Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants

Epigenetics

Volumn 8, Issue 4, 2013, Pages

  Labonne, Jonathan D J ^a   Dorweiler, Jane E ^b   McGinnis, Karen M ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

^b Marquette University   (United States)

Author keywords

Chromatin; Mediator of paramutation1; Nucleosome occupancy; Nucleosome position; RNA dependent DNA methylation; Transcription start sites; Zea mays

Indexed keywords

MEDIATOR OF PARAMUTATION1 PROTEIN; MICROCOCCAL NUCLEASE; MUTANT PROTEIN; RNA DIRECTED RNA POLYMERASE; UNCLASSIFIED DRUG; NUCLEOSOME; VEGETABLE PROTEIN;

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DNA METHYLATION; DNA MICROARRAY; DNA REPLICATION; DNA TRANSCRIPTION; GENE EXPRESSION; GENETIC ASSOCIATION; GENOTYPE; MAIZE; MICROARRAY ANALYSIS; MUTATION; NONHUMAN; NUCLEOSOME; ORTHOLOGY; REAL TIME POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION SITE; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENETIC EPIGENESIS; GENETICS; INFLORESCENCE; METABOLISM; PLANT GENE; PLANT LEAF; PLANT SEED;

CHROMATIN ASSEMBLY AND DISASSEMBLY; EPIGENESIS, GENETIC; GENES, PLANT; INFLORESCENCE; MUTATION; NUCLEOSOMES; PLANT LEAVES; PLANT PROTEINS; SEEDS; TRANSCRIPTION INITIATION SITE; ZEA MAYS;

EID: 84875873698     PISSN: 15592294     EISSN: 15592308     Source Type: Journal    
DOI: 10.4161/epi.24199     Document Type: Article

References (48)

