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Drosophila RNA decay

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https://www.readbyqxmd.com/read/28875934/me31b-globally-represses-maternal-mrnas-by-two-distinct-mechanisms-during-the-drosophila-maternal-to-zygotic-transition
#1
Miranda Wang, Michael Ly, Andrew Lugowski, John D Laver, Howard D Lipshitz, Craig A Smibert, Olivia S Rissland
In animal embryos, control of development is passed from exclusively maternal gene products to those encoded by the embryonic genome in a process referred to as the maternal-to-zygotic transition (MZT). We show that the RNA-binding protein, ME31B, binds to and represses the expression of thousands of maternal mRNAs during the Drosophila MZT. However, ME31B carries out repression in different ways during different phases of the MZT. Early, it represses translation while, later, its binding leads to mRNA destruction, most likely as a consequence of translational repression in the context of robust mRNA decay...
September 6, 2017: ELife
https://www.readbyqxmd.com/read/28771467/comprehensive-analysis-of-nucleocytoplasmic-dynamics-of-mrna-in-drosophila-cells
#2
Tao Chen, Bas van Steensel
Eukaryotic mRNAs undergo a cycle of transcription, nuclear export, and degradation. A major challenge is to obtain a global, quantitative view of these processes. Here we measured the genome-wide nucleocytoplasmic dynamics of mRNA in Drosophila cells by metabolic labeling in combination with cellular fractionation. By mathematical modeling of these data we determined rates of transcription, export and cytoplasmic decay for 5420 genes. We characterized these kinetic rates and investigated links with mRNA features, RNA-binding proteins (RBPs) and chromatin states...
August 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28606139/a-loss-of-pdxk-model-of-parkinson-disease-in-drosophila-can-be-suppressed-by-buffy
#3
P Githure M'Angale, Brian E Staveley
BACKGROUND: The identification of a DNA variant in pyridoxal kinase (Pdxk) associated with increased risk to Parkinson disease (PD) gene led us to study the inhibition of this gene in the Dopa decarboxylase (Ddc)-expressing neurons of the well-studied model organism Drosophila melanogaster. The multitude of biological functions attributable to the vitamers catalysed by this kinase reveal an overabundance of possible links to PD, that include dopamine synthesis, antioxidant activity and mitochondrial function...
June 12, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28445691/tis11-mediated-mrna-decay-promotes-the-reacquisition-of-drosophila-intestinal-stem-cell-quiescence
#4
Lindy McClelland, Heinrich Jasper, Benoît Biteau
Adult stem cell proliferation rates are precisely regulated to maintain long-term tissue homeostasis. Defects in the mechanisms controlling stem cell proliferation result in impaired regeneration and hyperproliferative diseases. Many stem cell populations increase proliferation in response to tissue damage and reacquire basal proliferation rates after tissue repair is completed. Although proliferative signals have been extensively studied, much less is known about the molecular mechanisms that restore stem cell quiescence...
June 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#5
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of 3 Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurologic processes. Here we synthesize 30 y of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/27729457/molecular-basis-for-cytoplasmic-rna-surveillance-by-uridylation-triggered-decay-in-drosophila
#6
Madalena M Reimão-Pinto, Raphael A Manzenreither, Thomas R Burkard, Pawel Sledz, Martin Jinek, Karl Mechtler, Stefan L Ameres
The posttranscriptional addition of nucleotides to the 3' end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. Here, we show that in flies, 3' terminal RNA uridylation triggers the processive, 3'-to-5' exoribonucleolytic decay via the RNase II/R enzyme CG16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. Together with the TUTase Tailor, dmDis3l2 forms the cytoplasmic, terminal RNA uridylation-mediated processing (TRUMP) complex that functionally cooperates in the degradation of structured RNA RNA immunoprecipitation and high-throughput sequencing reveals a variety of TRUMP complex substrates, including abundant non-coding RNA, such as 5S rRNA, tRNA, snRNA, snoRNA, and the essential RNase MRP Based on genetic and biochemical evidence, we propose a key function of the TRUMP complex in the cytoplasmic quality control of RNA polymerase III transcripts...
November 15, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27635759/acetylation-dependent-control-of-global-poly-a-rna-degradation-by-cbp-p300-and-hdac1-2
#7
Sahil Sharma, Fabian Poetz, Marius Bruer, Thi Bach Nga Ly-Hartig, Johanna Schott, Bertrand Séraphin, Georg Stoecklin
Acetylation of histones and transcription-related factors is known to exert epigenetic and transcriptional control of gene expression. Here we report that histone acetyltransferases (HATs) and histone deacetylases (HDACs) also regulate gene expression at the posttranscriptional level by controlling poly(A) RNA stability. Inhibition of HDAC1 and HDAC2 induces massive and widespread degradation of normally stable poly(A) RNA in mammalian and Drosophila cells. Acetylation-induced RNA decay depends on the HATs p300 and CBP, which acetylate the exoribonuclease CAF1a, a catalytic subunit of the CCR4-CAF1-NOT deadenlyase complex and thereby contribute to accelerating poly(A) RNA degradation...
