Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness
Abstract 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 an...
Guardado en:
| Autores principales: | , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Nature Portfolio
2017
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/1f4815366fd04629ad8147b4c54bb5ae |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:1f4815366fd04629ad8147b4c54bb5ae |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:1f4815366fd04629ad8147b4c54bb5ae2021-12-02T11:40:43ZGenome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness10.1038/s41598-017-04524-92045-2322https://doaj.org/article/1f4815366fd04629ad8147b4c54bb5ae2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-04524-9https://doaj.org/toc/2045-2322Abstract 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 ~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.Yue LiuWenli ZhangKang ZhangQi YouHengyu YanYuannian JiaoJiming JiangWenying XuZhen SuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Yue Liu Wenli Zhang Kang Zhang Qi You Hengyu Yan Yuannian Jiao Jiming Jiang Wenying Xu Zhen Su Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| description |
Abstract 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 ~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. |
| format |
article |
| author |
Yue Liu Wenli Zhang Kang Zhang Qi You Hengyu Yan Yuannian Jiao Jiming Jiang Wenying Xu Zhen Su |
| author_facet |
Yue Liu Wenli Zhang Kang Zhang Qi You Hengyu Yan Yuannian Jiao Jiming Jiang Wenying Xu Zhen Su |
| author_sort |
Yue Liu |
| title |
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| title_short |
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| title_full |
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| title_fullStr |
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| title_full_unstemmed |
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness |
| title_sort |
genome-wide mapping of dnase i hypersensitive sites reveals chromatin accessibility changes in arabidopsis euchromatin and heterochromatin regions under extended darkness |
| publisher |
Nature Portfolio |
| publishDate |
2017 |
| url |
https://doaj.org/article/1f4815366fd04629ad8147b4c54bb5ae |
| work_keys_str_mv |
AT yueliu genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT wenlizhang genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT kangzhang genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT qiyou genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT hengyuyan genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT yuannianjiao genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT jimingjiang genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT wenyingxu genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness AT zhensu genomewidemappingofdnaseihypersensitivesitesrevealschromatinaccessibilitychangesinarabidopsiseuchromatinandheterochromatinregionsunderextendeddarkness |
| _version_ |
1718395567707521024 |