Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives

PLOS ONE, Dec 2019

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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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. - 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)


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Shibin He, Shihan Yan, Pu Wang, Wei Zhu, Xiangwu Wang, Yao Shen, Kejia Shao, Haiping Xin, Shaohua Li, Lijia Li. Comparative Analysis of Genome-Wide Chromosomal Histone Modification Patterns in Maize Cultivars and Their Wild Relatives, PLOS ONE, 2014, Volume 9, Issue 5, DOI: 10.1371/journal.pone.0097364