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https://www.readbyqxmd.com/read/29141226/a-pan-cancer-analysis-of-the-expression-and-clinical-relevance-of-small-nucleolar-rnas-in-human-cancer
#1
Jing Gong, Yajuan Li, Chun-Jie Liu, Yu Xiang, Chunlai Li, Youqiong Ye, Zhao Zhang, David H Hawke, Peter K Park, Lixia Diao, John A Putkey, Liuqing Yang, An-Yuan Guo, Chunru Lin, Leng Han
Increasing evidence has demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in >10,000 samples across 31 cancer types from The Cancer Genome Atlas. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#2
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29132127/a-functional-connection-between-dyskerin-and-energy-metabolism
#3
Alberto Angrisani, Nunzia Matrone, Valentina Belli, Rosario Vicidomini, Nunzia Di Maio, Mimmo Turano, Filippo Scialò, Paolo Antonio Netti, Antonio Porcellini, Maria Furia
The human DKC1 gene encodes dyskerin, an evolutionarily conserved nuclear protein whose overexpression represents a common trait of many types of aggressive sporadic cancers. As a crucial component of the nuclear H/ACA snoRNP complexes, dyskerin is involved in a variety of essential processes, including telomere maintenance, splicing efficiency, ribosome biogenesis, snoRNAs stabilization and stress response. Although multiple minor dyskerin splicing isoforms have been identified, their functions remain to be defined...
November 6, 2017: Redox Biology
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#4
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29106639/mndr-v2-0-an-updated-resource-of-ncrna-disease-associations-in-mammals
#5
Tianyu Cui, Lin Zhang, Yan Huang, Ying Yi, Puwen Tan, Yue Zhao, Yongfei Hu, Liyan Xu, Enmin Li, Dong Wang
Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA-disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA-disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA-disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29089527/cross-platform-analysis-of-transcriptomic-data-identifies-ageing-has-distinct-and-opposite-effects-on-tendon-in-males-and-females
#6
Louise I Pease, Peter D Clegg, Carole J Proctor, Daryl J Shanley, Simon J Cockell, Mandy J Peffers
The development of tendinopathy is influenced by a variety of factors including age, gender, sex hormones and diabetes status. Cross platform comparative analysis of transcriptomic data elucidated the connections between these entities in the context of ageing. Tissue-engineered tendons differentiated from bone marrow derived mesenchymal stem cells from young (20-24 years) and old (54-70 years) donors were assayed using ribonucleic acid sequencing (RNA-seq). Extension of the experiment to microarray and RNA-seq data from tendon identified gender specific gene expression changes highlighting disparity with existing literature and published pathways...
October 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29064465/small-non-coding-rna-transcriptome-of-the-nci-60-cell-line-panel
#7
Erin A Marshall, Adam P Sage, Kevin W Ng, Victor D Martinez, Natalie S Firmino, Kevin L Bennewith, Wan L Lam
Only 3% of the transcribed human genome is translated into protein, and small non-coding RNAs from these untranslated regions have demonstrated critical roles in transcriptional and translational regulation of proteins. Here, we provide a resource that will facilitate cell line selection for gene expression studies involving sncRNAs in cancer research. As the most accessible and tractable models of tumours, cancer cell lines are widely used to study cancer development and progression. The NCI-60 panel of 59 cancer cell lines was curated to provide common models for drug screening in 9 tissue types; however, its prominence has extended to use in gene regulation, xenograft models, and beyond...
October 24, 2017: Scientific Data
https://www.readbyqxmd.com/read/29062204/repertoire-of-noncoding-rnas-in-corpus-luteum-of-early-pregnancy-in-buffalo-bubalus-bubalis
#8
A Jerome, S M K Thirumaran, S N Kala
AIM: The present study was designed to identify other noncoding RNAs (ncRNAs) in the corpus luteum (CL) during early pregnancy in buffalo. MATERIALS AND METHODS: For this study, CL (n=2) from two buffalo gravid uteri, obtained from the slaughter house, was transported to laboratory after snap freezing in liquid nitrogen (-196°C). The stage of pregnancy was determined by measuring the crown-rump region of the fetus. This was followed by isolation of RNA and deep sequencing...
