proceedings  
vitro, and to provide markers for predicting developmental competence of the embryo.  ...  Methylation of DNA and modification of histones regulate transcription, and mechanisms such as ubiquitinization, autophagy and microRNAs regulate development post-transcriptionally.  ...  , 2004-35205-15549, 2008-35205-05309), and Food for the 219 Century at the University of Missouri.  ... 
doi:10.1530/biosciprocs.18.0017 fatcat:d75kkjx7jrfcvoxgfvslfoehmy

Natural antisense transcripts

O. Khorkova, A. J. Myers, J. Hsiao, C. Wahlestedt
2014 Human Molecular Genetics  
Roughly defined as non-coding regulatory RNA transcribed from the opposite strand of a coding gene locus, NATs are proving to be a heterogeneous group with high potential for therapeutic application.  ...  These discoveries, fueled by the achievements of the FANTOM, and later GENCODE and ENCODE consortia, led to the recognition of the important regulatory roles of natural antisense transcripts (NATs) arising  ...  (22) found weak positive correlation in expression for coding/non-coding gene pairs at bidirectional promoters and for sense-antisense transcript pairs during a 120-h time course of differentiation  ... 
doi:10.1093/hmg/ddu207 pmid:24838284 pmcid:PMC4170719 fatcat:bbnx7447tzdm3fiskyeo4mcsfm

High-throughput discovery of post-transcriptional cis-regulatory elements

Erin M. Wissink, Elizabeth A. Fogarty, Andrew Grimson
2016 BMC Genomics  
We screened many thousands of short random sequences for their regulatory potential.  ...  Results: We created a high-throughput cell-based screen that enables identification of functional post-transcriptional 3′UTR regulatory elements.  ...  Because miRNAs increase the decay rate of their mRNA targets [31] , this 8mer's transcript is expected to be destabilized.  ... 
doi:10.1186/s12864-016-2479-7 pmid:26941072 pmcid:PMC4778349 fatcat:adrb2cqedzddplfomtkxxblihy

Understanding neuronal connectivity through the post-transcriptional toolkit

C. M. Loya, D. Van Vactor, T. A. Fulga
2010 Genes & Development  
It was shown that, of the FMRP-associated miRNAs, miR-132 and miR-125b differentially affect dendritic spine morphology in an FMRP-dependent fashion.  ...  In addition, negative regulation of NMDA receptor subunit NR2A involved both FMRP activity and miR-125b targeting of the NR2A 3'UTR.  ...  A recent study using a MARCM-based forward genetic screen in Drosophila identified the miRNA processing proteins pasha/DGRC8 and Dicer1 as crucial components in the establishment of wiring specificity  ... 
doi:10.1101/gad.1907710 pmid:20360381 pmcid:PMC2849119 fatcat:a3cvxavvmvhbrjhh6c4mklryi4

Post-transcriptional control of miRNA biogenesis

Gracjan Michlewski, Javier F. Cáceres
2018 RNA: A publication of the RNA Society  
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression.  ...  In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and  ...  ACKNOWLEDGMENTS We thank Fiona Haward (MRC HGU) for comments on this manuscript. We thank Craig Nicol (MRC HGU) for help with preparing the figures.  ... 
doi:10.1261/rna.068692.118 pmid:30333195 fatcat:ticcrkaczfeanan5ar6q2swwhy

A human 3′UTR clone collection to study post-transcriptional gene regulation

Kasuen Kotagama, Cody S. Babb, Justin M. Wolter, Ronan P. Murphy, Marco Mangone
2015 BMC Genomics  
We demonstrate the feasibility of the h3′ UTRome library by screening a panel of 87 3′UTRs for targeting by two miRNAs: let-7c, which is implicated in tumorigenesis, and miR-221, which is implicated in  ...  3′untranslated regions (3′UTRs) are poorly understood portions of eukaryotic mRNAs essential for post-transcriptional gene regulation.  ...  We thank Amanda Phomsavanah, Dasia Garcia and Christina Nguyen for help with the cloning of miR-221 and a portion of the clone library, and Thyu-Duyen Nguyen for suggestions and advice during the preparation  ... 
doi:10.1186/s12864-015-2238-1 pmid:26645212 pmcid:PMC4673713 fatcat:r7mqtrbnbfef5ebvqol7e4symy

The interplay between transcription factors and microRNAs in genome-scale regulatory networks

Natalia J. Martinez, Albertha J. M. Walhout
2009 Bioessays  
Differential gene expression is achieved through complex regulatory networks that are controlled in part by two types of trans-regulators: transcription factors (TFs) and microRNAs (miRNAs).  ...  TFs bind to cis-regulatory DNA elements that are often located in or near their target genes, while miRNAs hybridize to cis-regulatory RNA elements mostly located in the 3′ untranslated region of their  ...  Acknowledgments We thank members of the Walhout laboratory, Job Dekker, and Michael J. Krashes for comments and critical reading of the manuscript.  ... 
doi:10.1002/bies.200800212 pmid:19274664 pmcid:PMC3118512 fatcat:ozguxe7ivbczvmq3pfw6kavzhm

Post-transcriptional small RNA pathways in plants: mechanisms and regulations

H. Vaucheret
2006 Genes & Development  
They target endogenous mRNAs for cleavage and translational repression in plants and animals, and protect both plant and animal cells against virus infection through an RNA-based immune system.  ...  For a long period of time, DNA, the support of heredity, and proteins, the actors of the cellular machinery, have been considered the most important components of biological systems.  ...  Acknowledgments I thank Allison Mallory for critical reading of the manuscript and David Bartel and members of the Vaucheret and Bartel laboratories for fruitful discussions.  ... 
doi:10.1101/gad.1410506 pmid:16600909 fatcat:llvp4j7lxvglrn3te6fsulal5e
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