Genomes and Genes
Summary: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
- Liu A, Torchia B, Migeon B, Siliciano R. The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics. 1997;39:171-84 pubmed..Their proximity and shared expression pattern suggest a possible functional relationship. ..
- Zachar Z, Kramer J, Mims I, Bingham P. Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans. J Cell Biol. 1993;121:729-42 pubmed..We propose a simple model--based on channeled diffusion--for organization of intranuclear transport and metabolism of pre-mRNAs in polytene nuclei. We argue that this model can be generalized to all metazoan nuclei. ..
- Mankodi A, Lin X, Blaxall B, Swanson M, Thornton C. Nuclear RNA foci in the heart in myotonic dystrophy. Circ Res. 2005;97:1152-5 pubmed..A toxic effect of RNA with an expanded repeat may contribute to cardiac disease in DM1. ..
- Li H, Liu D, Waxman D. Transcriptional induction of hepatic NADPH: cytochrome P450 oxidoreductase by thyroid hormone. Mol Pharmacol. 2001;59:987-95 pubmed..P450R precursor RNA, followed by a decrease back to basal transcription levels at 24 h, consistent with the nuclear RNA profile...
- Yip P, Kwan H. Molecular identification of Astragalus membranaceus at the species and locality levels. J Ethnopharmacol. 2006;106:222-9 pubmed..Therefore, Astragalus membranaceus from these provinces, the major cultivation places in China, can be differentiated...
- Hugouvieux V, Murata Y, Young J, Kwak J, Mackesy D, Schroeder J. Localization, ion channel regulation, and genetic interactions during abscisic acid signaling of the nuclear mRNA cap-binding protein, ABH1. Plant Physiol. 2002;130:1276-87 pubmed..These data provide evidence for the model that the mRNA-processing proteins ABH1 and SAD1 function as negative regulators in guard cell ABA signaling. ..
- Okamoto M, Matsumoto K, Shibui A, Shibahara T, Ito A. Fundamental study of expression-library immunization against Taenia taeniaeformis in rats. Southeast Asian J Trop Med Public Health. 2005;36 Suppl 4:135-8 pubmed..Rats were immunized with expression-library and injected orally with 1,000 T. taeniaeformis eggs. However the protective effect of expression-library vaccine was not confirmed. ..
- García Varela M, Gonzalez Oliver A. The systematic position of Leptorhynchoides (Kostylew, 1924) and Pseudoleptorhynchoides (Salgado-Maldonado, 1976), inferred from nuclear and mitochondrial DNA gene sequences. J Parasitol. 2008;94:959-62 pubmed publisher..Maximum parsimony and maximum likelihood analyses were identical in placing both genera in the Illiosentidae. Bootstrap analyses also indicate that placement of these genera with members of Illiosentidae is reliably supported...
- Yu F, Gapor A, Bender W. Evidence for the preventive effect of the polyunsaturated phytol side chain in tocotrienols on 17beta-estradiol epoxidation. Cancer Detect Prev. 2005;29:383-8 pubmedWe found that 17beta-estradiol (E2) could be activated by epoxidation to bind DNA and to inhibit nuclear RNA synthesis. Vitamin E compounds are powerful antioxidants and chain-breaking free radical scavengers...
- Mix K, Mengshol J, Benbow U, Vincenti M, Sporn M, Brinckerhoff C. A synthetic triterpenoid selectively inhibits the induction of matrix metalloproteinases 1 and 13 by inflammatory cytokines. Arthritis Rheum. 2001;44:1096-104 pubmed..This study demonstrates that CDDO is a novel inhibitor of MMP-1 and MMP-13 gene expression mediated by inflammatory cytokines. Thus, CDDO may have therapeutic potential for the inhibition of joint degradation in osteoarthritis. ..
- Pederson T. Half a century of "the nuclear matrix". Mol Biol Cell. 2000;11:799-805 pubmed
- Boehm J, Orth T, Van Nguyen P, Söling H. Systemic lupus erythematosus is associated with increased auto-antibody titers against calreticulin and grp94, but calreticulin is not the Ro/SS-A antigen. Eur J Clin Invest. 1994;24:248-57 pubmed
- Bernard D, Prasanth K, Tripathi V, Colasse S, Nakamura T, Xuan Z, et al. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J. 2010;29:3082-93 pubmed publisher..Our results suggest that Malat1 regulates synapse formation by modulating the expression of genes involved in synapse formation and/or maintenance. ..
