ArticleNature communications2020
Epigenetic regulation of spurious transcription initiation in Arabidopsis.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 61 citations in OpenAlex.
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation.bioRxiv : the preprint server for biology · 2026Article
- GeneCAD: Plant Genome Annotation with a DNA Foundation Model.bioRxiv : the preprint server for biology · 2025Article
- Intra species dissection of phytophthora capsici resistance in black pepper.Journal of advanced research · 2025Article
- Are complex traits underpinned by polygenic molecular traits? A reflection on the complexity of gene expression.Plant & cell physiology · 2025Review
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- Whole Mount Staining and Immunolocalization Procedures for Developing Ovules of Vigna unguiculata.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Noncanonical transcription initiation is primarily tissue specific and epigenetically tuned in paleopolyploid plants.The Plant cell · 2024Article
- Distinct methylome profile of cfDNA in AMI patients reveals significant alteration in cAMP signaling pathway genes regulating cardiac muscle contraction.Clinical epigenetics · 2024Article
- Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.PLoS genetics · 2024Article
- AtSNP_TATAdb: Candidate Molecular Markers of Plant Advantages Related to Single Nucleotide Polymorphisms within Proximal Promoters ofInternational journal of molecular sciences · 2024Article
- Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat.Nature communications · 2023Article
- Article
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- Review
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin.Seminars in cell & developmental biology · 2023Review
- Genomic methylation patterns in pre-meiotic gynoecia of wild-type and RdDM mutants of Arabidopsis.Frontiers in plant science · 2023Article
- PSTVd infection inFrontiers in plant science · 2023Article
- LAFITE Reveals the Complexity of Transcript Isoforms in Subcellular Fractions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs.
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