ArticleProceedings of the National Academy of Sciences of the United States of America2020
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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61 citing papers in PubMed, 116 citations in OpenAlex.
- Functional genomic map of local adaptation in sorghum to guide allele mining.bioRxiv : the preprint server for biology · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Nanorate sequencing reveals theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Single-molecule views of chromatin accessibility and structure during photomorphogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Pangenome analysis provides insights into legume evolution and breeding.Nature genetics · 2025Article
- Integrative Analysis of Omics Reveals RdDM Pathway Participation in the Initiation of Rice Microspore Embryogenesis Under Cold Treatment.Plants (Basel, Switzerland) · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Transcription factor binding divergence drives transcriptional and phenotypic variation in maize.Nature plants · 2025Article
- Lost in translation: What we have learned from attributes that do not translate from Arabidopsis to other plants.The Plant cell · 2025Review
- Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.Nature communications · 2025Article
- Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- DNA methylation valley as a distinguishing feature occurs in root-specific expressed nicotine-related genes inFrontiers in plant science · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Epigenetic regulation of organ-specific functions in Mikania micrantha and Mikania cordata: insights from DNA methylation and siRNA integration.BMC plant biology · 2024Article
- Potent pollen gene regulation by DNA glycosylases in maize.Nature communications · 2024Article
- Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin inPlants (Basel, Switzerland) · 2024Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
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