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Vault RNA

Dmytro Ustianenko, Josef Pasulka, Zuzana Feketova, Lukas Bednarik, Dagmar Zigackova, Andrea Fortova, Mihaela Zavolan, Stepanka Vanacova
Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes...
September 19, 2016: EMBO Journal
Anna Łabno, Zbigniew Warkocki, Tomasz Kuliński, Paweł Szczepan Krawczyk, Krystian Bijata, Rafał Tomecki, Andrzej Dziembowski
The exosome-independent exoribonuclease DIS3L2 is mutated in Perlman syndrome. Here, we used extensive global transcriptomic and targeted biochemical analyses to identify novel DIS3L2 substrates in human cells. We show that DIS3L2 regulates pol II transcripts, comprising selected canonical and histone-coding mRNAs, and a novel FTL_short RNA from the ferritin mRNA 5' UTR. Importantly, DIS3L2 contributes to surveillance of maturing snRNAs during their cytoplasmic processing. Among pol III transcripts, DIS3L2 particularly targets vault and Y RNAs and an Alu-like element BC200 RNA, but not Alu repeats, which are removed by exosome-associated DIS3...
July 18, 2016: Nucleic Acids Research
Fabio Alexis Lefebvre, Louis Philip Benoit Bouvrette, Lilyanne Perras, Alexis Blanchet-Cohen, Delphine Garnier, Janusz Rak, Éric Lécuyer
Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts...
2016: Scientific Reports
Chunjie Meng, Zhiyun Wei, Yiting Zhang, Liang Yan, Hang He, Lirong Zhang, Qinghe Xing
Cytochrome P450 3A4 (CYP3A4) is the most abundant cytochrome P450 enzyme in human liver and intestine, contributing to the metabolism of >60% of all pharmaceuticals. The expression levels of hepatic CYP3A4 show great inter‑individual variation. However, the detailed regulatory mechanism of CYP3A4 expression has remained largely elusive. It has been reported that the non‑coding RNA small vault (sv)RNAb targets the 3' untranslated region (3'UTR) of CYP3A4 in MCF7 cells. However, to date, the role of svRNAb has not been examined in human liver tissue and hepatic cell lines such as HepG2, which was the aim of the present study...
July 2016: Molecular Medicine Reports
Nanfang Peng, Shi Liu, Zhangchuan Xia, Sheng Ren, Jian Feng, Mingzhen Jing, Xin Gao, Erik A C Wiemer, Ying Zhu
Pathogen invasion triggers robust antiviral cytokine production via different transcription factor signaling pathways. We have previously demonstrated that major vault protein (MVP) induces type I IFN production during viral infection; however, little is known about the role of MVP in proinflammatory responses. In this study, we found in vitro that expression of MVP, IL-6, and IL-8 was inducible upon dsRNA stimulation or viral infection. Moreover, MVP was essential for the induction of IL-6 and IL-8, as impaired expression of IL-6 and IL-8 in MVP-deficient human PBMCs, human lung epithelial cells (A549), and THP-1 monocytes, as well as in murine splenocytes, peritoneal macrophages, and PBMCs from MVP-knockout (MVP(-/-)) mice, was observed...
March 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
Shahid Y Khan, Sean F Hackett, S Amer Riazuddin
Non-coding RNAs (ncRNAs) are emerging as an important player in the regulation of genome integrity and gene expression, and they have been implicated in the pathogenesis of many diseases. The aim of the present study is to identify the repertoire of ncRNAs expressed in the developing mouse lens. We previously reported the mouse lens transcriptome, including mRNA and microRNA (miRNA) profiling at two embryonic (E15 and E18) and four postnatal (P0, P3, P6, and P9) time points. We analyzed the data from small RNA-Seq and mRNA-Seq libraries to investigate the ncRNA profile...
April 2016: Experimental Eye Research
Alexandra Søgaard Helbo, Marianne Treppendahl, Derya Aslan, Konstantinos Dimopoulos, Cecilie Nandrup-Bus, Mette Skov Holm, Mette Klarskov Andersen, Gangning Liang, Lasse Sommer Kristensen, Kirsten Grønbæk
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders. MDS is frequently associated with deletions on chromosome 5q as well as aberrant DNA methylation patterns including hypermethylation of key tumor suppressors. We have previously shown that hypermethylation and silencing of the non-coding RNA VTRNA2-1 are correlated with poor outcomes in acute myeloid leukemia patients. In this study, we find that VTRNA1-2 and VTRNA1-3, both located on chromosome 5q, can be regulated and silenced by promoter DNA methylation, and that the hypomethylating agent 5-aza-2-deoxycytidine causes reactivation these genes...
