Comparative analysis of genome-wide chromosomal histone modification patterns in maize cultivars and their wild relatives

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  He, Shibin ^a,b   Yan, Shihan ^a   Wang, Pu ^a   Zhu, Wei ^c   Wang, Xiangwu ^b   Shen, Yao ^b   Shao, Kejia ^b   Xin, Haiping ^c   Li, Shaohua ^c   Li, Jia ^a  

^a WUHAN UNIVERSITY   (China)

^b HENAN UNIVERSITY   (China)

^c Wuhan Institute of Botany Chinese Academy of Sciences   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME IDENTIFICATION; CONTROLLED STUDY; CULTIVAR; EPIGENETICS; EVOLUTION; HISTONE MODIFICATION; IMMUNOHISTOCHEMISTRY; INTERPHASE; KARYOTYPE; KARYOTYPING; MAIZE; METAPHASE; NONHUMAN; PLANT CHROMOSOME; PLANT GENOME; CELL NUCLEUS; COMPARATIVE STUDY; CYTOLOGY; GENETICS; GENOMICS; METABOLISM; MITOSIS;

HISTONE;

CELL NUCLEUS; CHROMOSOMES, PLANT; GENOME, PLANT; GENOMICS; HISTONES; INTERPHASE; KARYOTYPING; METAPHASE; MITOSIS; ZEA MAYS;

EID: 84901280420     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0097364     Document Type: Article

References (44)

