title: A conserved RNA polymerase III promoter required for gammaherpesvirus TMER transcription and microRNA processing.
abstract: Canonical RNA polymerase III (pol III) type 2 promoters contain a single A and B box and are well documented for their role in tRNA and SINE transcription in eukaryotic cells. The genome of Murid herpesvirus 4 (MuHV-4) contains eight polycistronic tRNA-microRNA encoded RNA (TMER) genes that are transcribed from a RNA pol III type 2-like promoter containing triplicated A box elements. Here, we demonstrate that the triplicated A box sequences are required in their entirety to produce functional MuHV-4 miRNAs. We also identify that these RNA pol III type 2-like promoters are conserved in eukaryotic genomes. Human and mouse predicted tRNA genes containing these promoters also show enrichment of alternative RNA pol III transcription termination sequences and are predicted to give rise to longer tRNA primary transcripts.
authors.affiliation: Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: kwdiebel@d.umn.edu.
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Diebel
authors.affiliation: Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Claypool
authors.affiliation: Program in Molecular Biology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Immunology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: Linda.VanDyk@ucdenver.edu.
authors.forename: Linda F
authors.initials: LF
authors.lastname: van Dyk
mesh_terms: D016475:3T3 Cells; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D005347:Fibroblasts / Q000378:metabolism / Q000821:virology; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral / Q000235:genetics; D054884:Host-Pathogen Interactions; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D020815:Polyproteins / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D059370:RNA Folding; D012320:RNA Polymerase III / Q000235:genetics*; D012323:RNA Processing, Post-Transcriptional; D012343:RNA, Transfer / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D018144:Rhadinovirus / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D020815:Polyproteins; D012367:RNA, Viral; D012343:RNA, Transfer; D012320:RNA Polymerase III
keywords: A box; Gammaherpesvirus 68; Type 2 promoter; tRNA
references.citation: Cell. 1982 Dec;31(3 Pt 2):543-51
references.pmid: 6297772
references.citation: PLoS One. 2009 Jun 15;4(6):e5908
references.pmid: 19526060
references.citation: Nucleic Acids Res. 2000 Mar 15;28(6):1283-98
references.pmid: 10684922
references.citation: J Virol. 2002 Jul;76(13):6532-44
references.pmid: 12050366
references.citation: Mol Cell Biol. 2001 Oct;21(20):6870-81
references.pmid: 11564871
references.citation: J Virol. 2004 Dec;78(23):12868-76
references.pmid: 15542639
references.citation: Genome Res. 2010 Jun;20(6):710-21
references.pmid: 20413673
references.citation: Nucleic Acids Res. 2007;35(8):2620-8
references.pmid: 17426139
references.citation: J Biol Chem. 1994 Nov 25;269(47):29752-9
references.pmid: 7525587
references.citation: Curr Opin Microbiol. 1999 Aug;2(4):403-9
references.pmid: 10458986
references.citation: J Biol Chem. 2006 Aug 18;281(33):23945-57
references.pmid: 16787917
references.citation: Cold Spring Harb Perspect Biol. 2011 Mar 01;3(3):
references.pmid: 20719877
references.citation: J Virol. 2006 Feb;80(3):1376-84
references.pmid: 16415015
references.citation: Acta Virol. 1980 Dec;24(6):468
references.pmid: 6111210
references.citation: J Virol. 2010 Oct;84(19):10344-53
references.pmid: 20660200
references.citation: Mol Cell. 2010 Jan 15;37(1):135-42
references.pmid: 20129062
references.citation: Nucleic Acids Res. 2011 Jul;39(13):5499-512
references.pmid: 21421562
references.citation: J Virol. 1997 Aug;71(8):5894-904
references.pmid: 9223479
references.citation: Nat Methods. 2005 Apr;2(4):269-76
references.pmid: 15782219
references.citation: J Gen Virol. 1997 Jul;78 ( Pt 7):1675-87
references.pmid: 9225045
references.citation: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
references.pmid: 15123812
references.citation: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references.pmid: 9023104
references.citation: FEBS Lett. 2006 Mar 6;580(6):1553-64
references.pmid: 16472808
references.citation: Cell. 1981 Apr;24(1):261-70
references.pmid: 6263489
references.citation: RNA. 2010 Jan;16(1):170-85
references.pmid: 19948768
references.citation: J Virol. 2005 Aug;79(15):9556-65
references.pmid: 16014917
references.citation: J Virol. 2010 Oct;84(19):10266-75
references.pmid: 20668074
references.citation: Annu Rev Immunol. 2011;29:351-97
references.pmid: 21219186
references.citation: J Gen Virol. 2003 Jan;84(Pt 1):99-109
references.pmid: 12533705
references.citation: Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1404-9
references.pmid: 23297232
references.citation: J Virol. 2003 Oct;77(19):10488-503
references.pmid: 12970434
references.citation: J Gen Virol. 1999 Jan;80 ( Pt 1):75-82
references.pmid: 9934687
references.citation: Antisense Nucleic Acid Drug Dev. 1998 Jun;8(3):185-97
references.pmid: 9669656
references.citation: Genes Dev. 2002 Oct 15;16(20):2593-620
references.pmid: 12381659
references.citation: FEBS Lett. 2009 Oct 6;583(19):3241-6
references.pmid: 19751732
references.citation: J Virol. 1991 Nov;65(11):5657-62
references.pmid: 1920611
references.citation: Trends Genet. 2007 Dec;23(12):614-22
references.pmid: 17977614
references.citation: Gene. 2012 Feb 10;493(2):185-94
references.pmid: 21712079
references.citation: Proc Natl Acad Sci U S A. 1981 Feb;78(2):805-9
references.pmid: 6262773
references.citation: RNA. 2010 Apr;16(4):673-95
references.pmid: 20181738
references.citation: Genes Dev. 2009 Nov 15;23(22):2639-49
references.pmid: 19933153
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references.pmid: 21037258
references.citation: J Mol Biol. 2003 Oct 10;333(1):1-20
references.pmid: 14516739
references.citation: Trends Microbiol. 1998 Jul;6(7):276-82
references.pmid: 9717216