September 15, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27502187/the-emerging-roles-of-the-ddx41-protein-in-immunity-and-diseases
#8
REVIEW
Yan Jiang, Yanping Zhu, Zhi-Jie Liu, Songying Ouyang
RNA helicases are involved in almost every aspect of RNA, from transcription to RNA decay. DExD/H-box helicases comprise the largest SF2 helicase superfamily, which are characterized by two conserved RecA-like domains. In recent years, an increasing number of unexpected functions of these proteins have been discovered. They play important roles not only in innate immune response but also in diseases like cancers and chronic hepatitis C. In this review, we summarize the recent literatures on one member of the SF2 superfamily, the DEAD-box protein DDX41...
February 2017: Protein & Cell
https://www.readbyqxmd.com/read/26930655/gw-bodies-and-p-bodies-constitute-two-separate-pools-of-sequestered-non-translating-rnas
#9
Prajal H Patel, Scott A Barbee, J Todd Blankenship
Non-translating RNAs that have undergone active translational repression are culled from the cytoplasm into P-bodies for decapping-dependent decay or for sequestration. Organisms that use microRNA-mediated RNA silencing have an additional pathway to remove RNAs from active translation. Consequently, proteins that govern microRNA-mediated silencing, such as GW182/Gw and AGO1, are often associated with the P-bodies of higher eukaryotic organisms. Due to the presence of Gw, these structures have been referred to as GW-bodies...
2016: PloS One
https://www.readbyqxmd.com/read/26786835/oligoadenylation-of-3-decay-intermediates-promotes-cytoplasmic-mrna-degradation-in-drosophila-cells
#10
Christiane Harnisch, Simona Cuzic-Feltens, Juliane C Dohm, Michael Götze, Heinz Himmelbauer, Elmar Wahle
Post-transcriptional 3' end addition of nucleotides is important in a variety of RNA decay pathways. We have examined the 3' end addition of nucleotides during the decay of the Hsp70 mRNA and a corresponding reporter RNA in Drosophila S2 cells by conventional sequencing of cDNAs obtained after mRNA circularization and by deep sequencing of dedicated libraries enriched for 3' decay intermediates along the length of the mRNA. Approximately 5%-10% of 3' decay intermediates carried nonencoded oligo(A) tails with a mean length of 2-3 nucleotides...
March 2016: RNA
https://www.readbyqxmd.com/read/26294687/extensive-cross-regulation-of-post-transcriptional-regulatory-networks-in-drosophila
#11
Marcus H Stoiber, Sara Olson, Gemma E May, Michael O Duff, Jan Manent, Robert Obar, K G Guruharsha, Peter J Bickel, Spyros Artavanis-Tsakonas, James B Brown, Brenton R Graveley, Susan E Celniker
In eukaryotic cells, RNAs exist as ribonucleoprotein particles (RNPs). Despite the importance of these complexes in many biological processes, including splicing, polyadenylation, stability, transportation, localization, and translation, their compositions are largely unknown. We affinity-purified 20 distinct RNA-binding proteins (RBPs) from cultured Drosophila melanogaster cells under native conditions and identified both the RNA and protein compositions of these RNP complexes. We identified "high occupancy target" (HOT) RNAs that interact with the majority of the RBPs we surveyed...
November 2015: Genome Research
https://www.readbyqxmd.com/read/26257181/aubergine-iclip-reveals-pirna-dependent-decay-of-mrnas-involved-in-germ-cell-development-in-the-early-embryo
#12
Bridlin Barckmann, Stéphanie Pierson, Jérémy Dufourt, Catherine Papin, Claudia Armenise, Fillip Port, Thomas Grentzinger, Séverine Chambeyron, Grégory Baronian, Jean-Pierre Desvignes, Tomaz Curk, Martine Simonelig
The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now emerging. Here, we perform iCLIP with the PIWI protein Aubergine (Aub) and identify hundreds of maternal mRNAs interacting with Aub in the early Drosophila embryo. Gene expression profiling reveals that a proportion of these mRNAs undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Strikingly, Aub-dependent unstable mRNAs encode germ cell determinants...
August 18, 2015: Cell Reports
https://www.readbyqxmd.com/read/26193331/the-3-to-5-exoribonuclease-dis3-from-structure-and-mechanisms-to-biological-functions-and-role-in-human-disease
#13
REVIEW
Sophie R Robinson, Antony W Oliver, Timothy J Chevassut, Sarah F Newbury
DIS3 is a conserved exoribonuclease and catalytic subunit of the exosome, a protein complex involved in the 3' to 5' degradation and processing of both nuclear and cytoplasmic RNA species. Recently, aberrant expression of DIS3 has been found to be implicated in a range of different cancers. Perhaps most striking is the finding that DIS3 is recurrently mutated in 11% of multiple myeloma patients. Much work has been done to elucidate the structural and biochemical characteristics of DIS3, including the mechanistic details of its role as an effector of RNA decay pathways...
