ArticleScientific reports2017
Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 22 citations in OpenAlex.
- Epigenetic crop improvement: Integrating ENCODE strategies into horticultural breeding.Horticulture research · 2025Article
- Strigolactone induces D14-dependent large-scale changes in gene expression requiring SWI/SNF chromatin remodellers.The Plant journal : for cell and molecular biology · 2024Article
- Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq.Genomics, proteomics & bioinformatics · 2024Article
- CScience advances · 2023Article
- Genome-wide association of the metabolic shifts underpinning dark-induced senescence in Arabidopsis.The Plant cell · 2022Article
- Untangling the crosstalk between BRCA1 and R-loops during DNA repair.Nucleic acids research · 2021Review
- Dark-Induced Barley Leaf Senescence - A Crop System for Studying Senescence and Autophagy Mechanisms.Frontiers in plant science · 2021Review
- Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Considerations in the analysis of plant chromatin accessibility data.Current opinion in plant biology · 2020Review
- Plant Chromatin Catches the Sun.Frontiers in plant science · 2019Review
- Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks ofFrontiers in genetics · 2019Article
- Retrograde Signals Navigate the Path to Chloroplast Development.Plant physiology · 2018Review
- PCSD: a plant chromatin state database.Nucleic acids research · 2018Article
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Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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