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Vault RNA

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https://www.readbyqxmd.com/read/29423138/developmental-constraint-through-negative-pleiotropy-in-the-zygomatic-arch
#1
Christopher J Percival, Rebecca Green, Charles C Roseman, Daniel M Gatti, Judith L Morgan, Stephen A Murray, Leah Rae Donahue, Jessica M Mayeux, K Michael Pollard, Kunjie Hua, Daniel Pomp, Ralph Marcucio, Benedikt Hallgrímsson
Background: Previous analysis suggested that the relative contribution of individual bones to regional skull lengths differ between inbred mouse strains. If the negative correlation of adjacent bone lengths is associated with genetic variation in a heterogeneous population, it would be an example of negative pleiotropy, which occurs when a genetic factor leads to opposite effects in two phenotypes. Confirming negative pleiotropy and determining its basis may reveal important information about the maintenance of overall skull integration and developmental constraint on skull morphology...
2018: EvoDevo
https://www.readbyqxmd.com/read/29394925/nc886-is-epigenetically-repressed-in-prostate-cancer-and-acts-as-a-tumor-suppressor-through-the-inhibition-of-cell-growth
#2
Rafael Sebastián Fort, Cecilia Mathó, Murilo Vieira Geraldo, María Carolina Ottati, Alex Shimura Yamashita, Kelly Cristina Saito, Katia Ramos Moreira Leite, Manuel Méndez, Noemí Maedo, Laura Méndez, Beatriz Garat, Edna Teruko Kimura, José Roberto Sotelo-Silveira, María Ana Duhagon
BACKGROUND: Nc886 is a 102 bp non-coding RNA transcript initially classified as a microRNA precursor (Pre-miR-886), later as a divergent homologue of the vault RNAs (vtRNA 2-1) and more recently as a novel type of RNA (nc886). Although nc886/vtRNA2-1/Pre-miR-886 identity is still controversial, it was shown to be epigenetically controlled, presenting both tumor suppressor and oncogenic function in different cancers. Here, we study for the first time the role of nc886 in prostate cancer...
February 2, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29346433/vault-rnas-partially-induces-drug-resistance-of-human-tumor-cells-mcf-7-by-binding-to-the-rna-dna-binding-protein-psf-and-inducing-oncogene-gage6
#3
Jianjun Chen, Hui OuYang, Xuemei An, Shixi Liu
BACKGROUND: Vault is the largest nonicosahedral cytosolic nucleoprotein particle, which is widely involved in induction of chemoresistance and lead to failure in long-term chemotherapy. Vault contains three different major vault proteins (MVPs) and four vault RNAs paralogues (vtRNAs, vtRNA1-1, vtRNA1-2, vtRNA1-3 and vtRNA2-1). Disruption of the MVPs do not induce hypersensitivity while expression of vtRNAs contributes to cells' drug resistance, indicates that vtRNAs, but not MVPs play an important role in causing drug resistance...
2018: PloS One
https://www.readbyqxmd.com/read/29343745/malaria-infected-red-blood-cells-release-small-regulatory-rnas-through-extracellular-vesicles
#4
Kehinde Adebayo Babatunde, Smart Mbagwu, María Andrea Hernández-Castañeda, Swamy R Adapa, Michael Walch, Luis Filgueira, Laurent Falquet, Rays H Y Jiang, Ionita Ghiran, Pierre-Yves Mantel
The parasite Plasmodium falciparum causes the most severe form of malaria. Cell communication between parasites is an important mechanism to control population density and differentiation. The infected red blood cells (iRBCs) release small extracellular vesicles (EVs) that transfer cargoes between cells. The EVs synchronize the differentiation of the asexual parasites into gametocytes to initiate the transmission to the mosquito. Beside their role in parasite communication, EVs regulate vascular function. So far, the exact cargoes responsible for cellular communication remain unknown...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29324814/comprehensive-molecular-profiling-of-advanced-metastatic-olfactory-neuroblastomas
#5
Jasmina Topcagic, Rebecca Feldman, Anatole Ghazalpour, Jeffrey Swensen, Zoran Gatalica, Semir Vranic
Olfactory neuroblastoma (ONB) is a rare, locally aggressive, malignant neoplasm originating in the olfactory epithelium in the nasal vault. The recurrence rate of ONB remains high and there are no specific treatment guidelines for recurrent/metastatic ONBs. This study retrospectively evaluated 23 ONB samples profiled at Caris Life Sciences (Phoenix, Arizona) using DNA sequencing (Sanger/NGS [Illumina], n = 15) and gene fusions (Archer FusionPlex, n = 6), whole genome RNA microarray (HumanHT-12 v4 beadChip, Illumina, n = 4), gene copy number assays (chromogenic and fluorescent in situ hybridization), and immunohistochemistry...
2018: PloS One
https://www.readbyqxmd.com/read/29219730/a-comprehensive-profile-of-circulating-rnas-in-human-serum
#6
Sinan Uğur Umu, Hilde Langseth, Cecilie Bucher-Johannessen, Bastian Fromm, Andreas Keller, Eckart Meese, Marianne Lauritzen, Magnus Leithaug, Robert Lyle, Trine B Rounge
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA)...