2015: Biomolecules
https://www.readbyqxmd.com/read/25962635/brain-tumor-is-a-sequence-specific-rna-binding-protein-that-directs-maternal-mrna-clearance-during-the-drosophila-maternal-to-zygotic-transition
#14
John D Laver, Xiao Li, Debashish Ray, Kate B Cook, Noah A Hahn, Syed Nabeel-Shah, Mariana Kekis, Hua Luo, Alexander J Marsolais, Karen Yy Fung, Timothy R Hughes, J Timothy Westwood, Sachdev S Sidhu, Quaid Morris, Howard D Lipshitz, Craig A Smibert
BACKGROUND: Brain tumor (BRAT) is a Drosophila member of the TRIM-NHL protein family. This family is conserved among metazoans and its members function as post-transcriptional regulators. BRAT was thought to be recruited to mRNAs indirectly through interaction with the RNA-binding protein Pumilio (PUM). However, it has recently been demonstrated that BRAT directly binds to RNA. The precise sequence recognized by BRAT, the extent of BRAT-mediated regulation, and the exact roles of PUM and BRAT in post-transcriptional regulation are unknown...
2015: Genome Biology
https://www.readbyqxmd.com/read/25364902/genome-wide-analyses-and-functional-classification-of-proline-repeat-rich-proteins-potential-role-of-eif5a-in-eukaryotic-evolution
#15
Ajeet Mandal, Swati Mandal, Myung Hee Park
The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in Saccharomyces cerevisiae, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens...
2014: PloS One
https://www.readbyqxmd.com/read/25342740/the-drosophila-tis11-protein-and-its-effects-on-mrna-expression-in-flies
#16
Youn-Jeong Choi, Wi S Lai, Robert Fedic, Deborah J Stumpo, Weichun Huang, Leping Li, Lalith Perera, Brandy Y Brewer, Gerald M Wilson, James M Mason, Perry J Blackshear
Members of the mammalian tristetraprolin family of CCCH tandem zinc finger proteins can bind to certain AU-rich elements (AREs) in mRNAs, leading to their deadenylation and destabilization. Mammals express three or four members of this family, but Drosophila melanogaster and other insects appear to contain a single gene, Tis11. We found that recombinant Drosophila Tis11 protein could bind to ARE-containing RNA oligonucleotides with low nanomolar affinity. Remarkably, co-expression in mammalian cells with "target" RNAs demonstrated that Tis11 could promote destabilization of ARE-containing mRNAs and that this was partially dependent on a conserved C-terminal sequence resembling the mammalian NOT1 binding domain...
December 19, 2014: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/25280104/micrornas-block-assembly-of-eif4f-translation-initiation-complex-in-drosophila
#17
Takashi Fukaya, Hiro-Oki Iwakawa, Yukihide Tomari
miRNAs silence their complementary target mRNAs by translational repression as well as by poly(A) shortening and mRNA decay. In Drosophila, miRNAs are typically incorporated into Argonaute1 (Ago1) to form the effector complex called RNA-induced silencing complex (RISC). Ago1-RISC associates with a scaffold protein GW182, which recruits additional silencing factors. We have previously shown that miRNAs repress translation initiation by blocking formation of the 48S and 80S ribosomal complexes. However, it remains unclear how ribosome recruitment is impeded...
October 2, 2014: Molecular Cell
https://www.readbyqxmd.com/read/25167966/brightness-through-local-constraint-lna-enhanced-fit-hybridization-probes-for-in-vivo-ribonucleotide-particle-tracking
#18
Felix Hövelmann, Imre Gaspar, Simon Loibl, Eugeny A Ermilov, Beate Röder, Jesper Wengel, Anne Ephrussi, Oliver Seitz
Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint...
October 13, 2014: Angewandte Chemie
https://www.readbyqxmd.com/read/25158797/purifying-selection-on-splice-related-motifs-not-expression-level-nor-rna-folding-explains-nearly-all-constraint-on-human-lincrnas
#19
Andreas Schüler, Avazeh T Ghanbarian, Laurence D Hurst
There are two strong and equally important predictors of rates of human protein evolution: The amount the gene is expressed and the proportion of exonic sequence devoted to control splicing, mediated largely by selection on exonic splice enhancer (ESE) motifs. Is the same true for noncoding RNAs, known to be under very weak purifying selection? Prior evidence suggests that selection at splice sites in long intergenic noncoding RNAs (lincRNAs) is important. We now report multiple lines of evidence indicating that the great majority of purifying selection operating on lincRNAs in humans is splice related...
December 2014: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/25110026/rna-granules-and-cytoskeletal-links
#20
REVIEW
Dipen Rajgor, Catherine M Shanahan
In eukaryotic cells, non-translating mRNAs can accumulate into cytoplasmic mRNP (messenger ribonucleoprotein) granules such as P-bodies (processing bodies) and SGs (stress granules). P-bodies contain the mRNA decay and translational repression machineries and are ubiquitously expressed in mammalian cells and lower eukaryote species including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. In contrast, SGs are only detected during cellular stress when translation is inhibited and form from aggregates of stalled pre-initiation complexes...
August 2014: Biochemical Society Transactions
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