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https://www.readbyqxmd.com/read/28338834/comparative-genomics-of-microsporidian-genomes-reveals-a-minimal-non-coding-rna-set-and-new-insights-for-transcription-in-minimal-eukaryotic-genomes
#1
Abdel Belkorchia, Jean-François Pombert, Valérie Polonais, Nicolas Parisot, Frédéric Delbac, Jean-François Brugère, Pierre Peyret, Christine Gaspin, Eric Peyretaillade
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments...
February 28, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#2
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28297668/mutually-exclusive-cbc-containing-complexes-contribute-to-rna-fate
#3
Simone Giacometti, Nour El Houda Benbahouche, Michal Domanski, Marie-Cécile Robert, Nicola Meola, Michal Lubas, Jakob Bukenborg, Jens S Andersen, Wiebke M Schulze, Celine Verheggen, Grzegorz Kudla, Torben Heick Jensen, Edouard Bertrand
The nuclear cap-binding complex (CBC) stimulates processing reactions of capped RNAs, including their splicing, 3'-end formation, degradation, and transport. CBC effects are particular for individual RNA families, but how such selectivity is achieved remains elusive. Here, we analyze three main CBC partners known to impact different RNA species. ARS2 stimulates 3'-end formation/transcription termination of several transcript types, ZC3H18 stimulates degradation of a diverse set of RNAs, and PHAX functions in pre-small nuclear RNA/small nucleolar RNA (pre-snRNA/snoRNA) transport...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28283058/5-end-nicotinamide-adenine-dinucleotide-cap-in-human-cells-promotes-rna-decay-through-dxo-mediated-denadding
#4
Xinfu Jiao, Selom K Doamekpor, Jeremy G Bird, Bryce E Nickels, Liang Tong, Ronald P Hart, Megerditch Kiledjian
Eukaryotic mRNAs generally possess a 5' end N7 methyl guanosine (m(7)G) cap that promotes their translation and stability. However, mammalian mRNAs can also carry a 5' end nicotinamide adenine dinucleotide (NAD(+)) cap that, in contrast to the m(7)G cap, does not support translation but instead promotes mRNA decay. The mammalian and fungal noncanonical DXO/Rai1 decapping enzymes efficiently remove NAD(+) caps, and cocrystal structures of DXO/Rai1 with 3'-NADP(+) illuminate the molecular mechanism for how the "deNADding" reaction produces NAD(+) and 5' phosphate RNA...
March 9, 2017: Cell
https://www.readbyqxmd.com/read/28254838/the-7sk-snrnp-associates-with-the-little-elongation-complex-to-promote-snrna-gene-expression
#5
Sylvain Egloff, Patrice Vitali, Michael Tellier, Raoul Raffel, Shona Murphy, Tamás Kiss
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, regulates the mRNA elongation capacity of RNA polymerase II (RNAPII) through controlling the nuclear activity of positive transcription elongation factor b (P-TEFb). Here, we demonstrate that the human 7SK snRNP also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes...
March 2, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28252005/serum-snornas-as-biomarkers-for-joint-ageing-and-post-traumatic-osteoarthritis
#6
Mandy M F Steinbusch, Yongxiang Fang, Peter I Milner, Peter D Clegg, David A Young, Tim J M Welting, Mandy J Peffers
The development of effective treatments for the age-related disease osteoarthritis and the ability to predict disease progression has been hampered by the lack of biomarkers able to demonstrate the course of the disease. Profiling the expression patterns of small nucleolar RNAs (snoRNAs) in joint ageing and OA may provide diagnostic biomarkers and therapeutic targets. This study determined expression patterns of snoRNAs in joint ageing and OA and examined them as potential biomarkers. Using SnoRNASeq and real-time quantitative PCR (qRT-PCR) we demonstrate snoRNA expression levels in murine ageing and OA joints and serum for the first time...
March 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28244370/molecular-architecture-of-the-90s-small-subunit-pre-ribosome
#7
Qi Sun, Xing Zhu, Jia Qi, Weidong An, Pengfei Lan, Dan Tan, Rongchang Chen, Bing Wang, Sanduo Zheng, Cheng Zhang, Xining Chen, Wei Zhang, Jing Chen, Meng-Qiu Dong, Keqiong Ye
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors...
