Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness

doi:10.3389/fpls.2017.00943

	Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness
	Liu, Yue ; Zhang, Wenli 1; Zhang, Kang ; You, Qi ; Yan, Hengyu ; Jiao, Yuannian2 ; Jiang, Jiming 3; Xu, Wenying ; Su, Zhen
	2017
发表期刊	SCIENTIFIC REPORTS
ISSN	2045-2322
卷号	7
摘要	Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis. We found that similar to 40% DHSs (DNaseI hypersensitive sites) were diminished under darkness. In non-TE regions, the majority of DHS-changed genes were DHS-diminished under darkness. A total of 519 down-regulated genes were associated with diminished DHSs under darkness, mainly involved in photosynthesis process and retrograde signaling, and were regulated by chloroplast maintenance master regulators such as GLK1. In TE regions, approximately half of the DHS-changed TEs were DHS-increased under darkness and were primarily associated with the LTR/Gypsy retrotransposons in the heterochromatin flanking the centromeres. In contrast, DHS-diminished TEs under darkness were enriched in Copia, LINE, and MuDR dispersed across chromosomes. Together, our results indicated that extended darkness resulted in more increased chromatin compaction in euchromatin and decompaction in heterochromatin, thus further leading to gene expression changes in Arabidopsis.
学科领域	Plant Sciences
DOI	10.3389/fpls.2017.00943
收录类别	SCI
语种	英语
WOS关键词	REGULATORY DNA ; ANALYSIS TOOLKIT ; LEAF SENESCENCE ; RNA-SEQ ; PHYTOCHROME ; EXPRESSION ; THALIANA ; ELEMENTS ; NETWORKS ; LEAVES
WOS记录号	WOS:000403043100001
出版者	NATURE PUBLISHING GROUP
文献子类	Article
出版地	LONDON
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31371291, 90817006] ; Direct For Biological SciencesNational Science Foundation (NSF)NSF - Directorate for Biological Sciences (BIO) [1822254] Funding Source: National Science Foundation
作者邮箱	zhensu@cau.edu.cn
作品OA属性	gold, Green Published
引用统计	被引频次：76[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/22291
专题	系统与进化植物学国家重点实验室
作者单位	1.China Agr Univ, State Key Lab Plant Physiol & Biochem, Coll Biol Sci, Beijing, Peoples R China 2.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, JCIC MCP, Nanjing, Jiangsu, Peoples R China 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 4.Univ Wisconsin, Dept Hort, 1575 Linden Dr, Madison, WI 53706 USA
推荐引用方式 GB/T 7714	Liu, Yue,Zhang, Wenli,Zhang, Kang,et al. Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness[J]. SCIENTIFIC REPORTS,2017,7.
APA	Liu, Yue.,Zhang, Wenli.,Zhang, Kang.,You, Qi.,Yan, Hengyu.,...&Su, Zhen.(2017).Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness.SCIENTIFIC REPORTS,7.
MLA	Liu, Yue,et al."Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness".SCIENTIFIC REPORTS 7(2017).

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