60 results match your criteria pol i-associated

RNA polymerase I (Pol I) passage through nucleosomes depends on Pol I subunits binding its lobe structure.

J Biol Chem 2020 04 14;295(15):4782-4795. Epub 2020 Feb 14.

Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany

RNA polymerase I (Pol I) is a highly efficient enzyme specialized in synthesizing most ribosomal RNAs. After nucleosome deposition at each round of rDNA replication, the Pol I transcription machinery has to deal with nucleosomal barriers. It has been suggested that Pol I-associated factors facilitate chromatin transcription, but it is unknown whether Pol I has an intrinsic capacity to transcribe through nucleosomes. Read More

View Article and Full-Text PDF

Antisense-Derived HIV-1 Cryptic Epitopes Are Not Major Drivers of Viral Evolution during the Acute Phase of Infection.

J Virol 2018 10 12;92(19). Epub 2018 Sep 12.

Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA

While prior studies have demonstrated that CD8 T cell responses to cryptic epitopes (CE) are readily detectable during HIV-1 infection, their ability to drive escape mutations following acute infection is unknown. We predicted 66 CE in a Zambian acute infection cohort based on escape mutations occurring within or near the putatively predicted HLA-I-restricted epitopes. The CE were evaluated for CD8 T cell responses for patients with chronic and acute HIV infections. Read More

View Article and Full-Text PDF
October 2018

Activation of γ2-AMPK Suppresses Ribosome Biogenesis and Protects Against Myocardial Ischemia/Reperfusion Injury.

Circ Res 2017 Oct 23;121(10):1182-1191. Epub 2017 Aug 23.

From the Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center (Y.C., N.B., M.K., T.L., R.T.) and Department of Biochemistry (R.D.P.), University of Washington, Seattle; Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark (P.Z., N.N., J.S.); and Howard Hughes Medical Institute, Seattle, WA (R.D.P.).

Rationale: AMPK (AMP-activated protein kinase) is a heterotrimeric protein that plays an important role in energy homeostasis and cardioprotection. Two isoforms of each subunit are expressed in the heart, but the isoform-specific function of AMPK remains unclear.

Objective: We sought to determine the role of γ2-AMPK in cardiac stress response using bioengineered cell lines and mouse models containing either isoform of the γ-subunit in the heart. Read More

View Article and Full-Text PDF
October 2017

Cystoisosporiasis-related human acalculous cholecystitis: the need for increased awareness.

Pol J Pathol 2016;67(3):270-276

Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. and

Cholecystitis is one of the common surgical indications affecting human beings in many countries. A variety of infectious agents can be associated with acute or chronic acalculous cholecystitis, especially in HIV/AIDS patients. In this investigation, the authors aim to describe two cases of histologically and molecularly documented cystoisosporiasis (syn. Read More

View Article and Full-Text PDF

Purification of RNA Polymerase I-Associated Chromatin from Yeast Cells.

Methods Mol Biol 2016 ;1455:213-23

Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie I, 93053, Regensburg, Germany.

The native template of all eukaryotic nuclear RNA polymerases is chromatin. To understand how transcription occurs in vivo, it is important to define the chromatin environment of transcribing RNA Pols. Here, we describe a method used to characterize the distribution and the protein environment of RNA Pol I on ribosomal DNA during transcription in the yeast S. Read More

View Article and Full-Text PDF
January 2018

A Combination of CRISPR/Cas9 and Standardized RNAi as a Versatile Platform for the Characterization of Gene Function.

G3 (Bethesda) 2016 08 9;6(8):2467-78. Epub 2016 Aug 9.

Institute of Molecular Biotechnology Austria, 1030 Vienna, Austria Gene Center, Ludwig-Maximilians-University Munich, 81377, Germany

Traditional loss-of-function studies in Drosophila suffer from a number of shortcomings, including off-target effects in the case of RNA interference (RNAi) or the stochastic nature of mosaic clonal analysis. Here, we describe minimal in vivo GFP interference (miGFPi) as a versatile strategy to characterize gene function and to conduct highly stringent, cell type-specific loss-of-function experiments in Drosophila miGFPi combines CRISPR/Cas9-mediated tagging of genes at their endogenous locus with an immunotag and an exogenous 21 nucleotide RNAi effector sequence with the use of a single reagent, highly validated RNAi line targeting this sequence. We demonstrate the utility and time effectiveness of this method by characterizing the function of the Polymerase I (Pol I)-associated transcription factor Tif-1a, and the previously uncharacterized gene MESR4, in the Drosophila female germline stem cell lineage. Read More

View Article and Full-Text PDF

Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic.

