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  • 1
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    A parsimonious model for gene regulation by miRNAs (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-02-05
    Description: MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) act with the Argonaute family of proteins to regulate target messenger RNAs (mRNAs) posttranscriptionally. SiRNAs typically induce endonucleolytic cleavage of mRNA with near-perfect complementarity. For targets with less complementarity, both translational repression and mRNA destabilization mechanisms have been implicated in miRNA-mediated gene repression, although the timing, coupling, and relative importance of these events have not been determined. Here, we review gene-specific and global approaches that probe miRNA function and mechanism, looking for a unifying model. More systematic analyses of the molecular specificities of the core components coupled with analysis of the relative timing of the different events will ultimately shed light on the mechanism of miRNA-mediated repression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955125/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955125/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djuranovic, Sergej -- Nahvi, Ali -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):550-3. doi: 10.1126/science.1191138.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI), Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292970" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Eukaryotic Initiation Factors/chemistry/metabolism ; *Gene Expression Regulation ; Humans ; MicroRNAs/*genetics/metabolism ; *Models, Genetic ; *Protein Biosynthesis ; *RNA Interference ; *RNA Stability ; RNA, Messenger/genetics/*metabolism ; Ribonucleoproteins/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    The genome of Tetranychus urticae reveals herbivorous pest adaptations (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-11-25
    Description: The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Grbic, Miodrag -- Van Leeuwen, Thomas -- Clark, Richard M -- Rombauts, Stephane -- Rouze, Pierre -- Grbic, Vojislava -- Osborne, Edward J -- Dermauw, Wannes -- Ngoc, Phuong Cao Thi -- Ortego, Felix -- Hernandez-Crespo, Pedro -- Diaz, Isabel -- Martinez, Manuel -- Navajas, Maria -- Sucena, Elio -- Magalhaes, Sara -- Nagy, Lisa -- Pace, Ryan M -- Djuranovic, Sergej -- Smagghe, Guy -- Iga, Masatoshi -- Christiaens, Olivier -- Veenstra, Jan A -- Ewer, John -- Villalobos, Rodrigo Mancilla -- Hutter, Jeffrey L -- Hudson, Stephen D -- Velez, Marisela -- Yi, Soojin V -- Zeng, Jia -- Pires-daSilva, Andre -- Roch, Fernando -- Cazaux, Marc -- Navarro, Marie -- Zhurov, Vladimir -- Acevedo, Gustavo -- Bjelica, Anica -- Fawcett, Jeffrey A -- Bonnet, Eric -- Martens, Cindy -- Baele, Guy -- Wissler, Lothar -- Sanchez-Rodriguez, Aminael -- Tirry, Luc -- Blais, Catherine -- Demeestere, Kristof -- Henz, Stefan R -- Gregory, T Ryan -- Mathieu, Johannes -- Verdon, Lou -- Farinelli, Laurent -- Schmutz, Jeremy -- Lindquist, Erika -- Feyereisen, Rene -- Van de Peer, Yves -- England -- Nature. 2011 Nov 23;479(7374):487-92. doi: 10.1038/nature10640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, The University of Western Ontario, London N6A 5B7, Canada. mgrbic@uwo.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22113690" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological/*genetics/physiology ; Animals ; Ecdysterone/analogs & derivatives/genetics ; Evolution, Molecular ; Fibroins/genetics ; Gene Expression Regulation ; Gene Transfer, Horizontal/genetics ; Genes, Homeobox/genetics ; Genome/*genetics ; Genomics ; Herbivory/*genetics/physiology ; Molecular Sequence Data ; Molting/genetics ; Multigene Family/genetics ; Nanostructures/chemistry ; Plants/parasitology ; Silk/biosynthesis/chemistry ; Tetranychidae/*genetics/*physiology ; Transcriptome/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-04-14
    Description: microRNAs (miRNAs) regulate gene expression through translational repression and/or messenger RNA (mRNA) deadenylation and decay. Because translation, deadenylation, and decay are closely linked processes, it is important to establish their ordering and thus to define the molecular mechanism of silencing. We have investigated the kinetics of these events in miRNA-mediated gene silencing by using a Drosophila S2 cell-based controllable expression system and show that mRNAs with both natural and engineered 3' untranslated regions with miRNA target sites are first subject to translational inhibition, followed by effects on deadenylation and decay. We next used a natural translational elongation stall to show that miRNA-mediated silencing inhibits translation at an early step, potentially translation initiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971879/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3971879/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Djuranovic, Sergej -- Nahvi, Ali -- Green, Rachel -- R01 GM059425/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Apr 13;336(6078):237-40. doi: 10.1126/science.1215691.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI) and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22499947" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions ; Animals ; Cell Line ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics/metabolism ; *Gene Silencing ; Kinetics ; MicroRNAs/*genetics/metabolism ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; *Protein Biosynthesis ; *RNA Stability ; RNA, Messenger/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Translational control by lysine-encoding A-rich sequences (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-07-26
    Description: Regulation of gene expression involves a wide array of cellular mechanisms that control the abundance of the RNA or protein products of that gene. We describe a gene regulatory mechanism that is based on polyadenylate [poly(A)] tracks that stall the translation apparatus. We show that creating longer or shorter runs of adenosine nucleotides, without changes in the amino acid sequence, alters the protein output and the stability of mRNA. Sometimes, these changes result in the production of an alternative "frameshifted" protein product. These observations are corroborated using reporter constructs and in the context of recombinant gene sequences. About 2% of genes in the human genome may be subject to this uncharacterized yet fundamental form of gene regulation. The potential pool of regulated genes encodes many proteins involved in nucleic acid binding. We hypothesize that the genes we identify are part of a large network whose expression is fine-tuned by poly(A) tracks, and we provide a mechanism through which synonymous mutations may influence gene expression in pathological states.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Molecular dissection of water and glycerol permeability of the aquaglyceroporin from Plasmodium falciparum by mutational analysis (2004)
    National Academy of Sciences
    Details
    Publication Date: 2004-01-20
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-30
    Description: The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus . As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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