2015: Genes
Lu Kong, Qi Hao, Ying Wang, Ping Zhou, Binbin Zou, Yu-xiang Zhang
nc886 or VRNA2-1 has recently been identified as a noncoding RNA instead of a vault RNA or a pre-microRNA. Several studies have reported that pre-miR-886 plays a tumor-suppressive role in a wide range of cancer cells through its activity as a cellular protein kinase RNA-activated (PKR) ligand and repressor. However, by sequencing stem-PCR products, we found that a microRNA originating from this precursor, vault RNA2-1-5p (VTRNA2-1-5p), occurs in cervical cancer cells. The expression levels of the predicted targets of VTRNA2-1-5p are negatively correlated with VTRNA2-1-5p levels by quantitative reversion transcription PCR (qRT-PCR)...
September 29, 2015: Oncotarget
Taral R Lunavat, Lesley Cheng, Dae-Kyum Kim, Joydeep Bhadury, Su Chul Jang, Cecilia Lässer, Robyn A Sharples, Marcela Dávila López, Jonas Nilsson, Yong Song Gho, Andrew F Hill, Jan Lötvall
Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform...
2015: RNA Biology
Bas W M van Balkom, Almut S Eisele, D Michiel Pegtel, Sander Bervoets, Marianne C Verhaar
Exosomes are small vesicles that mediate cell-cell communication. They contain proteins, lipids and RNA, and evidence is accumulating that these molecules are specifically sorted for release via exosomes. We recently showed that endothelial-cell-produced exosomes promote angiogenesis in vivo in a small RNA-dependent manner. Recent deep sequencing studies in exosomes from lymphocytic origin revealed a broad spectrum of small RNAs. However, selective depletion or incorporation of small RNA species into endothelial exosomes has not been studied extensively...
2015: Journal of Extracellular Vesicles
Melanie Amort, Birgit Nachbauer, Selma Tuzlak, Arnd Kieser, Aloys Schepers, Andreas Villunger, Norbert Polacek
Non-protein-coding RNAs are a functionally versatile class of transcripts exerting their biological roles on the RNA level. Recently, we demonstrated that the vault complex-associated RNAs (vtRNAs) are significantly upregulated in Epstein-Barr virus (EBV)-infected human B cells. Very little is known about the function(s) of the vtRNAs or the vault complex. Here, we individually express latent EBV-encoded proteins in B cells and identify the latent membrane protein 1 (LMP1) as trigger for vtRNA upregulation...
2015: Nature Communications
Hiroto Fukushima, Tetsuya Abe, Kazuki Sakamoto, Hiroaki Tsujimoto, Shinji Mizuarai, Shinji Oie
BACKGROUND: We previously reported that 3'-ethynylcytidine (ECyd, TAS-106), an RNA polymerases inhibitor, enhances the anti-tumor efficacy of platinum in several tumor types in both in vitro and in vivo tumor models. However, the molecular mechanisms underlying the ECyd-induced enhancement remain elusive. METHODS: Cisplatin (CDDP)-resistant head and neck cancer KB cells were established by stepwise dose escalation with CDDP. The combination effect of ECyd and CDDP were assessed using isobologram analysis...
2014: BMC Cancer
Kwang-Soo Lee, Jong-Lyul Park, Kwanbok Lee, Lauren E Richardson, Betty H Johnson, Hyun-Sung Lee, Ju-Seog Lee, Sang-Bae Kim, Oh-Hyung Kwon, Kyu Sang Song, Yong Sung Kim, Hassan Ashktorab, Duane T Smoot, Sung Ho Jeon, Seon-Young Kim, Yong Sun Lee
nc886 is a 101 nucleotide long non-coding RNA that has been designated as a precursor microRNA or a vault RNA based upon it sequence. nc886 has also been suggested to be a tumor suppressor, mainly inferred by its expression pattern as well as its genomic location at human chromosome 5q31, a locus for a tumor suppressor gene(s). However, legitimate data based on nc886's correct identity for its functional cellular roles as a tumor suppressor have not been provided yet. Here we have investigated nc886 in gastric cancer where its expression is suppressed due to CpG DNA hypermethylation at its promoter region in a cohort of paired tumor/normal tissues from 88 gastric cancer patients...
June 15, 2014: Oncotarget
Dimitry A Chistiakov, Vladimir P Chekhonin
Extracellular vesicles (EVs) are commonly used by normal and tumor cells for communication at long distances to exchange by complex molecular messages and deliver a variety of essential biomolecules. EVs (exosomes and microvesicles) released in large numbers by glioma cells represent a key mechanism of intercellular signaling. Tumor-derived EVs are produced to regulate all vital functions of tumor cells including growth, proliferation, migration, survival, malignancy, invasion, and resistance to host anti-tumor immunity and anti-cancer drugs...