1. Kornberg RD, Lorch Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 1999; 98:285-94; PMID:10458604; http:// dx.doi.org/10.1016/S0092-8674(00)81958-3.
2. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008; 132:887-98; PMID:18329373; http://dx.doi.org/10.1016/j. cell.2008.02.022.
3. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 2007; 39:1235-44; PMID:17873876; http://dx.doi.org/10.1038/ng2117.
4. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, et al. Relationship between nucleosome positioning and DNA methylation. Nature 2010; 466:388-92; PMID:20512117; http://dx.doi. org/10.1038/nature09147.
5. Gent JI, Schneider KL, Topp CN, Rodriguez C, Presting GG, Dawe RK. Distinct influences of tandem repeats and retrotransposons on CENH3 nucleosome positioning. Epigenetics Chromatin 2011; 4:3; PMID:21352520; http://dx.doi.org/10.1186/1756-8935-4-3.
6. Kornberg RD. The molecular basis of eukaryotic transcription. Proc Natl Acad Sci U S A 2007; 104:12955-61; PMID:17670940; http://dx.doi.org/10.1073/ pnas.0704138104.
7. Kornberg RD. The molecular basis of eucaryotic transcription. Cell Death Differ 2007; 14:1989-97; PMID:18007670; http://dx.doi.org/10.1038/ sj.cdd.4402251.
8. Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012; 32:1645-53; PMID:22354995; http://dx.doi. org/10.1128/MCB.06170-11.
9. Radman-Livaja M, Rando OJ. Nucleosome positioning: how is it established, and why does it matter? Dev Biol 2010; 339:258-66; PMID:19527704; http:// dx.doi.org/10.1016/j.ydbio.2009.06.012.
10. Kornberg RD, Klug A. The nucleosome. Sci Am 1981; 244:52-64; PMID:7209486; http://dx.doi. org/10.1038/scientificamerican0281-52.
11. Fedor MJ, Lue NF, Kornberg RD. Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol 1988; 204:109-27; PMID:3063825; http://dx.doi. org/10.1016/0022-2836(88)90603-1.
12. Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 2011; 332:977-80; PMID:21596991; http://dx.doi. org/10.1126/science.1200508.
13. Kornberg RD, Stryer L. Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism. Nucleic Acids Res 1988; 16(14A):6677-90; PMID:3399412; http://dx.doi.org/10.1093/ nar/16.14.6677.
14. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008; 18:1073-83; PMID:18550805; http://dx.doi.org/10.1101/ gr.078261.108.
15. Anderson JD, Widom J. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol 2001; 21:3830-9; PMID:11340174; http://dx.doi.org/10.1128/ MCB.21.11.3830-3839.2001.
16. Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nat Genet 2006; 38:1210-5; PMID:16964265; http:// dx.doi.org/10.1038/ng1878.
17. Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y, Moore IK, et al. A genomic code for nucleosome positioning. Nature 2006; 442:772-8; PMID:16862119; http://dx.doi.org/10.1038/ nature04979.
18. Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, et al. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011; 333:1758-60; PMID:21940898; http://dx.doi.org/10.1126/science. 1206097.
19. Hennig BP, Bendrin K, Zhou Y, Fischer T. Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription. EMBO Rep 2012; 13:997-1003; PMID:23032292; http://dx.doi. org/10.1038/embor.2012.146.
20. Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, et al. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 2012; 31:4388-403; PMID:23103765; http://dx.doi.org/10.1038/emboj.2012.289.
21. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 2003; 11:1587-98; PMID:12820971; http://dx.doi.org/10.1016/S1097-2765(03)00231-4.
22. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 2004; 14:667-73; PMID:15175161; http://dx.doi.org/10.1016/j.molcel. 2004.05.013.
23. Fazzio TG, Tsukiyama T. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Mol Cell 2003; 12:1333-40; PMID:14636590; http:// dx.doi.org/10.1016/S1097-2765(03)00436-2.
24. Whitehouse I, Tsukiyama T. Antagonistic forces that position nucleosomes in vivo. Nat Struct Mol Biol 2006; 13:633-40; PMID:16819518; http://dx.doi. org/10.1038/nsmb1111.
25. Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 1997; 90:145-55; PMID:9230310; http://dx.doi.org/10.1016/S0092-8674(00)80321-9.
26. Jiang C, Pugh BF. A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome. Genome Biol 2009; 10:R109; PMID:19814794; http://dx.doi.org/10.1186/gb-2009-10-10-r109.
27. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, et al. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 2005; 309:626-30; PMID:15961632; http://dx.doi. org/10.1126/science.1112178.
28. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, et al. Nucleosome organization in the Drosophila genome. Nature 2008; 453:358-62; PMID:18408708; http://dx.doi.org/10.1038/ nature06929.
29. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 2008; 18:1051-63; PMID:18477713; http://dx.doi. org/10.1101/gr.076463.108.
30. Pecinka A, Dinh HQ, Baubec T, Rosa M, Lettner N, Mittelsten Scheid O. Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell 2010; 22:3118-29; PMID:20876829; http://dx.doi.org/10.1105/ tpc.110.078493.
31. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, et al. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006; 442:295-8; PMID:16855589; http:// dx.doi.org/10.1038/nature04884.
32. Haag JR, Pikaard CS. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 2011; 12:483-92; PMID:21779025; http://dx.doi.org/10.1038/ nrm3152.
33. Jia Y, Lisch DR, Ohtsu K, Scanlon MJ, Nettleton D, Schnable PS. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24-nt small RNAs. PLoS Genet 2009; 5:e1000737; PMID:19936292; http://dx.doi.org/10.1371/journal. pgen.1000737.
34. Dorweiler JE, Carey CC, Kubo KM, Hollick JB, Kermicle JL, Chandler VL. Mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 2000; 12:2101-18; PMID:11090212.
35. Haring M, Bader R, Louwers M, Schwabe A, van Driel R, Stam M. The role of DNA methylation, nucleosome occupancy and histone modifications in paramutation. [Epub ahead of print]. Plant J 2010; PMID:20444233; http://dx.doi.org/10.1111/j.1365-313X.2010.04245.x.
36. Louwers M, Bader R, Haring M, van Driel R, de Laat W, Stam M. Tissue-and expression level-specific chromatin looping at maize b1 epialleles. Plant Cell 2009; 21:832-42; PMID:19336692; http://dx.doi. org/10.1105/tpc.108.064329.
37. Stam M, Belele C, Dorweiler JE, Chandler VL. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 2002; 16:1906-18; PMID:12154122; http://dx.doi.org/10.1101/ gad.1006702.
38. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci U S A 2001; 98:9161-6; PMID:11470895; http://dx.doi. org/10.1073/pnas.151244298.
39. Springer NM, Ying K, Fu Y, Ji T, Yeh CT, Jia Y, et al. Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genet 2009; 5:e1000734; PMID:19956538; http://dx.doi.org/10.1371/journal. pgen.1000734.
40. Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS. Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol 2008; 4:e1000134; PMID:18725940; http://dx.doi.org/10.1371/journal.pcbi.1000134.
41. Arteaga-Vazquez M, Sidorenko L, Rabanal FA, Shrivistava R, Nobuta K, Green PJ, et al. RNAmediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci U S A 2010; 107:12986-91; PMID:20616013; http:// dx.doi.org/10.1073/pnas.1007972107.
42. Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 2000; 101:543-53; PMID:10850496; http:// dx.doi.org/10.1016/S0092-8674(00)80864-8.
43. Mourrain P, Béclin C, Elmayan T, Feuerbach F, Godon C, Morel JB, et al. Arabidopsis SGS2 and SGS3 genes are required for posttranscriptional gene silencing and natural virus resistance. Cell 2000; 101:533-42; PMID:10850495; http://dx.doi.org/10.1016/S0092-8674(00)80863-6.
44. Deboo GB, Albertsen MC, Taylor LP. Flavanone 3-hydroxylase transcripts and flavonol accumulation are temporally coordinate in maize anthers. Plant J 1995; 7:703-13; PMID:7773305; http://dx.doi. org/10.1046/j.1365-313X.1995.07050703.x.
45. Goff SA, Klein TM, Roth BA, Fromm ME, Cone KC, Radicella JP, et al. Transactivation of anthocyanin biosynthetic genes following transfer of B regulatory genes into maize tissues. EMBO J 1990; 9:2517-22; PMID:2369901.
46. Labonne JJ, Goultiaeva A, Shore JS. High-resolution mapping of the S-locus in Turnera leads to the discovery of three genes tightly associated with the S-alleles. Mol Genet Genomics 2009; 281:673-85; PMID:19283410; http://dx.doi.org/10.1007/s00438-009-0439-5.
47. Steinmüller K, Apel K. A simple and efficient procedure for isolating plant chromatin which is suitable for studies of DNase I-sensitive domains and hypersensitive sites. Plant Mol Biol 1986; 7:87-94; http://dx.doi. org/10.1007/BF00040135.
48. Thuring RW, Sanders JP, Borst P. A freeze-squeeze method for recovering long DNA from agarose gels. Anal Biochem 1975; 66:213-20; PMID:1096670; http://dx.doi.org/10.1016/0003-2697(75)90739-3.