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https://www.readbyqxmd.com/read/28432181/dual-nature-of-pseudouridylation-in-u2-snrna-pus1p-dependent-and-pus1p-independent-activities-in-yeasts-and-higher-eukaryotes
#1
Svetlana Deryusheva, Joseph G Gall
The pseudouridine at position 43 in vertebrate U2 snRNA is one of the most conserved posttranscriptional modifications of spliceosomal snRNAs; the equivalent position is pseudouridylated in U2 snRNAs in different phyla including fungi, insects, and worms. Pseudouridine synthase Pus1p acts alone on U2 snRNA to form this pseudouridine in yeast Saccharomyces cerevisiae and mouse. Furthermore, in S. cerevisiae Pus1p is the only pseudouridine synthase for this position. Using an in vivo yeast cell system we tested enzymatic activity of Pus1p from the fission yeast Schizosaccharomyces pombe, the worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster and the frog Xenopus tropicalis...
April 21, 2017: RNA
https://www.readbyqxmd.com/read/28428330/genomic-responses-to-socio-sexual-environment-in-male-drosophila-melanogaster-exposed-to-conspecific-rivals
#2
Irina I Mohorianu, Amanda Bretman, Damian T Smith, Emily Fowler, Tamas Dalmay, Tracey Chapman
Socio-sexual environments have profound effects on fitness. Local sex ratios can alter the threat of sexual competition, to which males respond via plasticity in reproductive behaviours and ejaculate composition. In Drosophila melanogaster, males detect the presence of conspecific mating rivals prior to mating using multiple, redundant sensory cues. Males that respond to rivals gain significant fitness benefits by altering mating duration and ejaculate composition. Here we investigated the underlying genome-wide changes involved...
April 20, 2017: RNA
https://www.readbyqxmd.com/read/28428329/visualization-of-rna-structure-models-within-the-integrative-genomics-viewer
#3
Steven Busan, Kevin M Weeks
Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist...
April 20, 2017: RNA
https://www.readbyqxmd.com/read/28420675/integrative-analysis-unveils-new-functions-for-the-drosophila-cutoff-protein-in-non-coding-rna-biogenesis-and-gene-regulation
#4
Yuri Pritykin, Tarcisio Brito, Trudi Schupbach, Mona Singh, Attilio Pane
Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. Here we further elucidate the function of Cutoff and the RDC complex by performing genome-wide ChIP-seq and RNA-seq assays in the Drosophila germline and analyzing these data together with other publicly available data sets...
April 18, 2017: RNA
https://www.readbyqxmd.com/read/28416567/the-c-terminal-dsrna-binding-domain-of-drosophila-dicer-2-is-crucial-for-efficient-and-high-fidelity-production-of-sirna-and-loading-of-sirna-to-argonaute2
#5
Suresh K Kandasamy, Li Zhu, Ryuya Fukunaga
Drosophila Dicer-2 efficiently and precisely produces 21-nt siRNAs from long double-stranded RNA (dsRNA) substrates and loads these siRNAs onto the effector protein Argonaute2 for RNA silencing. The functional roles of each domain of the multi-domain Dicer-2 enzyme in the production and loading of siRNAs are not fully understood. Here we characterized Dicer-2 mutants lacking either the N-terminal helicase domain or C-terminal dsRNA-binding domain (CdsRBD) (ΔHelicase and ΔCdsRBD, respectively) in vivo and in vitro...
April 17, 2017: RNA
https://www.readbyqxmd.com/read/28416566/structure-of-deah-rha-atpase-prp43p-bound-to-rna-implicates-a-pair-of-hairpins-and-motif-va-in-translocation-along-rna
#6
Yangzi He, Jonathan P Staley, Gregers Rom Andersen, Klaus H Nielsen
Three families of nucleic acid-dependent ATPases (DEAH/RHA, Ski2-like and NS3/NPH-II), termed the DExH ATPases, are thought to execute myriad functions by processive, ATP-dependent, 3' to 5' translocation along single-stranded nucleic acid. While the mechanism of translocation of the viral NS3/NPH-II family has been studied extensively, it has not been clear if or how the principles that have emerged for this family extend to the other two families. Here we report the crystal structure of the yeast DEAH/RHA family ATPase Prp43p, which functions in splicing and ribosome biogenesis, in complex with poly-uracil and a non-hydrolysable ATP analogue...