December 8, 2017: RNA Biology
https://www.readbyqxmd.com/read/29073095/broad-role-for-ybx1-in-defining-the-small-noncoding-rna-composition-of-exosomes
#7
Matthew J Shurtleff, Jun Yao, Yidan Qin, Ryan M Nottingham, Morayma M Temoche-Diaz, Randy Schekman, Alan M Lambowitz
RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of conventional RNA-sequencing methods. Here we present our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to characterize the RNA extracted from HEK293T cell EVs isolated by flotation gradient ultracentrifugation and from exosomes containing the tetraspanin CD63 further purified from the gradient fractions by immunoisolation...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28877058/nonuniform-distribution-of-high-risk-human-papillomavirus-in-squamous-cell-carcinomas-of-the-oropharynx-rethinking-the-anatomic-boundaries-of-oral-and-oropharyngeal-carcinoma-from-an-oncologic-hpv-perspective
#8
Elise Gelwan, Ian-James Malm, Armen Khararjian, Carol Fakhry, Justin A Bishop, William H Westra
The oral cavity and oropharynx have historically been viewed as a single anatomic compartment of the head and neck. The practice of combining the oral cavity and oropharynx has recently been revised, largely owing to the observation that human papillomavirus (HPV)-related carcinogenesis has a strong predilection for the oropharynx but not the oral cavity. The purpose of this study was to determine whether HPV is evenly distributed across squamous cell carcinomas of the oropharynx including those sites that do not harbor tonsillar tissues such as the soft palate...
December 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28774579/afm-nanoindentation-of-protein-shells-expanding-the-approach-beyond-viruses
#9
REVIEW
Wouter H Roos
The archetypical protein nanoshell is the capsid that surrounds viral genomes. These capsids protect the viral RNA or DNA and function as transport vehicle for their nucleic acid. The material properties of a variety of viral capsids have been probed by Atomic Force Microscopy. In particular nanoindentation measurements revealed the complex mechanics of these shells and the intricate interplay of the capsid with its genomic content. Furthermore, effects of capsid protein mutations, capsid maturation and the effect of environmental changes have been probed...
July 31, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/27829009/the-morphogenesis-of-cranial-sutures-in-zebrafish
#10
Jolanta M Topczewska, Ramy A Shoela, Joanna P Tomaszewski, Rupa B Mirmira, Arun K Gosain
Using morphological, histological, and TEM analyses of the cranium, we provide a detailed description of bone and suture growth in zebrafish. Based on expression patterns and localization, we identified osteoblasts at different degrees of maturation. Our data confirm that, unlike in humans, zebrafish cranial sutures maintain lifelong patency to sustain skull growth. The cranial vault develops in a coordinated manner resulting in a structure that protects the brain. The zebrafish cranial roof parallels that of higher vertebrates and contains five major bones: one pair of frontal bones, one pair of parietal bones, and the supraoccipital bone...
2016: PloS One
https://www.readbyqxmd.com/read/27798849/dusp11-activity-on-triphosphorylated-transcripts-promotes-argonaute-association-with-noncanonical-viral-micrornas-and-regulates-steady-state-levels-of-cellular-noncoding-rnas
#11
James M Burke, Rodney P Kincaid, Ryan M Nottingham, Alan M Lambowitz, Christopher S Sullivan
RNA silencing is a conserved eukaryotic gene expression regulatory mechanism mediated by small RNAs. In Caenorhabditis elegans, the accumulation of a distinct class of siRNAs synthesized by an RNA-dependent RNA polymerase (RdRP) requires the PIR-1 phosphatase. However, the function of PIR-1 in RNAi has remained unclear. Since mammals lack an analogous siRNA biogenesis pathway, an RNA silencing role for the mammalian PIR-1 homolog (dual specificity phosphatase 11 [DUSP11]) was unexpected. Here, we show that the RNA triphosphatase activity of DUSP11 promotes the RNA silencing activity of viral microRNAs (miRNAs) derived from RNA polymerase III (RNAP III) transcribed precursors...
September 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27791479/two-distinct-extracellular-rna-signatures-released-by-a-single-cell-type-identified-by-microarray-and-next-generation-sequencing
#12
Cecilia Lässer, Ganesh Vilas Shelke, Ashish Yeri, Dae-Kyum Kim, Rossella Crescitelli, Stefania Raimondo, Margareta Sjöstrand, Yong Song Gho, Kendall Van Keuren Jensen, Jan Lötvall
Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated 2 distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not...
January 2, 2017: RNA Biology
https://www.readbyqxmd.com/read/27647875/tut-dis3l2-is-a-mammalian-surveillance-pathway-for-aberrant-structured-non-coding-rnas
#13
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...
October 17, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27431325/perlman-syndrome-nuclease-dis3l2-controls-cytoplasmic-non-coding-rnas-and-provides-surveillance-pathway-for-maturing-snrnas
#14
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...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27282340/comparative-transcriptomic-analysis-of-human-and-drosophila-extracellular-vesicles
#15
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
https://www.readbyqxmd.com/read/27177257/regulation-of-cytochrome-p450-3a4-by-small-vault-rnab-derived-from-the-non-coding-vault%C3%A2-rna1-of-multidrug-resistance-linked-vault-particle
#16
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
https://www.readbyqxmd.com/read/26843330/inducible-major-vault-protein-plays-a-pivotal-role-in-double-stranded-rna-or-virus-induced-proinflammatory-response
#17
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
https://www.readbyqxmd.com/read/26808486/non-coding-rna-profiling-of-the-developing-murine-lens
#18
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
https://www.readbyqxmd.com/read/26473932/hypermethylation-of-the-vtrna1-3-promoter-is-associated-with-poor-outcome-in-lower-risk-myelodysplastic-syndrome-patients
#19
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...
October 14, 2015: Genes
https://www.readbyqxmd.com/read/26318295/regulation-of-p53-expression-and-apoptosis-by-vault-rna2-1-5p-in-cervical-cancer-cells
#20
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
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