September 2017: Veterinary World
https://www.readbyqxmd.com/read/29051386/ets2-anchors-the-prometastatic-function-of-mutant-p53-in-osteosarcoma
#9
REVIEW
Daniel D Liu, Yibin Kang
Mutations in the tumor suppressor p53 occur in a majority of human cancers. Some gain-of-function (GOF) p53 mutations endow tumor cells with increased metastatic ability, although our understanding of the underlying mechanism remains incomplete. In this issue of Genes & Development, Pourebrahim and colleagues (pp. 1847-1857) develop a new mouse model of osteosarcoma in which a GOF mutant p53 allele is expressed specifically in osteoblasts, while the tumor microenvironment remains wild type for p53, allowing for the study of cell-autonomous functions...
September 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/29045842/the-conserved-rna-exonuclease-rexo5-is-required-for-3-end-maturation-of-28s-rrna-5s-rrna-and-snornas
#10
Stefanie Gerstberger, Cindy Meyer, Sigi Benjamin-Hong, Joe Rodriguez, Daniel Briskin, Claudia Bognanni, Kimberly Bogardus, Hermann Steller, Thomas Tuschl
Non-coding RNA biogenesis in higher eukaryotes has not been fully characterized. Here, we studied the Drosophila melanogaster Rexo5 (CG8368) protein, a metazoan-specific member of the DEDDh 3'-5' single-stranded RNA exonucleases, by genetic, biochemical, and RNA-sequencing approaches. Rexo5 is required for small nucleolar RNA (snoRNA) and rRNA biogenesis and is essential in D. melanogaster. Loss-of-function mutants accumulate improperly 3' end-trimmed 28S rRNA, 5S rRNA, and snoRNA precursors in vivo. Rexo5 is ubiquitously expressed at low levels in somatic metazoan cells but extremely elevated in male and female germ cells...
October 17, 2017: Cell Reports
https://www.readbyqxmd.com/read/29029611/identification-of-15-candidate-structured-noncoding-rna-motifs-in-fungi-by-comparative-genomics
#11
Sanshu Li, Ronald R Breaker
BACKGROUND: With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies...
October 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29021253/nuclear-export-factor-3-regulates-localization-of-small-nucleolar-rnas
#12
Melissa W Li, Arthur C Sletten, Jiyeon Lee, Kelly D Pyles, Scot J Matkovich, Daniel S Ory, Jean E Schaffer
Small nucleolar RNAs (snoRNAs) guide chemical modifications of ribosomal and small nuclear RNAs, functions that are carried out in the nucleus. While most snoRNAs reside in the nucleolus, a growing body of evidence indicates that snoRNAs are also present in the cytoplasm and that snoRNAs move between the nucleus and cytoplasm by a mechanism that is regulated by lipotoxic and oxidative stress. Here, in a genome-wide shRNA-based screen we identified nuclear export factor 3 (NXF3) as a transporter that alters the nucleocytoplasmic distribution of box C/D snoRNAs from the ribosomal protein L13a (Rpl13a) locus...
October 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29021240/integrative-genome-analysis-of-somatic-p53-mutant-osteosarcomas-identifies-ets2-dependent-regulation-of-small-nucleolar-rnas-by-mutant-p53-protein
#13
Rasoul Pourebrahim, Yun Zhang, Bin Liu, Ruli Gao, Shunbin Xiong, Patrick P Lin, Mark J McArthur, Michael C Ostrowski, Guillermina Lozano
TP53 is the most frequently mutated gene in human cancer. Many mutant p53 proteins exert oncogenic gain-of-function (GOF) properties that contribute to metastasis, but the mechanisms mediating these functions remain poorly defined in vivo. To elucidate how mutant p53 GOF drives metastasis, we developed a traceable somatic osteosarcoma mouse model that is initiated with either a single p53 mutation (p53R172H) or p53 loss in osteoblasts. Our study confirmed that p53 mutant mice developed osteosarcomas with increased metastasis as compared with p53-null mice...