- Umlauf S, Beverly B, Lantz O, Schwartz R. Regulation of interleukin 2 gene expression by CD28 costimulation in mouse T-cell clones: both nuclear and cytoplasmic RNAs are regulated with complex kinetics. Mol Cell Biol. 1995;15:3197-205 pubmed..This complexity suggests the existence of two interesting molecular mechanisms by which CD28 costimulates lymphokine gene expression. ..
- Chelomina G, Rozhkovan K, Kiselev K, Ivanov S, Bulgakov V. Multiplicity of alleles of nuclear 18S rRNA gene of Amur sturgeons: genes and pseudogenes?. Dokl Biochem Biophys. 2008;420:115-8 pubmed
- Barboro P, D Arrigo C, Repaci E, Bagnasco L, Orecchia P, Carnemolla B, et al. Proteomic analysis of the nuclear matrix in the early stages of rat liver carcinogenesis: identification of differentially expressed and MAR-binding proteins. Exp Cell Res. 2009;315:226-39 pubmed publisher..were synchronous with several modifications in both NM morphology and the ability of NM proteins to bind nuclear RNA and/or DNA containing MARs sequences...
- Paps J, Baguna J, Riutort M. Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. Proc Biol Sci. 2009;276:1245-54 pubmed publisher..Ribosomal RNA genes are thus a reliable source for the study of deep divergences in the metazoan tree, provided that the data are treated carefully. ..
- Schwanekamp J, Sartor M, Karyala S, Halbleib D, Medvedovic M, Tomlinson C. Genome-wide analyses show that nuclear and cytoplasmic RNA levels are differentially affected by dioxin. Biochim Biophys Acta. 2006;1759:388-402 pubmed..and TCDD-treated mouse embryonic fibroblasts (MEF) to test the hypotheses that (1) TCDD has a large impact on nuclear RNA levels and (2) that cytoplasmic RNA levels are dependent on nuclear RNA levels...
- Zhang Y, Zhang J, Huang M, Yang M, Cao H. Detection of genetic homogeneity of Panax notoginseng cultivars by sequencing nuclear 18S rRNA and plastid matK genes. Planta Med. 2006;72:860-2 pubmed..D85171 and AB027526). This phenomenon implies that the species is highly conserved, which is probably caused by the use of the same strain in cultivation and the lack of active mutation in these two genes. ..
- Nolan M, Jex A, Mansell P, Browning G, Gasser R. Genetic characterization of Cryptosporidium parvum from calves by mutation scanning and targeted sequencing--zoonotic implications. Electrophoresis. 2009;30:2640-7 pubmed publisher..Nucleotide sequences reported in this paper are available in the GenBank database under accession numbers FJ825018-FJ825029). ..
- Mastroyiannopoulos N, Shammas C, Phylactou L. Tackling the pathogenesis of RNA nuclear retention in myotonic dystrophy. Biol Cell. 2010;102:515-23 pubmed publisher..The purpose of the present review is to summarize the successful attempts to tackle the pathogenesis caused by nuclear retention of mutant transcripts in myotonic dystrophy and to discuss the possible gains from such approaches. ..
- Avivi S, Mor A, Dotan I, Tzadok S, Kanter I, Kinor N, et al. Visualizing nuclear RNAi activity in single living human cells. Proc Natl Acad Sci U S A. 2017;114:E8837-E8846 pubmed publisherb>Nuclear RNA interference (RNAi) is mediated by the canonical RNAi machinery and can lead to transcriptional silencing, transcriptional activation, or modulation of alternative splicing patterns...
- De La Fuente J, Almazan C, Van Den Bussche R, Bowman J, Yoshioka J, Kocan K. Characterization of genetic diversity in Dermacentor andersoni (Acari: Ixodidae) with body size and weight polymorphism. Exp Parasitol. 2005;109:16-26 pubmed..The results reported herein show that B ticks have a better reproductive success than S ticks and suggest partial reproductive isolation of S ticks. ..
- Kuldau G, Raju N, Glass N. Repeat-induced point mutations in Pad-1, a putative RNA splicing factor from Neurospora crassa, confer dominant lethal effects on ascus development. Fungal Genet Biol. 1998;23:169-80 pubmed..A mutant isolated from the Pad-1 RIP cross displayed a severe vegetative growth defect and dominant effects on ascus development, indicating that Pad-1 is essential for both asexual and sexual development. ..
- Shamovsky I, Gershon D. Novel regulatory factors of HSF-1 activation: facts and perspectives regarding their involvement in the age-associated attenuation of the heat shock response. Mech Ageing Dev. 2004;125:767-75 pubmed..It is proposed that structural changes in any one or a combination of these factors in response to heat shock may contribute to the age-associated attenuation in the response to stress. ..