J Virol 2016 02 11;90(3):1244-58. Epub 2015 Nov 11.

Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada

Unlabelled: Human leukocyte antigen (HLA) class I-associated polymorphisms in HIV-1 that persist upon transmission to HLA-mismatched hosts may spread in the population as the epidemic progresses. Transmission of HIV-1 sequences containing such adaptations may undermine cellular immune responses to the incoming virus in future hosts. Building upon previous work, we investigated the extent of HLA-associated polymorphism accumulation in HIV-1 polymerase (Pol) through comparative analysis of linked HIV-1/HLA class I genotypes sampled during historic (1979 to 1989; n = 338) and modern (2001 to 2011; n = 278) eras from across North America (Vancouver, BC, Canada; Boston, MA; New York, NY; and San Francisco, CA). Read More

View Article and Full-Text PDF
February 2016

Regulation of the association of the PAF53/PAF49 heterodimer with RNA polymerase I.

Gene 2015 Feb 16;556(1):61-7. Epub 2014 Sep 16.

Department of Cell Biology, University of Oklahoma College of Medicine, 940 Stanton L. Young Blvd., BMSB-553, Oklahoma City, OK 73104, USA. Electronic address:

Mammalian PAF49 and PAF53 form a heterodimer and are essential for transcription. However their roles in transcription have not been specifically defined. While the yeast homologues are "not essential" proteins, yeast cells deficient in the homologue of PAF53 grow at 50-66% the wild-type rate at 30°C, but fail to grow at 25°C (Liljelund et al. Read More

View Article and Full-Text PDF
February 2015

Selective inhibition of rDNA transcription by a small-molecule peptide that targets the interface between RNA polymerase I and Rrn3.

Mol Cancer Res 2014 Nov 17;12(11):1586-96. Epub 2014 Jul 17.

Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma.

Unlabelled: The interface between the polymerase I-associated factor Rrn3 and the 43-kDa subunit of RNA polymerase I is essential to the recruitment of Pol I to the preinitiation complex on the rDNA promoter. In silico analysis identified an evolutionarily conserved 22 amino acid peptide within rpa43 that is both necessary and sufficient to mediate the interaction between rpa43 and Rrn3. This peptide inhibited rDNA transcription in vitro, while a control peptide did not. Read More

View Article and Full-Text PDF
November 2014

Meeting report for Odd Pols 2012.

Gene 2013 Aug 20;526(1):1-6. Epub 2013 Apr 20.

Tulane Cancer Center, Dept. of Epidemiology, and Louisiana Cancer Research Consortium (LCRC), 1430 Tulane Ave, SL-66, New Orleans, LA 70112, USA.

The Eighth International Biennial Conference on RNA polymerases I and III (the 'Odd Pols') was held June 7-11, 2012 at The Airlie Center in Warrenton Virginia, USA. It was sponsored by the Universite Laval and the Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, and organized by Rich Maraia and Tom Moss. The meeting honored the memory of Pierre Thuriaux (Jan 1, 1950-March 18, 2012) and David Schneider reminisced on the important accomplishments his mentor Masayasu Nomura (1927-2011). Read More

View Article and Full-Text PDF

Characterization of the interactions of mammalian RNA polymerase I associated proteins PAF53 and PAF49.

Biochemistry 2012 Aug 8;51(33):6519-26. Epub 2012 Aug 8.

Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, USA.

Masami Muramatsu's laboratory demonstrated the critical role of RNA polymerase I (Pol I)-associated factor PAF53 in mammalian rRNA transcription. They have also identified a second polymerase associated factor, PAF49. Both PAF49 and PAF53 copurify with that fraction of the RNA polymerase I molecules that can function in transcription initiation in vitro. Read More

View Article and Full-Text PDF

Increasingly successful highly active antiretroviral therapy delays the emergence of new HLA class I-associated escape mutations in HIV-1.

Clin Infect Dis 2012 Jun 28;54(11):1652-9. Epub 2012 Mar 28.

BC Centre for Excellence in HIV/AIDS, Vancouver, Canada.

