College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China.
Nanjing Agricultural University, State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing, China.
Sci Rep. 2017 Jun 22;7(1):4093. doi: 10.1038/s41598-017-04524-9.
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.
光是光合作用中的能量来源，对植物的生长和发育至关重要。长时间的黑暗会导致基因表达发生显著变化。在这项研究中，我们应用 DNase-seq（DNase I 超敏位点测序）来研究拟南芥在长时间黑暗下常染色质和异染色质区域染色质可及性的变化。我们生成了 27Gb 的 DNase-seq 和 67.6Gb 的 RNA-seq 数据，以研究拟南芥在长时间黑暗和对照条件下染色质可及性变化和全局基因表达。我们发现，约 40%的 DHS（DNaseI 超敏位点）在黑暗下减少。在非转座元件区域，大多数 DHS 变化的基因在黑暗下是 DHS 减少的。共有 519 个下调基因与黑暗下 DHS 减少有关，主要涉及光合作用过程和逆行信号转导，并受 GLK1 等质体维持主调控因子的调节。在转座元件区域，约一半的 DHS 变化的转座元件在黑暗下是 DHS 增加的，主要与着丝粒周围异染色质侧翼的 LTR/Gypsy 反转录转座子有关。相比之下，黑暗下 DHS 减少的转座元件在 Copia、LINE 和 MuDR 中富集，分散在染色体上。总的来说，我们的结果表明，长时间的黑暗导致常染色质中染色质更加紧密，异染色质更加疏松，从而导致拟南芥基因表达的变化。