1. Li G, Reinberg D (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 21: 175-186.
2. Fuchs J, Schubert I (2012) Chromosomal Distribution and Functional Interpretation of Epigenetic Histone Marks in Plants. In: Bass HW, Birchler JA editors. Plant Cytogenetics: Genome Structure and Chromosome Function. Springer New York. pp. 231-253.
3. Terrenoire E, McRonald F, Halsall JA, Page P, Illingworth RS, et al. (2010) Immunostaining of modified histones defines high-level features of the human metaphase epigenome. Genome Biol 11: R110.
4. Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168: 81-91.
5. Pennisi E (2013) Evolution heresy? Epigenetics underlies heritable plant traits. Science 341: 1055.
6. Furusawa C, Kaneko K (2013) Epigenetic Feedback Regulation Accelerates Adaptation and Evolution. PLoS ONE 8: e61251. doi:10.1371/journal.pone.0061251
7. Schotta G, Lachner M, Sarma K, Ebert A, Sengupta R, et al. (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev 18: 1251-1262. (Pubitemid 38720593)
8. Fuchs J, Jovtchev G, Schubert I (2008) The chromosomal distribution of histone methylation marks in gymnosperms differs from that of angiosperms. Chromosome Res 16: 891-898.
9. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
10. Jin W, Lamb JC, Zhang W, Kolano B, Birchler JA, et al. (2008) Histone modifications associated with both A and B chromosomes of maize. Chromosome Res 16: 1203-1214.
11. Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, et al. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21: 6549-6559. (Pubitemid 35448432)
12. Shi J, Dawe RK (2006) Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173: 1571-1583. (Pubitemid 44127659)
13. Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns - from conservation to diversity. Trends Plant Sci 11: 199-208.
14. Carchilan M, Delgado M, Ribeiro T, Costa-Nunes P, Caperta A, et al. (2007) Transcriptionally active heterochromatin in rye B chromosomes. Plant Cell 19: 1738-1749. (Pubitemid 47218837)
15. Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, et al. (2012) Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing. PLoS ONE 7: e33071. doi:10.1371/journal.pone.0033071
16. Wei F, Coe E, Nelson W, Bharti AK, Engler F, et al. (2007) Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet 3: e123. doi:10.1371/journal.pgen.0030123
17. Li L, Yang J, Tong Q, Zhao L and Song Y (2005) A novel approach to prepare extended DNA fibers in plants. Cytometry A 63: 114-117. (Pubitemid 40224089)
18. Hu Y, Zhang L, Zhao L, Li J, He S, et al. (2011) Trichostatin A Selectively Suppresses the Cold-Induced Transcription of the ZmDREB1 Gene in Maize. PLoS ONE 6: e22132. doi:10.1371/journal.pone.0022132
19. He SB, Huang M, Huang J, Li J, Hu Y, et al. (2009) Dynamics of the Evolution of the Genus of Agrostis Revealed by GISH/FISH. Crop Science 49: 2285-2290.
20. Robinson TJ, Yang F (2012) Molecular cytogenetics: karyotype evolution, phylogenomics and future prospects. Heredity 108: 1-3.
21. Jeppesen P (1997) Histone acetylation: a possible mechanism for the inheritance of cell memory at mitosis. Bioessays 19: 67-74.
22. Kato A, Lamb JC, Birchler JA (2004) Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A 101: 13554-13559. (Pubitemid 39238441)
23. Morrell PL, Buckler ES, Ross-Ibarra J (2011) Crop genomics: advances and applications. Nat Rev Genet 13: 85-96.
24. Lai J, Li R, Xu X, Jin W, Xu M, et al. (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42: 1027-1030.
25. Anderson LK, Lai A, Stack SM, Rizzon C and Gaut BS (2006) Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res 16: 115-122. (Pubitemid 43048940)
26. Jasencakova Z, Meister A, Schubert I (2001) Chromatin organization and its relation to replication and histone acetylation during the cell cycle in barley. Chromosoma 110: 83-92. (Pubitemid 32529712)
27. Schneider R, Bannister AJ, Myers FA, Thorne AW, Crane-Robinson C, et al. (2004) Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat Cell Biol 6: 73-77. (Pubitemid 38425733)
28. Houben A, Demidov D, Gernand D, Meister A, Leach CR, et al. (2003) Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J 33: 967-973. (Pubitemid 36400279)
29. Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc Natl Acad Sci U S A 87: 9888-9892. (Pubitemid 120016549)
30. Ellneskog-Staam P, Henry Loaisiga C, Merker A (2007) Chromosome C-banding of the teosinte Zea nicaraguensis and comparison to other Zea species. Hereditas 144: 96-101. (Pubitemid 47108369)
31. Wang X, Elling AA, Li X, Li N, Peng Z, et al. (2009) Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant cell 21: 1053-1069.
32. Kruhlak MJ, Hendzel MJ, Fischle W, Bertos NR, Hameed S, et al. (2001) Regulation of global acetylation in mitosis through loss of histone acetyltransferases and deacetylases from chromatin. J Biol Chem 276: 38307-38319.
33. Liu JY, She CW, Hu ZL, Xiong ZY, Liu LH, et al. (2004) A new chromosome fluorescence banding technique combining DAPI staining with image analysis in plants. Chromosoma 113: 16-21. (Pubitemid 39236718)
34. Feng S, Jacobsen SE, Reik W (2010) Epigenetic reprogramming in plant and animal development. Science 330: 622-627.
35. Schwarz PM, Hansen JC (1994) Formation and stability of higher order chromatin structures. Contributions of the histone octamer. J Biol Chem 269: 16284-16289.
36. Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11: 285-296.
37. Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705.
38. Marks H, Chow JC, Denissov S, Francoijs KJ, Brockdorff N, et al. (2009) High-resolution analysis of epigenetic changes associated with X inactivation. Genome Res 19: 1361-1373.
39. Bonduriansky R, Day T (2009) Nongenetic Inheritance and Its Evolutionary Implications. Annu Rev Ecol Evol S 40: 103-125.
40. Vaughn MW, Tanurdzic M, Lippman Z, Jiang H, Carrasquillo R, et al. (2007) Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5: e174. doi:10.1371/journal.pbio.0050174
41. Moghaddam AM, Roudier F, Seifert M, Berard C, Magniette ML, et al. (2011) Additive inheritance of histone modifications in Arabidopsis thaliana intraspecific hybrids. Plant J 67: 691-700.
42. He G, Zhu X, Elling AA, Chen L, Wang X, et al. (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
43. He G, Chen B, Wang X, Li X, Li J, et al. (2013) Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids. Genome Biol 14: R57.
44. Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, et al. (2013) Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25: 780-793.