ArticlePlant physiology2015
Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants.
Article in Plant physiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 117 citations in OpenAlex.
- A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.The EMBO journal · 2026Article
- Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-COPlant communications · 2025Article
- Convergent Evolution and the Epigenome.Epigenomes · 2025Review
- Abundant clock proteins point to missing molecular regulation in the plant circadian clock.Molecular systems biology · 2025Article
- Heat stress causes chromatin accessibility and related gene expression changes in crown tissues of barley (Hordeum vulgare).Plant molecular biology · 2024Article
- Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Petal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases.Nature communications · 2024Article
- The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice.International journal of molecular sciences · 2024Article
- Predictions of DNA mechanical properties at a genomic scale reveal potentially new functional roles of DNA flexibility.NAR genomics and bioinformatics · 2023Article
- Different elongation factors distinctly modulate RNA polymerase II transcription in Arabidopsis.Nucleic acids research · 2023Article
- The role of transcript regions and amino acid choice in nucleosome positioning.NAR genomics and bioinformatics · 2023Article
- Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.BMC plant biology · 2023Article
- Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds.Tree physiology · 2023Article
- Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants.International journal of molecular sciences · 2022Review
- Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time.The Plant cell · 2022Article
- Epigenomic Features and Potential Functions of KInternational journal of molecular sciences · 2022Article
- NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps.PLoS computational biology · 2022Article
- Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in Arabidopsis.Nucleic acids research · 2022Article
- Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles.Plant physiology · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The fundamental unit of chromatin is the nucleosome that consists of a protein octamer composed of the four core histones (Hs; H3, H4, H2A, and H2B) wrapped by 147 bp of DNA. Nucleosome occupancy and positioning have proven to be dynamic and have a critical impact on expression, regulation, and evolution of eukaryotic genes. We developed nucleosome occupancy and positioning data sets using leaf tissue of rice (Oryza sativa) and both leaf and flower tissues of Arabidopsis (Arabidopsis thaliana). We show that model plant and animal species share the fundamental characteristics associated with nucleosome dynamics. Only 12% and 16% of the Arabidopsis and rice genomes, respectively, were occupied by well-positioned nucleosomes. The cores of positioned nucleosomes were enriched with G/C dinucleotides and showed a lower C→T mutation rate than the linker sequences. We discovered that nucleosomes associated with heterochromatic regions were more spaced with longer linkers than those in euchromatic regions in both plant species. Surprisingly, different nucleosome densities were found to be associated with chromatin in leaf and flower tissues in Arabidopsis. We show that deep MNase-seq data sets can be used to map nucleosome occupancy of specific genomic loci and reveal gene expression patterns correlated with chromatin dynamics in plant genomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.