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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
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28882366/editorial-commentary-let-it-snow-emerging-roles-for-snornas-in-cardiovascular-disease
#4
EDITORIAL
Mark W Feinberg
No abstract text is available yet for this article.
August 30, 2017: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28878772/lactobacillus-plantarum-strains-can-enhance-human-mucosal-and-systemic-immunity-and-prevent-non-steroidal-anti-inflammatory-drug-induced-reduction-in-t-regulatory-cells
#5
Paul de Vos, Zlatan Mujagic, Bart J de Haan, Roland J Siezen, Peter A Bron, Marjolein Meijerink, Jerry M Wells, Ad A M Masclee, Mark V Boekschoten, Marijke M Faas, Freddy J Troost
Orally ingested bacteria interact with intestinal mucosa and may impact immunity. However, insights in mechanisms involved are limited. In this randomized placebo-controlled cross-over trial, healthy human subjects were given Lactobacillus plantarum supplementation (strain TIFN101, CIP104448, or WCFS1) or placebo for 7 days. To determine whether L. plantarum can enhance immune response, we compared the effects of three stains on systemic and gut mucosal immunity, by among others assessing memory responses against tetanus toxoid (TT)-antigen, and mucosal gene transcription, in human volunteers during induction of mild immune stressor in the intestine, by giving a commonly used enteropathic drug, indomethacin [non-steroidal anti-inflammatory drug (NSAID)]...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28869095/biology-and-clinical-relevance-of-noncoding-sno-scarnas
#6
REVIEW
Thuy Cao, Sheeja Rajasingh, Saheli Samanta, Buddhadeb Dawn, Douglas C Bittel, Johnson Rajasingh
Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs that perform various biological functions, including biochemical modifications of other RNAs, precursors of miRNA, splicing, and telomerase activity. The small Cajal body-associated RNAs (scaRNAs) are a subset of the snoRNA family and collect in the Cajal body where they perform their canonical function to biochemically modify spliceosomal RNAs prior to maturation. Failure of sno/scaRNAs have been implicated in pathology such as congenital heart anomalies, neuromuscular disorders, and various malignancies...
August 12, 2017: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/28867607/tanshinone-iia-ameliorates-apoptosis-of-myocardiocytes-by-up-regulation-of-mir-133-and-suppression-of-caspase-9
#7
Tao Song, Yuan Yao, Teng Wang, He Huang, Hao Xia
To explore the potential protective effect of Tanshinone ⅡA on myocardial cell apoptosis and elucidate the underlying molecular mechanisms. The rat heart cell H9c2 was treated by either H2O2 or doxorubicin (DOX) to mimic oxidative stress and DNA damage conditions in vivo. Cell growth was monitored by optical microscope observation or CCK-8 counting kit. The relative expression of miR-133 and U6 snoRNA was semi-quantitated by RT-PCR or real-time PCR. Cell apoptosis was analyzed by flow cytometry with Annexin V/PI double staining...
August 31, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28855326/the-rna-modification-landscape-in-human-disease
#8
Nicky Jonkhout, Julia Tran, Martin Alexander Smith, Nicole Schonrock, John S Mattick, Eva Maria Novoa
RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs and snoRNAs. This view has changed dramatically in the recent years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination and stress responses...
August 30, 2017: RNA
https://www.readbyqxmd.com/read/28840253/interaction-and-cross-talk-between-non-coding-rnas
#9
REVIEW
Soichiro Yamamura, Mitsuho Imai-Sumida, Yuichiro Tanaka, Rajvir Dahiya
Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors...