February 28, 2017: ELife
https://www.readbyqxmd.com/read/28212545/snora74b-gene-silencing-inhibits-gallbladder-cancer-cells-by-inducing-phlpp-and-suppressing-akt-mtor-signaling
#8
Yiyu Qin, Li Meng, Yang Fu, Zhiwei Quan, Mingzhe Ma, Mingzhe Weng, Zhengdong Zhang, Cuixiang Gao, Xinghua Shi, Koulan Han
Small nucleolar RNAs (snoRNAs) have been implicated in the development of many cancers. We therefore examined the differential expression of snoRNAs between gallbladder cancer (GBC) tissues and matched adjacent non-tumor tissues using expression microarray analysis with confirmation by quantitative real-time PCR (qRT-PCR). Western blot analysis showed that SNORA74B levels were higher in GBC than non-tumor tissues. SNORA74B expression was positively associated with local invasion, advanced TNM stage, CA19-9 level, and Ki67 expression in patients with GBC, while it was negatively associated with expression of PHLPP, an endogenous Akt inhibitor...
February 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28139540/transcriptome-profiling-of-visceral-adipose-tissue-in-a-novel-obese-rat-model-wnin-ob-its-comparison-with-other-animal-models
#9
Siva Sankara Vara Prasad Sakamuri, Uday Kumar Putcha, Giridharan Nappan Veettil, Vajreswari Ayyalasomayajula
BACKGROUND & OBJECTIVES: Adipose tissue dysfunction in obesity is linked to the development of type 2 diabetes and cardiovascular diseases. We studied the differential gene expression in retroperitoneal adipose tissue of a novel obese rat model, WNIN/Ob, to understand the possible underlying transcriptional changes involved in the development of obesity and associatedcomorbidities in this model. METHODS: Four month old, male WNIN/Ob lean and obese rats were taken, blood was collected and tissues were dissected...
September 2016: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28127559/variety-of-rnas-in-peripheral-blood-cells-plasma-and-plasma-fractions
#10
Anna V Savelyeva, Elena V Kuligina, Dmitry N Bariakin, Vadim V Kozlov, Elena I Ryabchikova, Vladimir A Richter, Dmitry V Semenov
Human peripheral blood contains RNA in cells and in extracellular membrane vesicles, microvesicles and exosomes, as well as in cell-free ribonucleoproteins. Circulating mRNAs and noncoding RNAs, being internalized, possess the ability to modulate vital processes in recipient cells. In this study, with SOLiD sequencing technology, we performed identification, classification, and quantification of RNAs from blood fractions: cells, plasma, plasma vesicles pelleted at 16,000g and 160,000g, and vesicle-depleted plasma supernatant of healthy donors and non-small cell lung cancer (NSCLC) patients...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28110922/snornas-are-involved-in-the-progression-of-ulcerative-colitis-and-colorectal-cancer
#11
Xiao Yang, Yiming Li, Lianyun Li, Juan Liu, Min Wu, Mei Ye
BACKGROUND AND AIM: Emerging evidences indicate that small nucleolar RNAs (snoRNAs) are important regulatory molecules involved in various pathophysiological processes including inflammation and cancer. In the current study, we investigate whether snoRNAs dysregulate in colorectal cancer (CRC) and intestinal inflammation and contribute the pathogenesis of CRC. METHODS: We analyzed the snoRNAs expression profile in CRC patients by GeneChipR Array and validated candidate snoRNAs expression in 44 CRC tissues, as well as in 28 ulcerative colitis (UC) and 28 healthy controls using reverse transcription quantitative polymerase chain reaction...
January 5, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28105919/snoreport-2-0-new-features-and-a-refined-support-vector-machine-to-improve-snorna-identification
#12
João Victor de Araujo Oliveira, Fabrizio Costa, Rolf Backofen, Peter Florian Stadler, Maria Emília Machado Telles Walter, Jana Hertel
BACKGROUND: snoReport uses RNA secondary structure prediction combined with machine learning as the basis to identify the two main classes of small nucleolar RNAs, the box H/ACA snoRNAs and the box C/D snoRNAs. Here, we present snoReport 2.0, which substantially improves and extends in the original method by: extracting new features for both box C/D and H/ACA box snoRNAs; developing a more sophisticated technique in the SVM training phase with recent data from vertebrate organisms and a careful choice of the SVM parameters C and γ; and using updated versions of tools and databases used for the construction of the original version of snoReport...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#13
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
https://www.readbyqxmd.com/read/28053119/short-intron-derived-ncrnas
#14
Florent Hubé, Damien Ulveling, Alain Sureau, Sabrina Forveille, Claire Francastel
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2)...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28033303/strong-cis-acting-expression-quantitative-trait-loci-for-the-genes-encoding-snhg5-and-pex6
#15
Jihyeon Lee, Jihye Ryu, Chaeyoung Lee
Expression of quantitative trait loci (eQTLs) for the genes located in human chromosome 6 were examined. Data on RNA expression in lymphoblastoid cells of 373 unrelated Europeans were used to identify eQTLs.Genome-wide analysis resulted in 24,447 nucleotide variants associated with gene expression (P < 2.16 × 10). We found 36variants with P < 10, which were all associated with expression levels of the genes encoding small nucleolar RNA host gene 5 (SNHG5) and peroxisomal biogenesis factor 6 (PEX6)...