April 17, 2017: RNA
https://www.readbyqxmd.com/read/28411202/characterization-of-the-mammalian-dead-box-protein-ddx5-reveals-functional-conservation-with-s-cerevisiae-ortholog-dbp2-in-transcriptional-control-and-glucose-metabolism
#7
Zheng Xing, Siwen Wang, Elizabeth J Tran
DEAD-box proteins are a class of non-processive RNA helicases that dynamically modulate the structure of RNA and ribonucleoprotein complexes (RNPs). However, the precise roles of individual members are not well understood. Work from our lab revealed that the DEAD-box protein Dbp2 in Saccharomyces cerevisiae is an active RNA helicase in vitro that functions in transcription by promoting mRNP assembly, repressing cryptic transcription initiation, and regulating long non-coding RNA activity. Interestingly, Dbp2 is also linked to glucose sensing and hexose transporter gene expression...
April 14, 2017: RNA
https://www.readbyqxmd.com/read/28400409/drosha-targets-its-own-transcript-to-modulate-alternative-splicing
#8
Dooyoung Lee, Jin-Wu Nam, Chanseok Shin
The nuclear RNase III enzyme DROSHA interacts with its cofactor DGCR8 to form the Microprocessor complex, which initiates microRNA (miRNA) maturation by cleaving hairpin structures embedded in primary transcripts. Apart from its central role in the biogenesis of miRNAs, DROSHA is also known to recognize and cleave miRNA-like hairpins in a subset of transcripts without apparent small RNA production. Here, we report that the human DROSHA transcript is one such non-canonical target of DROSHA. Mammalian DROSHA genes have evolved a conserved hairpin structure spanning a specific exon-intron junction, which serves as a substrate for the Microprocessor in human cells but not in murine cells...
April 11, 2017: RNA
https://www.readbyqxmd.com/read/28396577/microrna-27b-functions-as-a-new-inhibitor-of-ovarian-cancer-mediated-vasculogenic-mimicry-through-suppression-of-ve-cadherin-expression
#9
Wenming Liu, Chunping Lv, Bin Zhang, Quansheng Zhou, Zhifei Cao
Aggressive cancer cells gain robust tumor vascular mimicry (VM) capability which promotes tumor growth and metastasis. VE-cadherin is aberrantly overexpressed in vasculogenic cancer cells and regarded as a master gene of tumor VM. Although micro RNAs (miRNAs) play an important role in modulating tumor angiogenesis and cancer metastasis, the miRNA which targets VE-cadherin expression in cancer cells to inhibit tumor cell-mediated VM is enigmatic. In this study, we found that miR-27b levels are negatively co-related to VE-cadherin expression in ovarian cancer cells and tumor cell-mediated VM, and demonstrated that miR-27b could bind to the 3'-untranslated region (3'-UTR) of VE-cadherin mRNA...
April 10, 2017: RNA
https://www.readbyqxmd.com/read/28396576/riboswitch-diversity-and-distribution
#10
Phillip J McCown, Keith A Corbino, Shira Stav, Madeline E Sherlock, Ronald R Breaker
Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands...
April 10, 2017: RNA
https://www.readbyqxmd.com/read/28389433/structure-of-a-smg8-smg9-complex-identifies-a-g-domain-heterodimer-in-the-nmd-effector-proteins
#11
Liang Li, Mahesh Lingaraju, Claire Basquin, Jerome Basquin, Elena Conti
Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA degradation pathway involved in surveillance and post-transcriptional regulation, and executed by the concerted action of several trans-acting factors. The SMG1 kinase is an essential NMD factor in metazoans and is associated with two recently identified and yet poorly characterized proteins, SMG8 and SMG9. We determined the 2.5 Å resolution crystal structure of a SMG8-SMG9 core complex from C. elegans. We found that SMG8-SMG9 is a G domain heterodimer with architectural similarities to the dynamin-like family of GTPases such as Atlastin and GBP1...
April 7, 2017: RNA
https://www.readbyqxmd.com/read/28389432/topological-and-thermodynamic-factors-that-influence-the-evolution-of-small-networks-of-catalytic-rna-species
#12
Jessica A M Yeates, Philippe Nghe, Niles Lehman
RNA-directed recombination reaction can result in a network of interacting RNA species. It is now becoming increasingly apparent that such networks would have been an important feature of the RNA world during the nascent evolution of life on the Earth. But the means by which such small RNA networks assimilate other available genotypes in the environment to grow and evolve into the more complex networks that are thought to have existed in the prebiotic milieu are not known. Here, we used the ability of fragments of the Azoarcus group I intron ribozyme to covalently self assemble via genotype-selfish and genotype-cooperative interactions into full-length ribozymes to investigate the dynamics of small (3- and 4-membered) networks...
