ArticleNature plants2024
Enhancers associated with unstable RNAs are rare in plants.
Article in Nature plants, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Positional grammar of transcription factor binding partitions developmental and stress-response regulation in plants.Nature communications · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Functional genomic map of local adaptation in sorghum to guide allele mining.bioRxiv : the preprint server for biology · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs.Nucleic acids research · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- Long Non-Coding RNAs in the Cold-Stress Response of Horticultural Plants: Molecular Mechanisms and Potential Applications.International journal of molecular sciences · 2025Review
- Transcriptional interference gates monogenic odorant receptor expression in ants.Current biology : CB · 2025Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- Transcriptional Interference Gates Monogenic Odorant Receptor Expression in Ants.bioRxiv : the preprint server for biology · 2025Article
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Integrated expression analysis to elucidate the role of miR394 during flowering in Arabidopsis thaliana.Plant cell reports · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Plant enhancers exhibit both cooperative and additive interactions among their functional elements.The Plant cell · 2024Article
- Genome organization and botanical diversity.The Plant cell · 2024Review
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7 authors.
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Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many 'distal' elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans.
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