title: Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants.
abstract: Nucleosomes facilitate compaction of DNA within the confines of the eukaryotic nucleus. This packaging of DNA and histone proteins must accommodate cellular processes, such as transcription and DNA replication. The repositioning of nucleosomes to facilitate cellular processes is likely regulated by several factors. In Zea mays, Mediator of paramutation1 (MOP1) has been demonstrated to be an epigenetic regulator of gene expression. Based on sequence orthology and mutant phenotypes, MOP1 is likely to function in an RNA-dependent pathway to mediate changes to chromatin. High-resolution microarrays were used to assay the distribution of nucleosomes across the transcription start sites (TSSs) of ~400 maize genes in wild type and mutant mop1-1 tissues. Analysis of nucleosome distribution in leaf, immature tassel and ear shoot tissues resulted in the identification of three genes showing consistent differences in nucleosome positioning and occupancy between wild type and mutant mop1-1. These specific changes in nucleosome distribution were located upstream as well as downstream of the TSS. No direct relationship between the specific changes in nucleosome distribution and transcription were observed through quantitative expression analysis in these tissues. In silico prediction suggests that nucleosome positioning is not dictated by intrinsic DNA sequence signals in the TSSs of two of the identified genes, suggesting a role for chromatin remodeling proteins in MOP1-mediated pathways. These results also indicate that MOP1 contributions to nucleosome position may be either separate from changes in gene expression, or cooperative with development and other levels of regulation in coordinating gene expression.
authors.affiliation: Department of Biological Science; Florida State University; Tallahassee, FL USA.
authors.forename: Jonathan D J
authors.initials: JD
authors.lastname: Labonne
authors.affiliation: Department of Biological Sciences; Marquette University; Milwaukee, WI USA.
authors.forename: Jane E
authors.initials: JE
authors.lastname: Dorweiler
authors.affiliation: Department of Biological Science; Florida State University; Tallahassee, FL USA.
authors.forename: Karen M
authors.initials: KM
authors.lastname: McGinnis
mesh_terms: D042002:Chromatin Assembly and Disassembly; D044127:Epigenesis, Genetic; D017343:Genes, Plant; D056626:Inflorescence / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D009707:Nucleosomes / Q000378:metabolism*; D018515:Plant Leaves / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012639:Seeds / Q000235:genetics* / Q000378:metabolism; D024363:Transcription Initiation Site; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism
chemical_list: D009707:Nucleosomes; D010940:Plant Proteins
keywords: RNA dependent DNA methylation; Zea mays; chromatin; mediator of paramutation1; nucleosome occupancy; nucleosome position; transcription start sites
references.citation: Sci Am. 1981 Feb;244(2):52-64
references.pmid: 7209486
references.citation: Nat Struct Mol Biol. 2006 Jul;13(7):633-40
references.pmid: 16819518
references.citation: Plant J. 1995 May;7(5):703-13
references.pmid: 7773305
references.citation: EMBO J. 1990 Aug;9(8):2517-22
references.pmid: 2369901
references.citation: Dev Biol. 2010 Mar 15;339(2):258-66
references.pmid: 19527704
references.citation: Mol Genet Genomics. 2009 Jun;281(6):673-85
references.pmid: 19283410
references.citation: Cell. 2008 Mar 7;132(5):887-98
references.pmid: 18329373
references.citation: Epigenetics Chromatin. 2011 Feb 25;4:3
references.pmid: 21352520
references.citation: Nature. 2010 Jul 15;466(7304):388-92
references.pmid: 20512117
references.citation: Cell. 2000 May 26;101(5):543-53
references.pmid: 10850496
references.citation: PLoS Comput Biol. 2008 Aug 22;4(8):e1000134
references.pmid: 18725940
references.citation: Mol Cell. 2004 Jun 4;14(5):667-73
references.pmid: 15175161
references.citation: Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12986-91
references.pmid: 20616013
references.citation: PLoS Genet. 2009 Nov;5(11):e1000734
references.pmid: 19956538
references.citation: Nat Rev Mol Cell Biol. 2011 Jul 22;12(8):483-92
references.pmid: 21779025
references.citation: Plant Mol Biol. 1986 Mar;7(2):87-94
references.pmid: 24302228
references.citation: Genome Biol. 2009;10(10):R109
references.pmid: 19814794
references.citation: Cell Death Differ. 2007 Dec;14(12):1989-97
references.pmid: 18007670
references.citation: Nature. 2006 Jul 20;442(7100):295-8
references.pmid: 16855589
references.citation: J Mol Biol. 1988 Nov 5;204(1):109-27
references.pmid: 3063825
references.citation: Genome Res. 2008 Jul;18(7):1051-63
references.pmid: 18477713
references.citation: Plant Cell. 2000 Nov;12(11):2101-18
references.pmid: 11090212
references.citation: Cell. 2000 May 26;101(5):533-42
references.pmid: 10850495
references.citation: Nat Genet. 2007 Oct;39(10):1235-44
references.pmid: 17873876
references.citation: Mol Cell Biol. 2001 Jun;21(11):3830-9
references.pmid: 11340174
references.citation: Plant J. 2010 Aug;63(3):366-78
references.pmid: 20444233
references.citation: Science. 2005 Jul 22;309(5734):626-30
references.pmid: 15961632
references.citation: PLoS Genet. 2009 Nov;5(11):e1000737
references.pmid: 19936292
references.citation: Mol Cell. 2003 Nov;12(5):1333-40
references.pmid: 14636590
references.citation: EMBO J. 2012 Nov 28;31(23):4388-403
references.pmid: 23103765
references.citation: Genes Dev. 2002 Aug 1;16(15):1906-18
references.pmid: 12154122
references.citation: Mol Cell Biol. 2012 May;32(9):1645-53
references.pmid: 22354995
references.citation: Proc Natl Acad Sci U S A. 2007 Aug 7;104(32):12955-61
references.pmid: 17670940
references.citation: Plant Cell. 2010 Sep;22(9):3118-29
references.pmid: 20876829
references.citation: EMBO Rep. 2012 Nov 6;13(11):997-1003
references.pmid: 23032292
references.citation: Science. 2011 May 20;332(6032):977-80
references.pmid: 21596991
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 31;98(16):9161-6
references.pmid: 11470895
references.citation: Mol Cell. 2003 Jun;11(6):1587-98
references.pmid: 12820971
references.citation: Anal Biochem. 1975 May 26;66(1):213-20
references.pmid: 1096670
references.citation: Nat Genet. 2006 Oct;38(10):1210-5
references.pmid: 16964265
references.citation: Plant Cell. 2009 Mar;21(3):832-42
references.pmid: 19336692
references.citation: Nature. 2008 May 15;453(7193):358-62
references.pmid: 18408708
references.citation: Cell. 1999 Aug 6;98(3):285-94
references.pmid: 10458604
references.citation: Nucleic Acids Res. 1988 Jul 25;16(14A):6677-90
references.pmid: 3399412
references.citation: Genome Res. 2008 Jul;18(7):1073-83
references.pmid: 18550805
references.citation: Cell. 1997 Jul 11;90(1):145-55
references.pmid: 9230310
references.citation: Science. 2011 Sep 23;333(6050):1758-60
references.pmid: 21940898
references.citation: Nature. 2006 Aug 17;442(7104):772-8
references.pmid: 16862119