- Isakova G, Zakharenko L, Abramova M. [Activity of embryonic mink genome during diapause (cytogenetic analysis): nucleolar and extranucleolar rna synthesis]. Ontogenez. 2001;32:302-8 pubmed..The data obtained suggest a differential and stage specific activity of the embryonic mRNA and rRNA synthesis during the period of delayed implantation. ..
- Hall L, Lawrence J. The cell biology of a novel chromosomal RNA: chromosome painting by XIST/Xist RNA initiates a remodeling cascade. Semin Cell Dev Biol. 2003;14:369-78 pubmed
- Raslova H, Roy L, Vourc h C, Le Couedic J, Brison O, Metivier D, et al. Megakaryocyte polyploidization is associated with a functional gene amplification. Blood. 2003;101:541-4 pubmed..Altogether, our results demonstrate that megakaryocyte polyploidization results in a functional gene amplification whose likely function is an increase in protein synthesis parallel with cell enlargement. ..
- Duborjal H, Beugnot R, Mousson de Camaret B, Issartel J. Large functional range of steady-state levels of nuclear and mitochondrial transcripts coding for the subunits of the human mitochondrial OXPHOS system. Genome Res. 2002;12:1901-9 pubmed..We also observed that in the different tissues and cells, there is a transcriptional coregulation of all the investigated nuclear genes. Nuclear OXPHOS gene expression seems to be finely regulated. ..
- Kohler S. Trypanosoma brucei: improved detection of nuclear transcripts reveals a genomic position effect on nuclearly accumulating NEO RNAs visualized in stably transformed cells. Exp Parasitol. 1999;92:249-62 pubmed..An improved fluorescent in situ hybridization method was used to visualize accumulations of nuclear RNA in procyclic Trypanosoma brucei that were stably transformed with a bacterial gene encoding neomycin ..
- Vitali P, Royo H, Marty V, Bortolin Cavaillé M, Cavaille J. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci. 2010;123:70-83 pubmed publisher..Our findings have repercussions for understanding the spatial organization of gene expression and the intra-nuclear fate of non-coding RNAs in the context of nuclear architecture. ..
- Ko Y, Kang Y, Kim E, Park S, Kim S. Nucleolar localization of human methionyl-tRNA synthetase and its role in ribosomal RNA synthesis. J Cell Biol. 2000;149:567-74 pubmed..Thus, human MRS plays a role in the biogenesis of rRNA in nucleoli, while it is catalytically involved in protein synthesis in cytoplasm. ..
- Politz J, Yarovoi S, Kilroy S, Gowda K, Zwieb C, Pederson T. Signal recognition particle components in the nucleolus. Proc Natl Acad Sci U S A. 2000;97:55-60 pubmed..Our findings support the notion that the nucleolus is the site of assembly and/or interaction between the family of ribonucleoproteins involved in protein synthesis, in addition to ribosomes themselves. ..
- Ideue T, Hino K, Kitao S, Yokoi T, Hirose T. Efficient oligonucleotide-mediated degradation of nuclear noncoding RNAs in mammalian cultured cells. RNA. 2009;15:1578-87 pubmed publisher..In summary, we believe that our system is a powerful tool to explore the biological functions of the large number of nuclear ncRNAs with unknown function. ..
- Deng Z, Norseen J, Wiedmer A, Riethman H, Lieberman P. TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol Cell. 2009;35:403-13 pubmed publisher..We conclude that TERRA facilitates TRF2 interaction with ORC and plays a central role in telomere structural maintenance and heterochromatin formation. ..
- Chen L, Carmichael G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell. 2009;35:467-78 pubmed publisher..Taken together, these results assign a biological function to a large noncoding nuclear RNA in the regulation of mRNA export.
- Santini R, Myrand S, Elferink C, Reiners J. Regulation of Cyp1a1 induction by dioxin as a function of cell cycle phase. J Pharmacol Exp Ther. 2001;299:718-28 pubmed..Quantitative reverse transcriptase-polymerase chain reaction analyses of CYP1A1 heterogeneous nuclear RNA (hnRNA) revealed that Cyp1a1 transcription was suppressed in G2/M cells...
- Chen L, Carmichael G. Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol. 2010;22:357-64 pubmed publisher..In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level. ..
- Bazett Jones D, Hendzel M, Kruhlak M. Stoichiometric analysis of protein- and nucleic acid-based structures in the cell nucleus. Micron. 1999;30:151-7 pubmed..In so doing, we demonstrate that these granules contain heterogeneous nuclear RNA, and have an average protein and RNA content of 3.094 and 1.672 MDa, respectively...
