Supplementary Data - Exonic enhancers are a widespread class of dual-function regulatory elements
Year: 2025
Type: supplementary-materials
Abstract: Description This repository accompanies our manuscript, “Exonic enhancers are a widespread class of dual-function regulatory elements,” in which we redefine the role of exonic regions in gene regulation. We demonstrate that many protein-coding exons also function as exonic enhancers (EEs) : previously underappreciated regulatory elements embedded within exons. By integrating TF ChIP-seq, chromatin accessibility data (DNase-seq/ATAC-seq), studying the impact of variants (common and cancer variants), high-throughput enhancer-reporter assays (STARR-seq, luciferase), and CRISPR-based validations, we show that EEs play critical roles in cis-regulatory networks while retaining protein-coding functionality. This repository provides the processed datasets, nd supporting materials used throughout the study, organized into thematic folders to facilitate easy navigation and reproducibility. Analysis scripts are both in Github and in another Zenodo. Key findings Identification of EEs Across Multiple Species - Systematic discovery of EEs using TF ChIP-seq, chromatin accessibility (DNase-seq/ATAC-seq), and STARR-seq data. - Many protein-coding exons exhibit enhancer activity. Dual Coding and Regulatory Roles - EEs retain coding functions while acting as cis-regulatory elements. - Both synonymous and nonsynonymous variants can disrupt enhancer activity and gene expression. Long-Range Interactions and Target Gene Regulation - Promoter capture Hi-C and eQTL integration confirm interactions between EEs and gene promoters. - CRISPR-mediated inactivation demonstrates that EEs regulate both host and distal gene expression. Clinical and Evolutionary Implications - TCGA cancer genome analysis reveals EE mutations correlate with altered target-gene expression and clinical outcomes. - Evolutionary conservation studies show that EEs are both functionally constrained and contribute to species-specific regulatory innovations. Repository Contents Below are the main folders included in this Zenodo repository. Each folder provides data or scripts relevant to the analyses described in the manuscript. 1_easy_accessContains the principal output files that may be of primary interest, including: ExonsEnhancers_all_species.tar.gz interactions_robust_EE_target_genes.tsv.gz STARR-seq_catalogs_all_species.tar.gz tcga_deseq_significative_results.tsv.gz tcga_variants_in_ee_per_patients_per_cancers_hg19.tsv.gz EE_selectionFinal lists used to define exonic enhancers (EEs) based on TF ChIP-seq peaks and filtering criteria. Control_selectionList of negative/positive control sets, ensuring consistent comparisons with EEs. Chromatin_accessibilityProcessed DNase-seq and ATAC-seq datasets used to assess open chromatin in exons and EEs across multiple species. Conservation_and_structureFiles related to multi-species alignments, phyloP conservation scores, MobiIDB disorder rates, AlphaFold structural data, and gene-age analysis for EEs. TF_randomisationResults for validating TF-binding enrichment in EEs through randomization tests. TFBS_in_EEMotif analysis outputs and JASPAR-based TFBS predictions overlapping EEs. STARR-seq_experimentNewly generated STARR-seq experimental data for exonic fragments. STARR-seq_catalogConsolidated catalogs of STARR-seq peaks from public sources, with annotations of EEs (overlap, signal, biotypes). G-quadruplexData examining the enrichment of G4-forming sequences within EEs relative to controls. Interaction_dataIntegration of promoter capture Hi-C, eQTL (GTEx), and ENCODE-rE2G resources to define robust EE–target gene interactions. gnomADv3_analysisVariant filtering and annotation pipelines used to intersect gnomAD v3 data (common variants) with EEs. GWAS_analysisOverlaps of GWAS loci with EEs to identify potential trait- and disease-associated variants in coding enhancer regions. PanCancer_analysisPan-cancer somatic mutation data (TCGA) intersected with EEs, files of differential expression. UCSC_trackhubReady-to-use track hub configurations for visualizing EEs, TF binding, and variant positions in the UCSC Genome Browser. How to Cite If you use this dataset or associated methods in your research, please cite both this Zenodo repository and the corresponding manuscript: Mouren J-C, Torres M, Van-Ouwerkerk A, Manosalva I, Gallardo F, Spicuglia S, Ballester B. Supplementary Data - Exonic enhancers are a widespread class of dual-function regulatory elements. Zenodo. [https://doi.org/10.5281/zenodo.15079251] Mouren J-C, Torres M, Van-Ouwerkerk A, Manosalva I, Gallardo F, Spicuglia S, Ballester B. Exonic enhancers are a widespread class of dual-function regulatory elements. (In prep - journal). [DOI] Contact For questions regarding the data, analysis scripts, or methods, please contact:Jean-Christophe Mouren & Benoit BallesterAix Marseille University, INSERM, TAGC, UMR [email protected] & [email protected] We hope this repository serves as a valuable resource for further research into exonic enhancers and their roles in gene regulation, evolution, and disease.
Authors: Mouren, Jean-Christophe, TORRES, Magali, van Ouwerkerk, Antoinette, Manosalva, Gallardo, Frederic, Spicuglia, Salvatore, Ballester, Benoit
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6912096795
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