September 2014: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Hirotaka Tomiyasu, Manabu Watanabe, Kanji Sugita, Yuko Goto-Koshino, Yasuhito Fujino, Koichi Ohno, Sumio Sugano, Hajime Tsujimoto
BACKGROUND: One of the major causes of failure in chemotherapy for patients with acute lymphoblastic leukemia (ALL) is the acquisition of multidrug resistance (MDR). Predominant mechanisms for MDR acquisition include the overexpression of efflux pumps. In the present study, the regulation of the expression of two genes that encode efflux pumps, ATP-binding cassette, sub-family B, member 1 (ABCB1) and ABCG2, through mitogen-activated protein kinase (MAPK) pathways was examined. MATERIALS AND METHODS: ABCB1 and ABCG2 mRNAs were quantified in a T-ALL cell line, CCRF-HSB-2 and a B-ALL cell line, YAMN90 using real-time RT-PCR...
December 2013: Anticancer Research
Ryuji Ikeda, Yukihiko Nishizawa, Yusuke Tajitsu, Kentaro Minami, Hironori Mataki, Shogo Masuda, Tatsuhiko Furukawa, Shin-Ichi Akiyama, Katsushi Yamada, Yasuo Takeda
Major vault protein (MVP) is the main constituent of the vault ribonucleoprotein particle and is identical to lung resistance-related protein (LRP). Although MVP is also expressed in several types of normal tissues, little is known about its physiological role. In the present study, we identified the crucial MVP promoter elements that regulate MVP expression. An examination of tissue expression profiles revealed that MVP was expressed in the heart, placenta, lung, liver, kidney and pancreas. Elements of the MVP promoter contain binding sites for transcription factors, STAT, p53, Sp1, E-box, GATA, MyoD and Y-box...
January 2014: Oncology Reports
Eneida V Reis, Roberta V Pereira, Matheus Gomes, Liana K Jannotti-Passos, Elio H Baba, Paulo Marcos Zech Coelho, Ana C A Mattos, Flávia F B Couto, William Castro-Borges, Renata Guerra-Sá
Vaults are ribonucleoproteins (13 MDa) highly conserved among lower and higher eukaryotes. Their association produces a complex composed of three proteins named Major Vault Protein (MVP), vault (PolyADP-ribose) polymerase (VPARP) and Telomerase-associated protein (TEP1), plus a small untranslated RNA. The exact function of this complex is unknown, although the biological role of vaults has been associated with multidrug resistance phenotypes and signal transduction pathways. Genomic analysis showed that model organisms, such as Caenorhabditis elegans and Drosophila melanogaster, do not possess genes encoding vaults...
February 2014: Parasitology International
Barbara Nasilowska-Adamska, Iwona Solarska, Monika Paluszewska, Iwona Malinowska, Wieslaw W Jedrzejczak, Krzysztof Warzocha
Fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) and mixed-lineage leukemia gene-partial tandem duplication (MLL-PTD) are aberrations associated with leukemia which indicate unsatisfactory prognosis. Downstream regulatory targets of FLT3-ITD and MLL-PTD are not well defined. We have analyzed the expression of MDR-1, multidrug resistant protein-1 (MRP-1), breast cancer resistance protein (BCRP), and lung resistance protein (LRP) messenger RNA (mRNA) in relation to the mutational status of FLT3-ITD and MLL-PTD in 185 acute myeloid leukemia (AML) adult patients...
April 2014: Annals of Hematology
Anupam Paliwal, Alexis M Temkin, Kristi Kerkel, Alexander Yale, Iveta Yotova, Natalia Drost, Simon Lax, Chia-Ling Nhan-Chang, Charles Powell, Alain Borczuk, Abraham Aviv, Ronald Wapner, Xiaowei Chen, Peter L Nagy, Nicholas Schork, Catherine Do, Ali Torkamani, Benjamin Tycko
Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM...
August 2013: PLoS Genetics
Peng Chen, Hao Chen, Xinjie Zang, Min Chen, Haoran Jiang, Shasha Han, Xianggen Wu
To investigate the expression profiles of efflux transporters in human ocular tissues, quantitative real-time polymerase chain reaction, Western blotting, and immunohistochemistry were used to obtain the relative mRNA and protein expressions of various efflux transporters in human ocular tissues. The cornea, conjunctiva, iris-ciliary body (ICB), retina and choroid, human corneal epithelial cell line (HCEC), and human retinal pigment epithelial cell line (ARPE-19) were examined for the expressions of multidrug resistance-associated proteins 1-7 (MRP1-7), multidrug resistance 1 (MDR1) P-glycoprotein, lung resistance protein (LRP), and breast cancer-resistance protein (BCRP)...
November 2013: Drug Metabolism and Disposition: the Biological Fate of Chemicals
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