ArticleGenetics2021
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- The genetic heist: how transposable elements capture and repurpose genes in plants.Genome biology · 2026Review
- A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily.Molecular biology and evolution · 2026Article
- Biotic and Abiotic Factors Influencing Maize Plant Height.International journal of molecular sciences · 2025Review
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Pangenome analysis provides insights into legume evolution and breeding.Nature genetics · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- The regulatory potential of transposable elements in maize.Nature plants · 2025Article
- The genetic architecture of cell type-specific cis regulation in maize.Science (New York, N.Y.) · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- The role of transposon activity in shapingGenome research · 2025Article
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa.Molecular biology and evolution · 2024Article
- The chromatin accessibility and transcriptomic landscape of the aging mice cochlea and the identification of potential functional super-enhancers in age-related hearing loss.Clinical epigenetics · 2024Article
- Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq.Genomics, proteomics & bioinformatics · 2024Article
- Review
- Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan.BMC plant biology · 2023Article
- Annotation of thePlants (Basel, Switzerland) · 2023Article
- Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.Genome biology · 2022Article
- Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
11 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.
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