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https://www.readbyqxmd.com/read/28212545/snora74b-gene-silencing-inhibits-gallbladder-cancer-cells-by-inducing-phlpp-and-suppressing-akt-mtor-signaling
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27965463/ameloblastoma-rna-profiling-uncovers-a-distinct-non-coding-rna-signature
#14
Haleh Davanian, Anangi Balasiddaiah, Robert Heymann, Magnus Sundström, Poppy Redenström, Mikael Silfverberg, David Brodin, Matti Sällberg, Sven Lindskog, Carina Kruger Weiner, Margaret Chen
Ameloblastoma of the jaws remains the top difficult to treat odontogenic tumour and has a high recurrence rate. New evidence suggests that non-coding RNAs (ncRNAs) play a critical role in tumourgenesis and prognosis of cancer. However, ameloblastoma ncRNA expression data is lacking. Here we present the first report of ameloblastoma ncRNA signatures. A total of 95 ameloblastoma cases and a global array transcriptome technology covering > 285.000 full-length transcripts were used in this two-step analysis...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27936807/trna-derived-rna-fragments-associate-with-human-multisynthetase-complex-msc-and-modulate-ribosomal-protein-translation
#15
Simon P Keam, Andrew Sobala, Sara Ten Have, Gyorgy Hutvagner
The functionality of small RNAs from abundant species of "housekeeping" noncoding RNAs (e.g., rRNA, tRNA, snRNA, snoRNA, etc.) remains a highly studied topic. The current state of research on short RNAs derived from transfer RNA (tRNA), called tRNA-derived fragments (tRFs), has been restricted largely to expression studies and limited functional studies. 5' tRFs are known translational inhibitors in mammalian cells, yet little is known about their functionality. Here we report on the first experimental evidence of the tRF protein interactome, identifying the mammalian multisynthetase complex as the primary interactor of the 5' tRF Gln19...
December 12, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27916288/small-non-coding-rna-expression-from-anterior-cingulate-cortex-in-schizophrenia-shows-sex-specific-regulation
#16
Chikako Ragan, Kalpana Patel, Janette Edson, Zong-Hong Zhang, Jacob Gratten, Bryan Mowry
MicroRNAs (miRNAs) are known to regulate the expression of genes that are important for brain development and function, but the roles of other classes of small non-coding RNAs (sncRNAs) are less well understood. Additionally, although miRNA expression studies have been conducted in post-mortem brain samples from schizophrenia (SCZ) patients, other classes of sncRNAs are yet to be investigated in SCZ. We profiled the expression of miRNAs, piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs) in SCZ by applying small RNA sequencing (RNA-Seq) to sncRNA isolated from post-mortem anterior cingulate cortex (ACC) of SCZ-affected individuals (n=22) and matched controls (n=22)...
December 1, 2016: Schizophrenia Research
https://www.readbyqxmd.com/read/27913571/snord126-promotes-hcc-and-crc-cell-growth-by-activating-the-pi3k-akt-pathway-through-fgfr2
#17
Xianlong Fang, Dongmei Yang, Hongping Luo, Shuai Wu, Wenjie Dong, Jing Xiao, Sujing Yuan, Aimin Ni, Kang-Jian Zhang, Xin-Yuan Liu, Liang Chu
Small nucleolar RNA (snoRNA) dysfunctions have been associated with cancer development. SNORD126 is an orphan C/D box snoRNA that is encoded within introns 5-6 of its host gene, cyclin B1-interacting protein 1 (CCNB1IP1) The cancer-associated molecular mechanisms triggered by SNORD126 are not fully understood. Here, we demonstrate that SNORD126 is highly expressed in hepatocellular carcinoma (HCC) and colorectal cancer (CRC) patient samples. SNORD126 increased Huh-7 and SW480 cell growth and tumorigenicity in nude mice...
December 2, 2016: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/27911188/tuning-the-ribosome-the-influence-of-rrna-modification-on-eukaryotic-ribosome-biogenesis-and-function
#18
Katherine E Sloan, Ahmed S Warda, Sunny Sharma, Karl-Dieter Entian, Denis L J Lafontaine, Markus T Bohnsack
rRNAs are extensively modified during their transcription and subsequent maturation in the nucleolus, nucleus and cytoplasm. RNA modifications, which are installed either by snoRNA-guided or by stand-alone enzymes, generally stabilize the structure of the ribosome. However, they also cluster at functionally important sites of the ribosome, such as the peptidyltransferase center and the decoding site, where they facilitate efficient and accurate protein synthesis. The recent identification of sites of substoichiometric 2'-O-methylation and pseudouridylation has overturned the notion that all rRNA modifications are constitutively present on ribosomes, highlighting nucleotide modifications as an important source of ribosomal heterogeneity...
December 2, 2016: RNA Biology
https://www.readbyqxmd.com/read/27899625/ym500v3-a-database-for-small-rna-sequencing-in-human-cancer-research
#19
I-Fang Chung, Shing-Jyh Chang, Chen-Yang Chen, Shu-Hsuan Liu, Chia-Yang Li, Chia-Hao Chan, Chuan-Chi Shih, Wei-Chung Cheng
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899618/rna-seq-mixology-designing-realistic-control-experiments-to-compare-protocols-and-analysis-methods
#20
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
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