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.
Highlights
Light is one of the essential environmental inputs for plant growth and development
Through genome-wide mapping of chromatin accessibility, we revealed the chromatin dynamics from control condition to extended darkness
We identified a total of 10,380 DNase I hypersensitive sites (DHSs) corresponding to control condition, and 5,948 DHSs under extended darkness
Summary
Light is one of the essential environmental inputs for plant growth and development. Several important genes (e.g., PHYA, PHYB, CRY2) have been shown to be responsible for plant adaptation to light conditions[1], and to lead to adaptive changes in cells and even the whole organism[2, 3]. Changes in chromatin structure affect the binding of TFs to regulatory elements, altering the expression of the associated genes[18]. DNase-seq (DNase I treatment coupled with high-throughput DNA sequencing) is a powerful technique for identifying cis-regulatory elements across the genome and is highly effective for comparing TF binding profiles in different development stages and environmental conditions. A large number of differentially expressed genes (DEGs) under extended darkness and control condition in Arabidopsis have been identified using ATH1 GeneChip or large-scale quantitative real-time PCR (qRT-PCR)[8, 27, 28]. To study the possible regulatory elements of DEGs under extended darkness in Arabidopsis, we conducted DNase-seq and RNA-seq to study chromatin accessibility and the association between DHSs and gene expression in Arabidopsis plants under extended darkness and control conditions. We used combinatorial analyses of DNase-seq and sRNA-seq to study the relationship between DHSs and siRNA changes in transposable element (TE) regions under these two conditions
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