Genome-wide nucleosome occupancy and positioning and their impact on gene expression and evolution in plants

Plant Physiology

Volumn 168, Issue 4, 2015, Pages 1406-1416

  Zhang, Tao ^a   Zhang, Wenli ^a,b   Jiang, Jiming ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA; ORYZA SATIVA;

CHROMATIN; HISTONE; NUCLEOSOME;

ANTIBODY SPECIFICITY; ARABIDOPSIS; CHROMATIN; EVOLUTION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NUCLEOSOME; ORYZA; PLANT GENOME;

ARABIDOPSIS; BIOLOGICAL EVOLUTION; CHROMATIN; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HISTONES; NUCLEOSOMES; ORGAN SPECIFICITY; ORYZA;

EID: 84939184200     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.15.00125     Document Type: Article

References (44)

1. Bell O, Tiwari VK, Thomä NH, Schübeler D (2011) Determinants and dynamics of genome accessibility. Nat Rev Genet 12: 554-564
2. Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43: 956-963
3. Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W (2013) DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res 23: 341-351
4. Chen W, Liu Y, Zhu S, Green CD, Wei G, Han JDJ (2014) Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data. Nat Commun 5: 4909
5. Chen X, Chen Z, Chen H, Su Z, Yang J, Lin F, Shi S, He X (2012) Nucleosomes suppress spontaneous mutations base-specifically in eukaryotes. Science 335: 1235-1238
6. Cheng Z, Buell CR, Wing RA, Gu M, Jiang J (2001) Toward a cytological characterization of the rice genome. Genome Res 11: 2133-2141
7. Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, et al (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392
8. Flores O, Orozco M (2011) nucleR: a package for non-parametric nucleosome positioning. Bioinformatics 27: 2149-2150
9. Fransz P, De Jong JH, Lysak M, Castiglione MR, Schubert I (2002) Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc Natl Acad Sci USA 99: 14584-14589
10. Fransz PF, Armstrong S, de Jong JH, Parnell LD, van Drunen C, Dean C, Zabel P, Bisseling T, Jones GH (2000) Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100: 367-376
11. Hacia JG, Fan JB, Ryder O, Jin L, Edgemon K, Ghandour G, Mayer RA, Sun B, Hsie L, Robbins CM, et al (1999) Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat Genet 22: 164-167
12. Higo K, Ugawa Y, Iwamoto M, Korenaga T (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27: 297-300
13. Huang H, Tudor M, Weiss CA, Hu Y, Ma H (1995) The Arabidopsis MADSbox gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Mol Biol 28: 549-567
14. Huang X, Zhao Y, Wei X, Li C,Wang A, Zhao Q, LiW, Guo Y, Deng L, Zhu C, et al (2012) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44: 32-39
15. Hughes AL, Jin Y, Rando OJ, Struhl K (2012) A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 48: 5-15
16. Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, et al (2011) ARTADE2DB: improved statistical inferences for Arabidopsis gene functions and structure predictions by dynamic structure-based dynamic expression (DSDE) analyses. Plant Cell Physiol 52: 254-264
17. Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ (2006) Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Res 16: 1505-1516
18. Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: an armchair guide. Nat Rev Genet 6: 688-698
19. Langley SA, Karpen GH, Langley CH (2014) Nucleosomes shape DNA polymorphism and divergence. PLoS Genet 10: e1004457
20. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
21. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244
22. Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L (2014) ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J 78: 706-714
23. Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV (2010) Highthroughput sequencing reveals a simple model of nucleosome energetics. Proc Natl Acad Sci USA 107: 20998-21003
24. Lynch M, Sung W, Morris K, Coffey N, Landry CR, Dopman EB, Dickinson WJ, Okamoto K, Kulkarni S, Hartl DL, et al (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proc Natl Acad Sci USA 105: 9272-9277
25. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF (2008a) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083
26. Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, et al (2008b) Nucleosome organization in the Drosophila genome. Nature 453: 358-362
27. Prendergast JGD, Semple CAM (2011) Widespread signatures of recent selection linked to nucleosome positioning in the human lineage. Genome Res 21: 1777-1787
28. Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, Zeevi D, Sharon E, Weinberger A, Segal E (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 44: 743-750
29. Richmond TJ, Davey CA (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150
30. Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto S, Ogawa M, Matsushima K, Gu SGP, Kasahara M, Ahsan B, et al (2009) Chromatinassociated periodicity in genetic variation downstream of transcriptional start sites. Science 323: 401-404
31. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A,Wang Z,Wei G, Zhao K (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132: 887-898
32. Segal E, Widom J (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71
33. Struhl K, Segal E (2013) Determinants of nucleosome positioning. Nat Struct Mol Biol 20: 267-273
34. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063
35. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516-520
36. Vera DL, Madzima TF, Labonne JD, AlamMP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW (2014) Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell 26: 3883-3893
37. Wu MF, Sang Y, Bezhani S, Yamaguchi N, Han SK, Li Z, Su Y, Slewinski TL, Wagner D (2012) SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proc Natl Acad Sci USA 109: 3576-3581
38. Wu Y, Zhang W, Jiang J (2014) Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet 10: e1004378
39. Yilmaz A, Mejia-Guerra MK, Kurz K, Liang X, Welch L, Grotewold E (2011) AGRIS: the Arabidopsis gene regulatory Information server, an update. Nucleic Acids Res 39: D1118-D1122
40. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630
41. Zaret KS, Carroll JS (2011) Pioneer transcription factors: establishing competence for gene expression. Genes Dev 25: 2227-2241
42. Zhang T, Talbert PB, Zhang W, Wu Y, Yang Z, Henikoff JG, Henikoff S, Jiang J (2013) The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci USA 110: E4875-E4883
43. Zhang W, Zhang T, Wu Y, Jiang J (2012) Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24: 2719-2731
44. Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K (2009) Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 16: 847-852