ArticleMolecular biology and evolution2018
Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression.Nature biotechnology · 2026Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- The role of DNA content in shaping chromatin architecture and gene expression.The Plant journal : for cell and molecular biology · 2025Article
- Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa.Molecular biology and evolution · 2024Article
- Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2024Article
- Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.BMC plant biology · 2023Article
- CScience advances · 2023Article
- Increased chromatin accessibility promotes the evolution of a transcriptional silencer inScience advances · 2023Article
- Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.Genome biology · 2022Article
- Single-cell genomics in plants: current state, future directions, and hurdles to overcome.Plant physiology · 2022Article
- Selection on Accessible Chromatin Regions in Capsella grandiflora.Molecular biology and evolution · 2021Article
- Potentials of single-cell genomics in deciphering cellular phenotypes.Current opinion in plant biology · 2021Review
- Genome accessibility dynamics in response to phosphate limitation is controlled by the PHR1 family of transcription factors inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana.Molecular biology and evolution · 2021Article
- The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution.Nature communications · 2021Article
- Anno genominis XX: 20 years of Arabidopsis genomics.The Plant cell · 2021Review
- Considerations in the analysis of plant chromatin accessibility data.Current opinion in plant biology · 2020Review
- Accelerating structure-function mapping using the ViVa webtool to mine natural variation.Plant direct · 2019Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Dynamics of Gene Expression in Single Root Cells ofThe Plant cell · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
16 authors.
Funding
Abstract
Variation in regulatory DNA is thought to drive phenotypic variation, evolution, and disease. Prior studies of regulatory DNA and transcription factors across animal species highlighted a fundamental conundrum: Transcription factor binding domains and cognate binding sites are conserved, while regulatory DNA sequences are not. It remains unclear how conserved transcription factors and dynamic regulatory sites produce conserved expression patterns across species. Here, we explore regulatory DNA variation and its functional consequences within Arabidopsis thaliana, using chromatin accessibility to delineate regulatory DNA genome-wide. Unlike in previous cross-species comparisons, the positional homology of regulatory DNA is maintained among A. thaliana ecotypes and less nucleotide divergence has occurred. Of the ∼50,000 regulatory sites in A. thaliana, we found that 15% varied in accessibility among ecotypes. Some of these accessibility differences were associated with extensive, previously unannotated sequence variation, encompassing many deletions and ancient hypervariable alleles. Unexpectedly, for the majority of such regulatory sites, nearby gene expression was unaffected. Nevertheless, regulatory sites with high levels of sequence variation and differential chromatin accessibility were the most likely to be associated with differential gene expression. Finally, and most surprising, we found that the vast majority of differentially accessible sites show no underlying sequence variation. We argue that these surprising results highlight the necessity to consider higher-order regulatory context in evaluating regulatory variation and predicting its phenotypic consequences.
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