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 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.

Induction of C4genes evolved through changes incisallowing integration into ancestral C3gene regulatory networks

“…Consistent with previous work 33 with them repressing gene expression in mesophyll cells 12,13 . In the current dataset, we found that transcription factor binding events predicted to be positive activators were 1.6 and 2.9 times more likely to be found in promoters and introns respectively compared to predicted negative regulators.…”

“…3b). This is consistent with the notion that exposure to light leads to a rapid increase in open chromatin around gene bodies 33 . To further investigate the extent to which accessible chromatin changed over the entire time-course, the proportion of DHS that were shared between time-points was examined (Fig.…”

“…gynandra. This finding is consistent with loci becoming more accessible in light 33 . However, for early responding genes changes in accessibility in DHS's (dDHS) was not associated with increased gene expression ( Supplementary Fig.…”

PCSD: a plant chromatin state database

“…The public data sets were downloaded from NCBI Gene Expression Omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) ( 38 ) and Sequence Read Archive ( http://www.ncbi.nlm.nih.gov/sra ) ( 39 ). The in-house data sets of Arabidopsis and rice were previously published ( 34 – 37 ).…”

“…ChIP-seq data for various histone modifications, histone variants and TFs have accumulated in public databases for studies on the regulation of gene expression in developmental processes and in response to environmental treatments in Arabidopsis, rice and maize ( 24 – 33 ). In addition, our group also accumulated in-house epigenomic data sets, such as DNase-seq and ChIP-seq data for histone modifications and variants in Arabidopsis and rice ( 34 – 37 ). The abundance of epigenomic data sets enabled construction of a plant chromatin state database to better decode chromatin states with epigenomic data sets and to discover causal functions hidden in plant chromatin.…”