ArticleGenomics, proteomics & bioinformatics2019
Global Quantitative Mapping of Enhancers in Rice by STARR-seq.
Article in Genomics, proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- KAS-Seq Captures Global Transcription Dynamics and Active Single-Stranded Enhancers in Rice.Plant biotechnology journal · 2026Article
- H3K4 Methylation Readers in Plants: Recognition Mechanisms and Biological Functions.International journal of molecular sciences · 2026Review
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification and application of bioparts for plant synthetic biology.Molecules and cells · 2025Review
- Review
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- High-throughput quantitative assessment of ABA-responsive elements at single-nucleotide resolution.Quantitative biology (Beijing, China) · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.BMC genomics · 2025Article
- A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation.Frontiers in plant science · 2025Article
- Recent advances in designing synthetic plant regulatory modules.Frontiers in plant science · 2025Review
- Widespread position-dependent transcriptional regulatory sequences in plants.Nature genetics · 2024Article
- Identification of Highly Repetitive Enhancers with Long-range Regulation Potential in Barley via STARR-seq.Genomics, proteomics & bioinformatics · 2024Article
- Modeling 0.6 million genes for the rational design of functionalProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Precise integration of large DNA sequences in plant genomes using PrimeRoot editors.Nature biotechnology · 2024Article
- Synthetic directed evolution for targeted engineering of plant traits.Frontiers in plant science · 2024Review
- Sea-ATI unravels novel vocabularies of plant active cistrome.Nucleic acids research · 2023Article
- From qualitative to quantitative: the state of the art and challenges for plant synthetic biology.Quantitative biology (Beijing, China) · 2023Review
- Epigenetic Regulation of Subgenomic Gene Expression in AllotetraploidPlants (Basel, Switzerland) · 2023Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
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Authors and funding
8 authors.
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Abstract
Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.
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