April 7, 2017: RNA
https://www.readbyqxmd.com/read/28386015/lncatlas-database-for-subcellular-localisation-of-long-noncoding-rnas
#13
David Mas-Ponte, Joana Carlevaro-Fita, Emilio Palumbo, Toni Hermoso Pulido, Roderic Guigo, Rory Johnson
The subcellular localisation of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localisation of newly-discovered lncRNAs involves time-consuming and costly experimental methods. We have created "LncATLAS", a comprehensive resource of lncRNA localisation in human cells based on RNA-sequencing datasets. Altogether, 6,768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce "Relative concentration index" (RCI) as a useful measure of localisation derived from ensemble RNAseq measurements...
April 6, 2017: RNA
https://www.readbyqxmd.com/read/28373290/a-genetic-screen-implicates-a-cwc16-yju2-ccdc130-protein-and-smu1-in-alternative-splicing-in-arabidopsis-thaliana
#14
Tatsuo Kanno, Wen-Dar Lin, Jason Fu, Antonius Matzke, Marjori Matzke
To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively-spliced GFP reporter gene in Arabidopsis thaliana. In wild-type plants, three major splice variants issue from the GFP gene but only one represents a translatable GFP mRNA. Compared to wild-type seedlings, which exhibit an intermediate level of GFP expression, mutants identified in the screen feature either a 'GFP-weak' or 'Hyper-GFP' phenotype depending on the ratio of the three splice variants...
April 3, 2017: RNA
https://www.readbyqxmd.com/read/28363900/computational-analysis-of-nascent-peptides-that-induce-ribosome-stalling-and-their-proteomic-distribution-in-saccharomyces-cerevisiae
#15
Renana Sabi, Tamir Tuller
Interactions between the ribosomal exit tunnel and the nascent peptide can affect translation elongation rates. While previous studies have already demonstrated the feasibility of such interactions, little is known about the nature of the stalling peptide sequences and their distribution in the proteome. Here we ask which peptide sequences tend to occupy the tunnel of stalled ribosomes and how they are distributed in the proteome. Using computational analysis of ribosome profiling data from S. cerevisiae, we identified for the first time dozens of short stalling peptide sequences and studied their statistical properties...
March 31, 2017: RNA
https://www.readbyqxmd.com/read/28351886/3-uridylation-controls-mature-microrna-turnover-during-cd4-t-cell-activation
#16
Cristina Gutierrez-Vazquez, Anton J Enright, Ana Rodríguez-Galán, Arantxa Perez-García, Paul Collier, Matthew R Jones, Vladimir Benes, Joseph P Mizgerd, María Mittelbrunn, Almudena R Ramiro, Francisco Sanchez-Madrid
Activation of T lymphocytes requires a tight regulation of microRNAs (miRNAs) expression. Terminal uridyltransferases (TUTases) catalyze 3' non-templated nucleotide addition (3'NTA) to miRNAs which may influence miRNA stability and function. Here, we investigated 3'NTA to mature miRNA in CD4 T lymphocytes by deep sequencing. Upon T cell activation, miRNA sequences bearing terminal uridines are specifically decreased, concomitantly with downregulation of TUT4 and TUT7 enzymes. Analyzing TUT4 deficient T lymphocytes, we proved that this terminal uridyltransferase is essential for the maintenance of miRNA uridylation in steady state of T lymphocytes...
March 28, 2017: RNA
https://www.readbyqxmd.com/read/28351885/loss-of-the-rna-helicase-skiv2l2-impairs-mitotic-progression-and-replication-dependent-histone-mrna-turnover-in-murine-cell-lines
#17
Alexis M Onderak, James T Anderson
RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by thirty percent. Propidium iodide-based cell cycle analysis of Skiv2l2 knockdown cells revealed defective progression through G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression...
March 28, 2017: RNA
https://www.readbyqxmd.com/read/28348170/crystal-structure-of-u2-snrnp-sf3b-components-hsh49p-in-complex-with-cus1p-binding-domain
#18
Anne-Marie A M van Roon, Chris Oubridge, Eiji Obayashi, Benedetta Sposito, Andrew James Newman, Bertrand Seraphin, Kiyoshi Nagai
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA binding surface available to bind RNA...
March 27, 2017: RNA
https://www.readbyqxmd.com/read/28341704/structural-landscape-of-base-pairs-containing-post-transcriptional-modifications-in-rna
#19
Preethi P Seelam, Purshotam Sharma, Abhijit Mitra
Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures, and most commonly involve guanine or uridine modifications...
March 24, 2017: RNA
https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#20
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
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