August 24, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28817650/snorna-and-pirna-expression-levels-modified-by-tobacco-use-in-women-with-lung-adenocarcinoma
#10
Natasha Andressa Nogueira Jorge, Gabriel Wajnberg, Carlos Gil Ferreira, Benilton de Sa Carvalho, Fabio Passetti
Lung cancer is one of the most frequent types of cancer worldwide. Most patients are diagnosed at advanced stage and thus have poor prognosis. Smoking is a risk factor for lung cancer, however most smokers do not develop lung cancer while 20% of women with lung adenocarcinoma are non-smokers. Therefore, it is possible that these two groups present differences besides the smoking status, including differences in their gene expression signature. The altered expression patterns of non-coding RNAs in complex diseases make them potential biomarkers for diagnosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28761171/genomewide-analysis-of-clp1-function-in-transcription-in-budding-yeast
#11
Nadra Al-Husini, Ali Sharifi, Seyed Ahmad Mousavi, Hamidreza Chitsaz, Athar Ansari
In budding yeast, the 3' end processing of mRNA and the coupled termination of transcription by RNAPII requires the CF IA complex. We have earlier demonstrated a role for the Clp1 subunit of this complex in termination and promoter-associated transcription of CHA1. To assess the generality of the observed function of Clp1 in transcription, we tested the effect of Clp1 on transcription on a genomewide scale using the Global Run-On-Seq (GRO-Seq) approach. GRO-Seq analysis showed the polymerase reading through the termination signal in the downstream region of highly transcribed genes in a temperature-sensitive mutant of Clp1 at elevated temperature...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28734806/snora21-an-oncogenic-small-nucleolar-rna-with-a-prognostic-biomarker-potential-in-human-colorectal-cancer
#12
Kazuhiro Yoshida, Shusuke Toden, Wenhao Weng, Kunitoshi Shigeyasu, Jinsei Miyoshi, Jacob Turner, Takeshi Nagasaka, Yanlei Ma, Tetsuji Takayama, Toshiyoshi Fujiwara, Ajay Goel
BACKGROUND: Emerging evidence indicates that small nucleolar RNAs (snoRNAs) play a central role in oncogenesis. Herein, we systematically evaluated expression profiles of snoRNAs in colorectal cancer (CRC) and investigated their clinical and functional role in this malignancy. METHODS: We compared expression levels of snoRNAs between cancer and normal tissues using publicly available datasets and identified the most differentially expressed and commonly upregulated snoRNAs in CRC...
August 2017: EBioMedicine
https://www.readbyqxmd.com/read/28702505/human-snorna-93-is-processed-into-a-microrna-like-rna-that-promotes-breast-cancer-cell-invasion
#13
Dillon G Patterson, Justin T Roberts, Valeria M King, Dominika Houserova, Emmaline C Barnhill, Aline Crucello, Caroline J Polska, Lucas W Brantley, Garrett C Kaufman, Michael Nguyen, Megann W Santana, Ian A Schiller, Julius S Spicciani, Anastasia K Zapata, Molly M Miller, Timothy D Sherman, Ruixia Ma, Hongyou Zhao, Ritu Arora, Alexander B Coley, Melody M Zeidan, Ming Tan, Yaguang Xi, Glen M Borchert
Genetic searches for tumor suppressors have recently linked small nucleolar RNA misregulations with tumorigenesis. In addition to their classically defined functions, several small nucleolar RNAs are now known to be processed into short microRNA-like fragments called small nucleolar RNA-derived RNAs. To determine if any small nucleolar RNA-derived RNAs contribute to breast malignancy, we recently performed a RNA-seq-based comparison of the small nucleolar RNA-derived RNAs of two breast cancer cell lines (MCF-7 and MDA-MB-231) and identified small nucleolar RNA-derived RNAs derived from 13 small nucleolar RNAs overexpressed in MDA-MB-231s...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28678681/profiling-of-oxbs-450k-5-hydroxymethylcytosine-in-human-placenta-and-brain-reveals-enrichment-at-imprinted-loci
#14
Jose Ramon Hernandez Mora, Marta Sanchez-Delgado, Paolo Petazzi, Sebastian Moran, Manel Esteller, Isabel Iglesias-Platas, David Monk
DNA methylation (5-methylcytosine, 5mC) is involved in many cellular processes and is an epigenetic mechanism primarily associated with transcriptional repression. The recent discovery that 5mC can be oxidized to 5-hydromethylcytosine (5hmC) by TET proteins has revealed the "sixth base" of DNA and provides additional complexity to what was originally thought to be a stable repressive mark. However, our knowledge of the genome-wide distribution of 5hmC in different tissues is currently limited. Here, we sought to define loci enriched for 5hmC in the placenta genome by combining oxidative bisulphite (oxBS) treatment with high-density Illumina Infinium HumanMethylation450 methylation arrays and to compare our results with those obtained in brain...
