ArticleNucleic acids research2020
Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed, 134 citations in OpenAlex.
- Temporal dynamics of intragenic enhancer RNAs regulate Lin28a expression in response to external stimuli in embryonic stem cells.Nucleic acids research · 2026Article
- Enhancer RNA transcription near segmentation gene enhancers can be analyzed in situ using FISH.G3 (Bethesda, Md.) · 2026Article
- Subtype-specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers.Molecular oncology · 2026Article
- Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance.Genome biology · 2026Article
- Super Enhancer RNAs Rewrite the Molecular Script of Complex Gene Regulation in the MDD Brain.Communications biology · 2026Article
- How intrinsically disordered regions shape the function of CREB-binding protein.Biochemical Society transactions · 2026Review
- Emerging roles of circular RNAs and enhancer RNAs: new insights into the development and management of neurodegenerative disorders.Biomarker research · 2026Review
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Enhancer-dependent gene regulation in space, time, and malignancies.International journal of cancer · 2026Review
- Emerging insights into enhancer RNAs: biogenesis, function, mechanism, and disease implication.Briefings in bioinformatics · 2026Review
- Enhancer Trajectories in Lineage Commitment: Regulatory Logic of States and Cooperation.Biomolecules · 2026Review
- Unveiling the regulatory potential of the non-coding genome: Insights from the human genome project to precision medicine.Genes & diseases · 2025Review
- Targeting eRNA-Producing Super-Enhancers Regulates TNFα Expression and Mitigates Chronic Inflammation in Mice and Patient-Derived Immune Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Improving confidence of differential transcription calls in enhancers.bioRxiv : the preprint server for biology · 2025Article
- iEnhancer-GDM: A Deep Learning Framework Based on Generative Adversarial Network and Multi-head Attention Mechanism to Identify Enhancers and Their Strength.Interdisciplinary sciences, computational life sciences · 2025Article
- A Bayesian nonparametric method for jointly clustering multiple spatial transcriptomic datasets and simultaneous gene selection.Scientific reports · 2025Article
- Automated high-throughput profiling of single-cell total transcriptome with scComplete-seq.Nucleic acids research · 2025Article
- Biological roles of enhancer RNA m6A modification and its implications in cancer.Cell communication and signaling : CCS · 2025Review
- Reelin marks cocaine-activated striatal neurons, promotes neuronal excitability, and regulates cocaine reward.Science advances · 2025Article
- Stimulus-Dependent Expression ofThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2025Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
Genomic enhancer elements regulate gene expression programs important for neuronal fate and function and are implicated in brain disease states. Enhancers undergo bidirectional transcription to generate non-coding enhancer RNAs (eRNAs). However, eRNA function remains controversial. Here, we combined Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq) and RNA-Seq datasets from three distinct neuronal culture systems in two activity states, enabling genome-wide enhancer identification and prediction of putative enhancer-gene pairs based on correlation of transcriptional output. Notably, stimulus-dependent enhancer transcription preceded mRNA induction, and CRISPR-based activation of eRNA synthesis increased mRNA at paired genes, functionally validating enhancer-gene predictions. Focusing on enhancers surrounding the Fos gene, we report that targeted eRNA manipulation bidirectionally modulates Fos mRNA, and that Fos eRNAs directly interact with the histone acetyltransferase domain of the enhancer-linked transcriptional co-activator CREB-binding protein (CBP). Together, these results highlight the unique role of eRNAs in neuronal gene regulation and demonstrate that eRNAs can be used to identify putative target 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 OpenQuestion graph.