ArticleThe Plant cell2021
Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed, 97 citations in OpenAlex.
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- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Gene body methylation buffers noise in gene expression in plants.Nucleic acids research · 2026Article
- Ribozyme-Enabled Tissue Specificity (RETS): A System for Precise Gene Expression without Specialized Promoters.ACS synthetic biology · 2026Article
- Evolutionary dynamics and transcriptional diversification of GAD gene family in plants: a pan-species perspective in silico analysis.BMC plant biology · 2025Article
- Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.bioRxiv : the preprint server for biology · 2025Article
- Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum.BMC plant biology · 2025Article
- Elucidating design principles for Ribozyme-Enabled Tissue Specificity (RETS) to allow precise expression without specialized promoters.bioRxiv : the preprint server for biology · 2025Article
- Chromatin accessibility dynamics and transcriptional regulatory networks underlying the primary nitrogen response in rice roots.Plant communications · 2025Article
- Deciphering ABA/PYL gene family in flax: evolutionary analysis, and abiotic stress response.Plant cell reports · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Ethylene response factor SlERF.D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Arabidopsis thaliana core splicing factor PORCUPINE/SmE1 requires intron-mediated expression.PloS one · 2025Article
- Genome-wide characterization of the GmLUX binding preferences and its epigenic features in the soybean genome.Frontiers in plant science · 2025Article
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8 authors at 4 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
Enhancers located in introns are abundant and play a major role in the regulation of gene expression in mammalian species. By contrast, the functions of intronic enhancers in plants have largely been unexplored and only a handful of plant intronic enhancers have been reported. We performed a genome-wide prediction of intronic enhancers in Arabidopsis thaliana using open chromatin signatures based on DNase I sequencing. We identified 941 candidate intronic enhancers associated with 806 genes in seedling tissue and 1,271 intronic enhancers associated with 1,069 genes in floral tissue. We validated the function of 15 of 21 (71%) of the predicted intronic enhancers in transgenic assays using a reporter gene. We also created deletion lines of three intronic enhancers associated with two different genes using CRISPR/Cas. Deletion of these enhancers, which span key transcription factor binding sites, did not abolish gene expression but caused varying levels of transcriptional repression of their cognate genes. Remarkably, the transcriptional repression of the deletion lines occurred at specific developmental stages and resulted in distinct phenotypic effects on plant morphology and development. Clearly, these three intronic enhancers are important in fine-tuning tissue- and development-specific expression of their cognate genes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.