Background: HLA class I-restricted cytotoxic T lymphocytes and highly active antiretroviral therapy (HAART) exert strong selective pressures on human immunodeficiency virus type 1 (HIV-1), leading to escape mutations compromising virologic control. Immune responses continue to shape HIV-1 evolution after HAART initiation, but the extent and rate at which this occurs remain incompletely quantified. Here, we characterize the incidence and clinical correlates of HLA-associated evolution in HIV-1 Pol after HAART initiation in a large, population-based observational cohort. Read More

View Article and Full-Text PDF

hALP, a novel transcriptional U three protein (t-UTP), activates RNA polymerase I transcription by binding and acetylating the upstream binding factor (UBF).

J Biol Chem 2011 Mar 22;286(9):7139-48. Epub 2010 Dec 22.

Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing 100142, China.

Transcription of ribosome RNA precursor (pre-rRNA) and pre-rRNA processing are coordinated by a subset of U three proteins (UTPs) known as transcriptional UTPs (t-UTPs), which participate in pre-rRNA transcription in addition to participation in 18 S rRNA processing. However, the mechanism by which t-UTPs function in pre-rRNA transcription remains undetermined. In the present study, we identified hALP, a histone acetyl-transferase as a novel t-UTP. Read More

View Article and Full-Text PDF

Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers.

J Acquir Immune Defic Syndr 2011 Feb;56(2):100-8

Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.

Background: Identifying viral and host determinants of HIV-1 elite control may help inform novel therapeutic and/or vaccination strategies. Previously, we observed decreased replication capacity in controller-derived viruses suggesting that fitness consequences of human leukocyte antigen (HLA) class I-associated escape mutations in Gag may contribute to this phenotype. This study examines whether similar functional defects occur in Pol proteins of elite controllers. Read More

View Article and Full-Text PDF
February 2011

Co-transcriptional RNA cleavage provides a failsafe termination mechanism for yeast RNA polymerase I.

Nucleic Acids Res 2011 Mar 23;39(4):1439-48. Epub 2010 Oct 23.

Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.

Ribosomal RNA, transcribed by RNA polymerase (Pol) I, accounts for most cellular RNA. Since Pol I transcribes rDNA repeats with high processivity and polymerase density, transcription termination is a critical process. Early in vitro studies proposed polymerase pausing by Reb1 and transcript release at the T-rich element T1 determined transcription termination. Read More

View Article and Full-Text PDF

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription.

J Exp Med 2010 Jan 11;207(1):51-9. Epub 2010 Jan 11.

Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). Read More

View Article and Full-Text PDF
January 2010

AMP-activated protein kinase adapts rRNA synthesis to cellular energy supply.

Proc Natl Acad Sci U S A 2009 Oct 6;106(42):17781-6. Epub 2009 Oct 6.

Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, INF 581, D-69120 Heidelberg, Germany.

AMP-activated protein kinase (AMPK) senses changes in the intracellular AMP/ATP ratio, switching off energy-consuming processes and switching on catabolic pathways in response to energy depletion. Here, we show that AMPK down-regulates rRNA synthesis under glucose restriction by phosphorylating the RNA polymerase I (Pol I)-associated transcription factor TIF-IA at a single serine residue (Ser-635). Phosphorylation by AMPK impairs the interaction of TIF-IA with the TBP-containing promoter selectivity factor SL1, thereby precluding the assembly of functional transcription initiation complexes. Read More

View Article and Full-Text PDF
October 2009

Suppression of human T-cell leukemia virus I gene expression by pokeweed antiviral protein.

J Biol Chem 2009 Nov 11;284(45):31453-62. Epub 2009 Sep 11.

Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.

Human T-cell leukemia virus I (HTLV-I) is a deltaretrovirus that is the causative agent of adult T-cell leukemia and the neurological disorder HTLV-I-associated myelopathy/tropical spastic paraparesis. Currently, no effective antiretroviral treatment options are available to restrict the development of diseases associated with the virus. In this work, we investigated the activity of pokeweed antiviral protein (PAP) on HTLV-I, when expressed from a proviral clone in 293T cells or in an HTLV-I immortalized cell line. Read More

View Article and Full-Text PDF
November 2009

Protective HLA class I alleles that restrict acute-phase CD8+ T-cell responses are associated with viral escape mutations located in highly conserved regions of human immunodeficiency virus type 1.

J Virol 2009 Feb 26;83(4):1845-55. Epub 2008 Nov 26.

Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA.