July 5, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28671581/pleiotropic-roles-of-non-coding-rnas-in-tgf-%C3%AE-mediated-epithelial-mesenchymal-transition-and-their-functions-in-tumor-progression
#15
REVIEW
Simon Grelet, Ariel McShane, Renaud Geslain, Philip H Howe
Epithelial-mesenchymal transition (EMT) is a spatially- and temporally-regulated process involved in physiological and pathological transformations, such as embryonic development and tumor progression. While the role of TGF-β as an EMT-inducer has been extensively documented, the molecular mechanisms regulating this transition and their implications in tumor metastasis are still subjects of intensive debates and investigations. TGF-β regulates EMT through both transcriptional and post-transcriptional mechanisms, and recent advances underline the critical roles of non-coding RNAs in these processes...
July 1, 2017: Cancers
https://www.readbyqxmd.com/read/28663102/rnase-h1-dependent-antisense-oligonucleotides-are-robustly-active-in-directing-rna-cleavage-in-both-the-cytoplasm-and-the-nucleus
#16
Xue-Hai Liang, Hong Sun, Joshua G Nichols, Stanley T Crooke
RNase H1-dependent antisense oligonucleotides (ASOs) are active in reducing levels of both cytoplasmic mRNAs and nuclear retained RNAs. Although ASO activity in the nucleus has been well demonstrated, the cytoplasmic activity of ASOs is less clear. Using kinetic and subcellular fractionation studies, we evaluated ASO activity in the cytoplasm. Upon transfection, ASOs targeting exonic regions rapidly reduced cytoplasmically enriched mRNAs, whereas an intron-targeting ASO that only degrades the nuclear pre-mRNA reduced mRNA levels at a slower rate, similar to normal mRNA decay...
September 6, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28659642/snornas-contribute-to-myeloid-leukaemogenesis
#17
Mona Khalaj, Christopher Y Park
The mechanism of action of oncogenes in acute myeloid leukaemia is poorly understood. A study now shows that the fusion oncoprotein AML1-ETO regulates leukaemogenesis by increasing the expression of small nucleolar RNAs through post-transcriptional mechanisms, resulting in increased ribosomal RNA methylation, protein translation, and promotion of leukaemic-cell self-renewal and growth.
June 29, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28650479/aml1-eto-requires-enhanced-c-d-box-snorna-rnp-formation-to-induce-self-renewal-and-leukaemia
#18
Fengbiao Zhou, Yi Liu, Christian Rohde, Cornelius Pauli, Dennis Gerloff, Marcel Köhn, Danny Misiak, Nicole Bäumer, Chunhong Cui, Stefanie Göllner, Thomas Oellerich, Hubert Serve, Maria-Paz Garcia-Cuellar, Robert Slany, Jaroslaw P Maciejewski, Bartlomiej Przychodzen, Barbara Seliger, Hans-Ulrich Klein, Christoph Bartenhagen, Wolfgang E Berdel, Martin Dugas, Makoto Mark Taketo, Daneyal Farouq, Schraga Schwartz, Aviv Regev, Josée Hébert, Guy Sauvageau, Caroline Pabst, Stefan Hüttelmaier, Carsten Müller-Tidow
Leukaemogenesis requires enhanced self-renewal, which is induced by oncogenes. The underlying molecular mechanisms remain incompletely understood. Here, we identified C/D box snoRNAs and rRNA 2'-O-methylation as critical determinants of leukaemic stem cell activity. Leukaemogenesis by AML1-ETO required expression of the groucho-related amino-terminal enhancer of split (AES). AES functioned by inducing snoRNA/RNP formation via interaction with the RNA helicase DDX21. Similarly, global loss of C/D box snoRNAs with concomitant loss of rRNA 2'-O-methylation resulted in decreased leukaemia self-renewal potential...
July 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28629949/the-diversity-of-long-noncoding-rnas-and-their-generation
#19
REVIEW
Huang Wu, Li Yang, Ling-Ling Chen
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures...
June 16, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28623187/control-of-box-c-d-snornp-assembly-by-n-6-methylation-of-adenine
#20
Lin Huang, Saira Ashraf, Jia Wang, David Mj Lilley
N(6)-methyladenine is the most widespread mRNA modification. A subset of human box C/D snoRNA species have target GAC sequences that lead to formation of N(6)-methyladenine at a key trans Hoogsteen-sugar A·G base pair, of which half are methylated in vivo The GAC target is conserved only in those that are methylated. Methylation prevents binding of the 15.5-kDa protein and the induced folding of the RNA Thus, the assembly of the box C/D snoRNP could in principle be regulated by RNA methylation at its critical first stage...
September 2017: EMBO Reports
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