Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness
文献类型：期刊论文
| 作者 | Liu, Yue; Zhang, Wenli2; Zhang, Kang; You, Qi; Yan, Hengyu; Jiao, Yuannian3 ; Jiang, Jiming1; Xu, Wenying; Su, Zhen
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| 刊名 | SCIENTIFIC REPORTS
 |
| 出版日期 | 2017 |
| 卷号 | 7 |
| ISSN号 | 2045-2322 |
| DOI | 10.3389/fpls.2017.00943 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Plant Sciences |
| 出版地 | LONDON |
| WOS关键词 | REGULATORY DNA ; ANALYSIS TOOLKIT ; LEAF SENESCENCE ; RNA-SEQ ; PHYTOCHROME ; EXPRESSION ; THALIANA ; ELEMENTS ; NETWORKS ; LEAVES |
| 语种 | 英语 |
| WOS记录号 | WOS:000403043100001 |
| 出版者 | NATURE PUBLISHING GROUP |
| 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 |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/22291]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 作者单位 | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.China Agr Univ, State Key Lab Plant Physiol & Biochem, Coll Biol Sci, Beijing, Peoples R China 3.Nanjing Agr Univ, State Key Lab Crop Genet & Germplasm Enhancement, JCIC MCP, Nanjing, Jiangsu, 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). |
入库方式： OAI收割
来源：植物研究所
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