October 11, 2017: Genes & Development
https://www.readbyqxmd.com/read/28981840/the-sirna-suppressor-rtl1-is-redox-regulated-through-glutathionylation-of-a-conserved-cysteine-in-the-double-stranded-rna-binding-domain
#14
Cyril Charbonnel, Adnan K Niazi, Emilie Elvira-Matelot, Elzbieta Nowak, Matthias Zytnicki, Anne de Bures, Edouard Jobet, Alisson Opsomer, Nahid Shamandi, Marcin Nowotny, Christine Carapito, Jean-Philippe Reichheld, Hervé Vaucheret, Julio Sáez-Vásquez
RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28977534/fractionation-iclip-detects-persistent-sr-protein-binding-to-conserved-retained-introns-in-chromatin-nucleoplasm-and-cytoplasm
#15
Mattia Brugiolo, Valentina Botti, Na Liu, Michaela Müller-McNicoll, Karla M Neugebauer
RNA binding proteins (RBPs) regulate the lives of all RNAs from transcription, processing, and function to decay. How RNA-protein interactions change over time and space to support these roles is poorly understood. Towards this end, we sought to determine how two SR proteins-SRSF3 and SRSF7, regulators of pre-mRNA splicing, nuclear export and translation-interact with RNA in different cellular compartments. To do so, we developed Fractionation iCLIP (Fr-iCLIP), in which chromatin, nucleoplasmic and cytoplasmic fractions are prepared from UV-crosslinked cells and then subjected to iCLIP...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28973544/loss-of-the-imprinted-non-coding-snord116-gene-cluster-in-the-interval-deleted-in-the-prader-willi-syndrome-results-in-murine-neuronal-and-endocrine-pancreatic-developmental-phenotypes
#16
Lisa Cole Burnett, Gabriela Hubner, Charles LeDuc, Michael V Morabito, Jayne F Martin Carli, Rudolph L Leibel
Global neurodevelopmental delay is a prominent characteristic of individuals with Prader-Willi syndrome (PWS). The neuromolecular bases for these delays are unknown. We identified neuroanatomical changes in the brains of mice deficient for a gene in the minimal critical deletion region for PWS (Snord116p-/m+). In Snord116p-/m+ mice, reduced primary forebrain neuron cell body size is apparent in embryonic day 15.5 fetuses, and persists until postnatal day 30 in cerebellar purkinje neurons. Snord116 is a snoRNA gene cluster of unknown function that can localize to the nucleolus...
September 6, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28943972/small-non-coding-rna-abundance-in-adrenocortical-carcinoma-a-footprint-of-a-rare-cancer
#17
Srinivas V Koduru, Ashley N Leberfinger, Dino J Ravnic
BACKGROUND: Adrenocortical carcinoma (ACC) is a relatively rare, but aggressive type of cancer, which affects both children and adults. OBJECTIVE: Small non-coding RNAs (sncRNAs) play important roles and may serve as biomarkers for disease diagnosis, prognosis and treatment. METHODS: In our study, we sought to identify sncRNAs associated with malignant adrenal tumors. We obtained publicly available, small RNA sequencing data derived from 45 ACC and 30 benign tumors arising from the cortex of the adrenal gland, adrenocortical adenomas (ACA), and compared their sncRNA expression profiles...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28934414/mrna-seq-reveals-accumulation-followed-by-reduction-of-small-nuclear-and-nucleolar-rnas-in-yeast-exposed-to-antiviral-ribavirin
#18
Siyu Xu, Naomichi Yamamoto
Ribavirin is an antiviral drug that is used to treat a wide range of human viral infections. However, the side effects are reported, and the mechanisms on eukaryotic cells are still largely unknown. Here we report our observation of accumulation followed by reduction of small nuclear (sn)RNAs and small nucleolar (sno)RNAs in Saccharomyces cerevisiae exposed to ribavirin. The three strains reported to contain dsRNA virus-like particle(s) were exposed to 100 μM of ribavirin, and snRNAs and snoRNAs from a total of 31 snR genes were differentially detected between the samples exposed to ribavirin and the respective negative controls by mRNA-Seq...
November 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28911119/a-snorna-modulates-mrna-3-end-processing-and-regulates-the-expression-of-a-subset-of-mrnas
#19
Chunliu Huang, Junjie Shi, Yibin Guo, Weijun Huang, Shanshan Huang, Siqi Ming, Xingui Wu, Rui Zhang, Junjun Ding, Wei Zhao, Jie Jia, Xi Huang, Andy Peng Xiang, Yongsheng Shi, Chengguo Yao
mRNA 3' end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3' processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3' processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF)...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904332/identification-of-sites-of-2-o-methylation-vulnerability-in-human-ribosomal-rnas-by-systematic-mapping
#20
Sunny Sharma, Virginie Marchand, Yuri Motorin, Denis L J Lafontaine
Ribosomal RNA modifications are important in optimizing ribosome function. Sugar 2'-O-methylation performed by fibrillarin-associated box C/D antisense guide snoRNAs impacts all steps of translation, playing a role in disease etiology (cancer). As it renders adjacent phosphodiester bonds resistant to alkaline treatment, 2'-O-methylation can be monitored qualitatively and quantitatively by applying next-generation sequencing to fragments of randomly cleaved RNA. We remapped all sites of 2'-O-methylation in human rRNAs in two isogenic diploid cell lines, one producing and one not producing the antitumor protein p53...
September 13, 2017: Scientific Reports
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