Sessions allow users to save snapshots of the Genome Browser and its current configuration, including displayed tracks, position, and custom track data. The Public Sessions tool allows users to easily share those sessions that they deem interesting with the rest of the world's researchers. You can add your own sessions to this list by checking the appropriate box on the Session Management page.
Description: Exonic enhancers (EEs) are a newly characterized class of dual-function regulatory elements that reside in protein-coding regions yet retain bona fide enhancer activity. In our study, we integrated transcription factor (TF) binding profiles (ReMap), chromatin accessibility data (DNase, ATAC), and high-throughput reporter assays (STARR-seq, luciferase) to show that many exons can act as cis-regulatory modules. These EEs display hallmark epigenomic signatures, often form long-range interactions with promoters, and are sensitive to both nonsynonymous and synonymous mutations. Functional assays, including CRISPR-based silencing, demonstrate their involvement in regulating host and distal genes. Large-scale cancer genomics analyses reveal that EE variants are associated with dysregulated gene expression and clinical outcomes, underscoring their importance in disease. Evolutionary comparisons further indicate that EEs combine deep sequence conservation with lineage-specific innovation, revealing how coding regions can simultaneously encode protein domains and regulatory activities.
This UCSC public session provides direct visualization of these findings, featuring our custom track hub: https://remap.univ-amu.fr/storage/public/hubEE/hub.txt.
Researchers can explore TF occupancy, open chromatin marks, STARR-seq signals, and EE annotations genome-wide, offering a comprehensive resource to investigate how exons function as both protein-coding and cis-regulatory elements. Author: Benoit Ballester Session Name: hg38_ExonEnhancers_gnomAD Genome Assembly: hg38 Creation Date: 2025-03-21 Views: 4
Description: Exonic enhancers (EEs) are a newly characterized class of dual-function regulatory elements that reside in protein-coding regions yet retain bona fide enhancer activity. In our study, we integrated transcription factor (TF) binding profiles (ReMap), chromatin accessibility data (DNase, ATAC), and high-throughput reporter assays (STARR-seq, luciferase) to show that many exons can act as cis-regulatory modules. These EEs display hallmark epigenomic signatures, often form long-range interactions with promoters, and are sensitive to both nonsynonymous and synonymous mutations. Functional assays, including CRISPR-based silencing, demonstrate their involvement in regulating host and distal genes. Large-scale cancer genomics analyses reveal that EE variants are associated with dysregulated gene expression and clinical outcomes, underscoring their importance in disease. Evolutionary comparisons further indicate that EEs combine deep sequence conservation with lineage-specific innovation, revealing how coding regions can simultaneously encode protein domains and regulatory activities.
This UCSC public session provides direct visualization of these findings, featuring our custom track hub: https://remap.univ-amu.fr/storage/public/hubEE/hub.txt.
Researchers can explore TF occupancy, open chromatin marks, STARR-seq signals, and EE annotations genome-wide, offering a comprehensive resource to investigate how exons function as both protein-coding and cis-regulatory elements. Author: Benoit Ballester Session Name: hg19_ExonEnhancers_TCGA Genome Assembly: hg19 Creation Date: 2025-03-21 Views: 6
Description: This public session offers access to a track hub containing 25,000 predicted forebrain enhancers within the hg19 human genome assembly. These enhancers were identified through a DNA-sequence-based prediction pipeline that integrates tissue-specific transcription factor occupancy patterns. Essential for regulating gene expression during brain development, these enhancers were further validated using chromatin marks, DNase hypersensitivity data, GWAS-based SNP data, and in vivo zebrafish models (https://doi.org/10.1002/1873-3468.15030).
Additionally, this session includes an extra track for a subset of 2,614 predicted forebrain enhancers, representing a portion of the full set. This subset specifically reveals the binding patterns of the HES5-FOXP2-GATA3 triad, with FOXP2 binding positioned between HES5 and GATA3, helping define the forebrain transcription factor binding syntax (https://doi.org/10.1242/bio.061751).
Together, the forebrain enhancer data presented in this public track hub provides a valuable resource for investigating the genetic regulatory mechanisms underlying brain development and related diseases. It also offers a platform for exploring the role of these predicted enhancers in mammalian and primate brain evolution. Author: abbasiam Session Name: hg19_Predicted human forebrain enhancers_hg19 Genome Assembly: hg19 Creation Date: 2025-03-20 Views: 24
Description: This session give an overview of the human CHD1 gene encoding the clinically relevant E-Cadherin/Cadherin-1 protein. Disease susceptibility is associated with variants in CDH-1 including gastric cancer and lobular breast cancer. Data tracks demonstrating disease-associated alleles, protein domains, and conservation have been included. Author: renkejhsph Session Name: hg38 CDH1 gene Genome Assembly: hg38 Creation Date: 2025-03-20 Views: 6
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