Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives
et al. (2014) Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars
and Their Wild Relatives. PLoS ONE 9(5): e97364. doi:10.1371/journal.pone.0097364
Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives
Shibin He 0
Shihan Yan 0
Pu Wang 0
Wei Zhu 0
Xiangwu Wang 0
Yao Shen 0
Kejia Shao 0
Haiping Xin 0
Shaohua Li 0
Lijia Li 0
Michael Freitag, Oregon State University, United States of America
0 1 State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University , Wuhan , China , 2 State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University , Kaifeng , China , 3 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture , Wuhan Botanical Garden , The Chinese Academy of Sciences , Wuhan , China , 4 School of Physics and Electronics, Henan University , Kaifeng , China
Recent advances demonstrate that epigenome changes can also cause phenotypic diversity and can be heritable across generations, indicating that they may play an important role in evolutionary processes. In this study, we analyzed the chromosomal distribution of several histone modifications in five elite maize cultivars (B73, Mo17, Chang7-2, Zheng58, ZD958) and their two wild relatives (Zea mays L. ssp. parviglumis and Zea nicaraguensis) using a three-dimensional (3D) epigenome karyotyping approach by combining immunostaining and 3D reconstruction with deconvolution techniques. The distribution of these histone modifications along chromosomes demonstrated that the histone modification patterns are conserved at the chromosomal level and have not changed significantly following domestication. The comparison of histone modification patterns between metaphase chromosomes and interphase nuclei showed that some of the histone modifications were retained as the cell progressed from interphase into metaphase, although remodelling existed. This study will increase comprehension of the function of epigenetic modifications in the structure and evolution of the maize genome.
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Funding: This work was supported by the NSFC (No. 31171186; http://www.nsfc.gov.cn/publish/portal0/default.htm), Hubei Province Natural Science Fund,
Fundamental Research Funds for the Central Universities (No. 2012204020202), Henan University Research Fund (No. 2012YBZR028) and Henan Province
Postdoctoral Science Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
Chromatin in eukaryotes is composed of DNA and its associated
core histones and is subject to various post-translational
modifications in the amino-terminal tails of histones and methylation in
the cytosine residues of DNA [1]. Some modifications such as
histone acetylation and H3K4 methylation are enriched in
euchromatin, while H3K9 methylation, H3K27 methylation,
and DNA methylation are generally thought to be the marks of
condensed heterochromatin [2,3]. These epigenetic modifications
have an effect on gene expression and phenotype and can be
heritable across generations, indicating that they also play a role in
evolution [46]. Although histones and their modifications are
conserved, extensive studies have revealed that there are some
differences in the distributions and functional meanings of histone
modifications between the genomes of animals and plants as well
as between different plant species [2]. In mouse nuclei, H3K9
trimethylation and H4K20 trimethylation preferentially mark
constitutive heterochromatin [7], whereas in Arabidopsis thaliana,
they are not typical marks for heterochromatin [2]. H3K9me1, a
heterochromatin-specific mark in angiosperms has been found to
be enriched in euchromatic domains in gymnosperm species [8].
However, very little is known about how the histone modification
patterns change during plant evolution from wild species to
cultivated species.
Genome-wide analysis of the epigenome can be revealed at the
molecular level by the chromatin immunoprecipitation-sequencing
(ChIP-seq) technique [9]. However, highly repetitive DNAs hinder
sequencing-based analysis of the plant genome and ChIP-seq is
not suitable for non-sequenced genomes [10]. There are some
changes in epigenetic states from interphase to metaphase, but
ChIP-seq cannot distinguish cells in different phases of the cell
cycle. Immunocytological analysis with antibodies specific to
histone modification and DNA methylation is a powerful
technique for identifying individual chromosomes and analysis of
the entire epigenome at the chromosomal level [3]. The
distribution of histone modifications can be traced along
metaphase chromosomes of animals and plants by this technique
[2,3]. Many plants such as A. thaliana [11], Zea mays [12], Vicia faba
[13] and Secale cereale [14] have been investigated so far with regard
to (...truncated)