The control of human immunodeficiency virus type 1 (HIV-1) associated with particular HLA class I alleles suggests that some CD8(+) T-cell responses may be more effective than others at containing HIV-1. Unfortunately, substantial diversities in the breadth, magnitude, and function of these responses have impaired our ability to identify responses most critical to this control. It has been proposed that CD8 responses targeting conserved regions of the virus may be particularly effective, since the development of cytotoxic T-lymphocyte (CTL) escape mutations in these regions may significantly impair viral replication. Read More

View Article and Full-Text PDF
February 2009

Budding yeast RNA polymerases I and II employ parallel mechanisms of transcriptional termination.

Genes Dev 2008 Apr;22(8):1082-92

Sir William Dunn School of Pathology, Oxford OX1 3RE, United Kingdom.

Both RNA polymerase I and II (Pol I and Pol II) in budding yeast employ a functionally homologous "torpedo-like" mechanism to promote transcriptional termination. For two well-defined Pol II-transcribed genes, CYC1 and PMA1, we demonstrate that both Rat1p exonuclease and Sen1p helicase are required for efficient termination by promoting degradation of the nascent transcript associated with Pol II, following mRNA 3' end processing. Similarly, Pol I termination relies on prior Rnt1p cleavage at the 3' end of the pre-rRNA 35S transcript. Read More

View Article and Full-Text PDF

RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor.

Mol Cell Biol 2006 Jul;26(14):5436-48

Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, United Kingdom.

Eukaryotic RNA polymerases are large complexes, 12 subunits of which are structurally or functionally homologous across the three polymerase classes. Each class has a set of specific subunits, likely targets of their cognate transcription factors. We have identified and characterized a human RNA polymerase I (Pol I)-specific subunit, previously identified as ASE-1 (antisense of ERCC1) and as CD3epsilon-associated signal transducer (CAST), and here termed CAST or human Pol I-associated factor of 49 kDa (hPAF49), after mouse orthologue PAF49. Read More

View Article and Full-Text PDF

RNA-templated replication of hepatitis delta virus: genomic and antigenomic RNAs associate with different nuclear bodies.

J Virol 2006 Jul;80(13):6478-86

Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, 2011 Zonal Ave., Los Angeles, CA 90033-1054, USA.

Lacking an RNA-dependent RNA polymerase, hepatitis delta virus (HDV), which contains a circular RNA of 1.7 kilobases, is nonetheless able to replicate its RNA by use of cellular transcription machineries. Previously, we have shown that the replications of genomic- and antigenomic-strand HDV RNAs have different sensitivities to alpha-amanitin, suggesting that these two strands are synthesized in different transcription machineries in the cells, but the nature of these transcription machineries is not clear. Read More

View Article and Full-Text PDF

Nucleolar protein upstream binding factor is sequestered into adenovirus DNA replication centres during infection without affecting RNA polymerase I location or ablating rRNA synthesis.

J Cell Sci 2006 Jun;119(Pt 12):2621-31

Division of Virology, Department of Cellular and Molecular Medicine, University Walk, University of Bristol, Bristol, BS8 1TD, UK.

When human adenovirus infects human cells there is disruption of rRNA biogenesis. This report examines the effect of adenovirus infection on the nucleolar protein, upstream binding factor (UBF) which plays a major role in regulating rRNA synthesis. We determined that early after infection, UBF associates with the replication of viral DNA, preferentially associating with the ends of the linear viral genome, and that addition of anti-UBF serum to in vitro replication assays markedly reduced viral DNA replication. Read More

View Article and Full-Text PDF

Acetylation of UBF changes during the cell cycle and regulates the interaction of UBF with RNA polymerase I.

Nucleic Acids Res 2006 31;34(6):1798-806. Epub 2006 Mar 31.

Division of Molecular Biology, Biocenter, Innsbruck Medical University, A-6020 Innsbruck, Austria.

The upstream binding factor UBF, an activator of RNA polymerase I transcription, is posttranslationally modified by phosphorylation and acetylation. We found that in NIH3T3 cells, UBF is acetylated in S-phase but not in G1-phase. To assess the role of acetylation in regulation of UBF activity, we have established an NIH3T3 cell line that inducibly overexpresses HDAC1. Read More

View Article and Full-Text PDF

Human T-cell lymphotropic virus type I (HTLV-I) proviral DNA viral load among asymptomatic patients and patients with HTLV-I-associated myelopathy/tropical spastic paraparesis.

Braz J Med Biol Res 2005 Nov 26;38(11):1643-7. Epub 2005 Oct 26.

Departamento de Dermatologia, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP, Brazil.