December 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28031372/high-throughput-identification-of-c-d-box-snorna-targets-with-clip-and-ribometh-seq
#16
Rafal Gumienny, Dominik J Jedlinski, Alexander Schmidt, Foivos Gypas, Georges Martin, Arnau Vina-Vilaseca, Mihaela Zavolan
High-throughput sequencing has greatly facilitated the discovery of long and short non-coding RNAs (ncRNAs), which frequently guide ribonucleoprotein complexes to RNA targets, to modulate their metabolism and expression. However, for many ncRNAs, the targets remain to be discovered. In this study, we developed computational methods to map C/D box snoRNA target sites using data from core small nucleolar ribonucleoprotein crosslinking and immunoprecipitation and from transcriptome-wide mapping of 2'-O-ribose methylation sites...
December 27, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/28024084/targeting-the-histone-methyltransferase-g9a-activates-imprinted-genes-and-improves-survival-of-a-mouse-model-of-prader-willi-syndrome
#17
Yuna Kim, Hyeong-Min Lee, Yan Xiong, Noah Sciaky, Samuel W Hulbert, Xinyu Cao, Jeffrey I Everitt, Jian Jin, Bryan L Roth, Yong-Hui Jiang
Prader-Willi syndrome (PWS) is an imprinting disorder caused by a deficiency of paternally expressed gene(s) in the 15q11-q13 chromosomal region. The regulation of imprinted gene expression in this region is coordinated by an imprinting center (PWS-IC). In individuals with PWS, genes responsible for PWS on the maternal chromosome are present, but repressed epigenetically, which provides an opportunity for the use of epigenetic therapy to restore expression from the maternal copies of PWS-associated genes. Through a high-content screen (HCS) of >9,000 small molecules, we discovered that UNC0638 and UNC0642-two selective inhibitors of euchromatic histone lysine N-methyltransferase-2 (EHMT2, also known as G9a)-activated the maternal (m) copy of candidate genes underlying PWS, including the SnoRNA cluster SNORD116, in cells from humans with PWS and also from a mouse model of PWS carrying a paternal (p) deletion from small nuclear ribonucleoprotein N (Snrpn (S)) to ubiquitin protein ligase E3A (Ube3a (U)) (mouse model referred to hereafter as m(+)/p(ΔS-U))...
February 2017: Nature Medicine
https://www.readbyqxmd.com/read/28007835/paralog-specific-functions-of-rpl7a-and-rpl7b-mediated-by-ribosomal-protein-or-snorna-dosage-in-saccharomyces-cerevisiae
#18
Ryan J Palumbo, Gabriele Fuchs, Sheila Lutz, M Joan Curcio
Most ribosomal proteins in Saccharomyces cerevisiae are encoded by two paralogs that additively produce the optimal protein level for cell growth. Nonetheless, deleting one paralog of most ribosomal protein gene pairs results in a variety of phenotypes not observed when the other paralog is deleted. To determine whether paralog-specific phenotypes associated with deleting RPL7A or RPL7B stem from distinct functions or different levels of the encoded isoforms, the coding region and introns of one paralog, including an intron-embedded snoRNA (small nucleolar RNA) gene, were exchanged with that of the other paralog...
December 22, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27999395/stem-loop-rt-qpcr-as-an-efficient-tool-for-the-detection-and-quantification-of-small-rnas-in-giardia-lamblia
#19
Jaime Marcial-Quino, Saúl Gómez-Manzo, Francisco Fierro, America Vanoye-Carlo, Yadira Rufino-González, Edgar Sierra-Palacios, Adriana Castillo-Villanueva, Rosa Angélica Castillo-Rodríguez, Eduardo Rodríguez-Bustamante, Roberto Arreguin-Espinosa, Horacio Reyes-Vivas
Stem-loop quantitative reverse transcription PCR (RT-qPCR) is a molecular technique used for identification and quantification of individual small RNAs in cells. In this work, we used a Universal ProbeLibrary (UPL)-based design to detect-in a rapid, sensitive, specific, and reproducible way-the small nucleolar RNA (snoRNA) GlsR17 and its derived miRNA (miR2) of Giardia lamblia using a stem-loop RT-qPCR approach. Both small RNAs could be isolated from both total RNA and small RNA samples. Identification of the two small RNAs was carried out by sequencing the PCR-amplified small RNA products upon ligation into the pJET1...
December 20, 2016: Genes
https://www.readbyqxmd.com/read/27980088/architecture-of-the-yeast-small-subunit-processome
#20
Malik Chaker-Margot, Jonas Barandun, Mirjam Hunziker, Sebastian Klinge
The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains...
January 13, 2017: Science
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