- Tycowski K, Shu M, Steitz J. Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal RNA maturation. Science. 1994;266:1558-61 pubmed..The appearance of 18S rRNA was restored by injection of in vitro-synthesized U22 RNA. These results identify a cellular function for an intron-encoded small RNA. ..
- Liao X, Selinger D, Althoff S, Chiang A, Hamilton D, Ma M, et al. Random mutagenesis of Schizosaccharomyces pombe SRP RNA: lethal and conditional lesions cluster in presumptive protein binding sites. Nucleic Acids Res. 1992;20:1607-15 pubmed
- Puranam R, Attardi G. The RNase P associated with HeLa cell mitochondria contains an essential RNA component identical in sequence to that of the nuclear RNase P. Mol Cell Biol. 2001;21:548-61 pubmed..The available evidence indicates that the levels of mtRNase P detected in HeLa cells should be fully adequate to satisfy the mitochondrial tRNA synthesis requirements of these cells. ..
- Meru N, Jung A, Lisner R, Niedobitek G. Expression of the recombination activating genes (RAG1 and RAG2) is not detectable in Epstein-Barr virus-associated human lymphomas. Int J Cancer. 2001;92:75-8 pubmed..Moreover, our study shows that in situ hybridization is a suitable method for the analysis of RAG expression in human tissue sections. ..
- Shav Tal Y, Blechman J, Darzacq X, Montagna C, Dye B, Patton J, et al. Dynamic sorting of nuclear components into distinct nucleolar caps during transcriptional inhibition. Mol Biol Cell. 2005;16:2395-413 pubmed
- Ulvé V, Sevin E, Chéron A, Barloy Hubler F. Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021. BMC Genomics. 2007;8:467 pubmed..Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium. ..
- Armando Sánchez J, Lasker H, Taylor D. Phylogenetic analyses among octocorals (Cnidaria): mitochondrial and nuclear DNA sequences (lsu-rRNA, 16S and ssu-rRNA, 18S) support two convergent clades of branching gorgonians. Mol Phylogenet Evol. 2003;29:31-42 pubmed..ribosomal subunit of the mitochondrial RNA (lsu-rRNA, 16S: 524bp and 21 species) and the small subunit of the nuclear RNA (ssu-rRNA, 18S: 1815bp and 13 spp) using information from insertions-deletions (INDELS) and the predicted ..
- Raska I, Shaw P, Cmarko D. New insights into nucleolar architecture and activity. Int Rev Cytol. 2006;255:177-235 pubmed..However, the present power of light and electron microscopy (EM) techniques means that a description of nucleolar processes at the molecular level is now achievable, and the time is ripe for such an effort...
- Qi Y, Ding B. Differential subnuclear localization of RNA strands of opposite polarity derived from an autonomously replicating viroid. Plant Cell. 2003;15:2566-77 pubmed
- Giorgobiani N, Dzidziguri D, Rusishvili L, Giorgobiani E, Chkhobadze M, Tumanishvili G. [Investigation of properties of the thermostable protein complex obtained from the myocardium left ventricles of adult white rats]. Tsitologiia. 2006;48:443-9 pubmed..Besides, it is planned to produce antibodies against TSPC fractions with the purpose to block its inhibitory effect on myocyte regeneration in the damaged myocardium. ..
- Kohtz J, Fishell G. Developmental regulation of EVF-1, a novel non-coding RNA transcribed upstream of the mouse Dlx6 gene. Gene Expr Patterns. 2004;4:407-12 pubmed..EVF-1 expression is linked to Shh and the Dlx family of proteins, genes with a demonstrated importance to ventral forebrain and craniofacial development. ..
- Bridger J, Kalla C, Wodrich H, Weitz S, King J, Khazaie K, et al. Nuclear RNAs confined to a reticular compartment between chromosome territories. Exp Cell Res. 2005;302:180-93 pubmed..Co-delineation of the RNA transcripts with Cajal bodies and chromosome territories indicated the organization of nuclear RNA transcripts in a reticular interchromosome domain compartment.
- Bass B, Hellwig S, Hundley H. A nuclear RNA is cut out for translation. Cell. 2005;123:181-3 pubmed..It is then transported to the cytoplasm and translated into protein. These findings suggest that the nucleus may store RNAs destined for translation that then can be released, as needed, in response to specific cellular signals. ..
- Finn J, MacLachlan I, Cullis P. Factors limiting autogene-based cytoplasmic expression systems. FASEB J. 2005;19:608-10 pubmed..It follows that mRNA production, as well as translation, are important factors limiting autogene-based cytoplasmic expression. ..