To evaluate the human T-cell lymphotropic virus type I (HTLV-I) proviral DNA load among asymptomatic HTLV-I-infected carriers and patients with HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP), real time PCR using TaqMan probes for the pol gene was performed in two million peripheral blood mononuclear cells (PBMC). The albumin gene was the internal genomic control and MT2 cells were used as positive control. The results are reported as copies/10,000 PBMC, and the detection limit was 10 copies. Read More

View Article and Full-Text PDF
November 2005

Regulation of ribosomal RNA gene expression in porcine oocytes.

Anim Reprod Sci 2004 Jul;82-83:605-16

Department of Animal and Veterinary Basic Sciences, The Royal Veterinary and Agricultural University, Groennegaardsvej 7, DK-1870 Frederiksberg C, Denmark.

In vitro production (IVP) of porcine embryos including in vitro maturation (IVM) of oocytes followed by in vitro fertilization (IVF) and in vitro culture (IVC) of the resultant embryos may result in live offspring, but it is still associated with great inefficiencies probably due to incomplete cytoplasmic maturation of the oocytes in vitro. Therefore, fundamental knowledge on the regulation of transcription during the oocyte growth phase when the messengers and protein synthetic machinery necessary for oocyte developmental competence are formed, is of great importance. In mammals, synthesis of RNA, up to 60-70% of which is ribosomal (rRNA), increases during oocyte growth and reaches a peak at the beginning of follicular antrum formation. Read More

View Article and Full-Text PDF

Multiple protein-protein interactions by RNA polymerase I-associated factor PAF49 and role of PAF49 in rRNA transcription.

Mol Cell Biol 2004 Jul;24(14):6338-49

Department of Biochemistry, Saitama Medical School, Iruma-gun, Japan.

We previously demonstrated the critical role of RNA polymerase I (Pol I)-associated factor PAF53 in mammalian rRNA transcription. Here, we report the isolation and characterization of another Pol I-associated factor, PAF49. Mouse PAF49 shows striking homology to the human nucleolar protein ASE-1, so that they are considered orthologues. Read More

View Article and Full-Text PDF

Expression of nucleolar-related proteins in porcine preimplantation embryos produced in vivo and in vitro.

Biol Reprod 2004 Apr 29;70(4):867-76. Epub 2003 Oct 29.

Department of Anatomy and Physiology, Royal Veterinary and Agricultural University, 1870 Frederiksberg C, Denmark.

The expression of nucleolar-related proteins was studied as an indirect marker of the ribosomal RNA (rRNA) gene activation in porcine embryos up to the blastocyst stage produced in vivo and in vitro. A group of the in vivo-developed embryos were cultured with alpha-amanitin to block the de novo embryonic mRNA transcription. Localization of proteins involved in the rRNA transcription (upstream binding factor [UBF], topoisomerase I, RNA polymerase I [RNA Pol I], and the RNA Pol I-associated factor PAF53) and processing (fibrillarin, nucleophosmin, and nucleolin) was assessed by immunocytochemistry and confocal laser-scanning microscopy, and mRNA expression was determined by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). Read More

View Article and Full-Text PDF

Defective human T-cell lymphotropic virus type I (HTLV-I) provirus in seronegative tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM) patients.

Virus Res 2003 Feb;91(2):231-9

Section of Virology, Public Health Institute of Chile, Avenida Marathon 1000, Santiago, Chile.

Infection with human T-cell lymphotropic virus type I (HTLV-I) have been associated with the development of the tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM). We studied the presence of HTLV-I provirus in peripheral blood mononuclear cells (PBMC) from 72 Chilean patients with progressive spastic paraparesis by polymerase chain reaction: 32 seropositive and 40 seronegative cases. We amplified different genomic regions of HTLV-I using primers of 5' ltr, tax, env/tax, pX, pol and env genes. Read More

View Article and Full-Text PDF
February 2003

Genetic characterization and phylogeny of human T-cell lymphotropic virus type I from Chile.

Virus Res 2002 Mar;84(1-2):135-49

Department of Virology, Public Health Institute of Chile, Av. Marathon 1000, Santiago, Chile.

Infection with Human T-Cell Lymphotropic Virus type I (HTLV-I) have been associated with the development of the HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP). Phylogenetic analyses of HTLV-I isolates have revealed that HTLV-I can be classified into three major groups: the Cosmopolitan, Central African and Melanesian. In the present study, we analyzed the tax, 5' ltr, gag, pol, and env sequences of proviruses of PBMC from ten HAM/TSP patients to investigate the phylogenetic characterization of HTLV-I in Chilean patients. Read More

View Article and Full-Text PDF