title: Nascent transcription affected by RNA polymerase IV in Zea mays.
abstract: All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3'-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.
authors: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102.
authors: Karl F
authors: KF
authors: Erhard
authors: Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200 Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
authors: Joy-El R B
authors: http://orcid.org/0000-0001-5334-3806
authors: JE
authors: Talbot
authors: Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
authors: Natalie C
authors: http://orcid.org/0000-0001-9749-7647
authors: NC
authors: Deans
authors: Department of Biology, Albion College, Albion, Michigan 49224.
authors: Allison E
authors: AE
authors: McClish
authors: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102 Department of Molecular Genetics, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210 hollick.3@osu.edu.
authors: Jay B
authors: JB
authors: Hollick
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D036226:Seedlings / Q000235:genetics; D014158:Transcription, Genetic; D059467:Transcriptome; D003313:Zea mays / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D012321:DNA-Directed RNA Polymerases
keywords: RNA polymerase IV; gene regulation; paramutation; transcription; transposons
references: Nat Rev Genet. 2014 Jun;15(6):394-408
references: 24805120
references: Science. 2009 Feb 27;323(5918):1201-5
references: 19251626
references: Genetics. 1961 Jul;46(7):707-10
references: 17248053
references: Nat Genet. 2011 Oct;43(10):1035-9
references: 21873998
references: Cold Spring Harb Symp Quant Biol. 2010;75:285-97
references: 21447813
references: Cell Rep. 2012 Oct 25;2(4):1025-35
references: 23062713
references: PLoS Biol. 2007 Oct 16;5(10):e275
references: 17941719
references: Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10444-9
references: 22689990
references: Plant Cell. 2012 May;24(5):1761-75
references: 22562610
references: Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3145-50
references: 18287047
references: Mol Cell. 2013 Mar 7;49(5):783-94
references: 23473599
references: Genetics. 2007 Jun;176(2):829-39
references: 17435245
references: PLoS Genet. 2012;8(12):e1003127
references: 23271981
references: Curr Opin Plant Biol. 2012 Nov;15(5):536-43
references: 23017240
references: PLoS Biol. 2006 Oct;4(10):e339
references: 16968137
references: PLoS Genet. 2009 Nov;5(11):e1000740
references: 19936069
references: Science. 2008 Dec 19;322(5909):1845-8
references: 19056941
references: Genome Res. 2015 Feb;25(2):235-45
references: 25414514
references: Genome Biol. 2010;11(10):R106
references: 20979621
references: Elife. 2013;2:e00808
references: 23795297
references: Cell Rep. 2014 Oct 9;9(1):378-90
references: 25284785
references: Cell. 2012 Jul 6;150(1):65-77
references: 22738726
references: PLoS Genet. 2009 Nov;5(11):e1000737
references: 19936292
references: Science. 2008 Dec 19;322(5909):1849-51
references: 19056940
references: Science. 2009 Nov 20;326(5956):1112-5
references: 19965430
references: Plant Mol Biol. 1993 Jul;22(4):561-72
references: 8343595
references: Genetics. 2007 Dec;177(4):1975-85
references: 18073417
references: Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4536-41
references: 17360559
references: Plant Cell. 2014 Dec;26(12):4602-16
references: 25527708
references: Genetics. 2005 Oct;171(2):725-40
references: 16020780
references: Cell. 1988 Sep 9;54(6):795-804
references: 3136931
references: Mol Cell. 2014 Aug 7;55(3):383-96
references: 25018019
references: Genes Dev. 2002 Aug 1;16(15):1906-18
references: 12154122
references: Nature. 2006 May 25;441(7092):469-74
references: 16724059
references: Epigenetics. 2011 May;6(5):650-60
references: 21521939
references: Cold Spring Harb Symp Quant Biol. 1951;16:13-47
references: 14942727
references: Mol Cell. 2012 Dec 14;48(5):811-8
references: 23142082
references: Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17644-9
references: 17101975
references: Bioinformatics. 2010 Mar 15;26(6):841-2
references: 20110278
references: PLoS Genet. 2009 Nov;5(11):e1000725
references: 19936058
references: Genetics. 1956 Nov;41(6):872-89
references: 17247669
references: Biology (Basel). 2013 Sep 30;2(4):1210-23
references: 24833221
references: Proc Natl Acad Sci U S A. 2006 May 2;103(18):6853-8
references: 16624880
references: Curr Opin Plant Biol. 2007 Oct;10(5):520-7
references: 17709278
references: Cell. 2013 Jan 17;152(1-2):352-64
references: 23313553
references: Cell Cycle. 2009 Aug 15;8(16):2557-64
references: 19597342
references: Cold Spring Harb Symp Quant Biol. 1958;23:379-91
references: 13635569
references: Cell. 2012 Jul 6;150(1):88-99
references: 22738725
references: Plant Cell. 2014 Dec;26(12):4903-17
references: 25465407
references: Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3570-5
references: 22331882
references: PLoS Genet. 2009 Aug;5(8):e1000598
references: 19680464
references: Dev Biol. 2007 Aug 15;308(2):462-73
references: 17612519
references: Genome Biol. 2009;10(3):R25
references: 19261174
references: Annu Rev Plant Biol. 2015;66:243-67
references: 25494460
references: Genetics. 1995 Oct;141(2):709-19
references: 8647404
references: Science. 2005 Apr 1;308(5718):118-20
references: 15692015
references: Curr Opin Plant Biol. 2007 Oct;10(5):512-9
references: 17702644
references: Genes Dev. 2005 Sep 1;19(17):2030-40
references: 16140984
references: Proc Natl Acad Sci U S A. 2011 Feb 8;108(6):2322-7
references: 21252301
references: Plant Physiol. 2011 Oct;157(2):790-803
references: 21825105
references: Plant Cell. 2013 Mar;25(3):808-19
references: 23512852
references: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14958-63
references: 18815367
references: Plant Cell. 2001 Feb;13(2):319-35
references: 11226188
references: Mol Cell. 2009 Jan 30;33(2):192-203
references: 19110459
references: J Mol Evol. 2007 Jan;64(1):101-12
references: 17160640
references: Nature. 2012 Oct 4;490(7418):112-5
references: 22922650
references: Cell. 2005 Mar 11;120(5):613-22
references: 15766525
references: Nucleic Acids Res. 2012 Feb;40(4):1550-60
references: 22058126
references: Nat Rev Genet. 2004 Jul;5(7):532-44
references: 15211355
references: Genetics. 2014 Nov;198(3):1031-42
references: 25164883
references: Cell Rep. 2014 Feb 13;6(3):455-66
references: 24485661
references: Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3633-8
references: 17360694
references: Nature. 2006 Jul 20;442(7100):295-8
references: 16855589
references: Genetics. 1998 Apr;148(4):1973-81
references: 9560410
references: Plant Cell. 2009 Mar;21(3):832-42
references: 19336692
references: Theor Appl Genet. 1978 May;53(3):113-23
references: 24311343
references: PLoS Genet. 2009 Nov;5(11):e1000732
references: 19936065
references: PLoS Genet. 2009 Nov;5(11):e1000706
references: 19936246
references: Sci Rep. 2014;4:4519
references: 24682209
references: Genome Res. 2013 Apr;23(4):628-37
references: 23269663
references: Heredity (Edinb). 2009 Mar;102(3):236-45
references: 18781168
references: Nat Struct Mol Biol. 2012 Sep;19(9):870-5
references: 22864289