ArticleEpigenetics & chromatin2015
Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.
Article in Epigenetics & chromatin, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed, 121 citations in OpenAlex.
- A chromatin-informed transcriptional regulatory framework to stratify patients and guide therapy selection in triple-negative breast cancer.Nature communications · 2026Article
- Distinct and compensatory roles of STAG1 and STAG2 in post-mitotic genome refolding.Nature communications · 2026Article
- Variant-to-function dissection of the 17q21.31 locus resolves ANKRD1 as a convergent regulatory target.BMC medical genomics · 2026Article
- Microglial epigenetic memory is associated with accelerated resolution of inflammatory pain induced by prophylactic macrophage-derived small extracellular vesicles.bioRxiv : the preprint server for biology · 2026Article
- Microglial Epigenetic Memory is Associated with Accelerated Resolution of Inflammatory Pain Induced by Prophylactic Macrophage-Derived Small Extracellular Vesicles.Journal of inflammation research · 2026Article
- Discovering the complete enhancer map of human herpesviruses using a natural language processing model.Nature communications · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- Article
- Combinatorial transcription factor binding encodes cis-regulatory wiring of mouse forebrain GABAergic neurogenesis.Developmental cell · 2025Article
- LDB1 establishes multi-enhancer networks to regulate gene expression.Molecular cell · 2025Article
- LDB1 establishes multi-enhancer networks to regulate gene expression.bioRxiv : the preprint server for biology · 2024Article
- Genome folding principles uncovered in condensin-depleted mitotic chromosomes.Nature genetics · 2024Article
- Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids.Scientific reports · 2024Article
- Genome folding principles revealed in condensin-depleted mitotic chromosomes.bioRxiv : the preprint server for biology · 2023Article
- Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids.bioRxiv : the preprint server for biology · 2023Article
- A generalizable framework to comprehensively predict epigenome, chromatin organization, and transcriptome.Nucleic acids research · 2023Article
- A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.Nature communications · 2023Article
- Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences.BMC genomics · 2023Article
- Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique.Frontiers in cellular and infection microbiology · 2023Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
15 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 7 institutions in 1 country.
Funding
Abstract
backgroundRegulated gene expression controls organismal development, and variation in regulatory patterns has been implicated in complex traits. Thus accurate prediction of enhancers is important for further understanding of these processes. Genome-wide measurement of epigenetic features, such as histone modifications and occupancy by transcription factors, is improving enhancer predictions, but the contribution of these features to prediction accuracy is not known. Given the importance of the hematopoietic transcription factor TAL1 for erythroid gene activation, we predicted candidate enhancers based on genomic occupancy by TAL1 and measured their activity. Contributions of multiple features to enhancer prediction were evaluated based on the results of these and other studies.
resultsTAL1-bound DNA segments were active enhancers at a high rate both in transient transfections of cultured cells (39 of 79, or 56%) and transgenic mice (43 of 66, or 65%). The level of binding signal for TAL1 or GATA1 did not help distinguish TAL1-bound DNA segments as active versus inactive enhancers, nor did the density of regulation-related histone modifications. A meta-analysis of results from this and other studies (273 tested predicted enhancers) showed that the presence of TAL1, GATA1, EP300, SMAD1, H3K4 methylation, H3K27ac, and CAGE tags at DNase hypersensitive sites gave the most accurate predictors of enhancer activity, with a success rate over 80% and a median threefold increase in activity. Chromatin accessibility assays and the histone modifications H3K4me1 and H3K27ac were sensitive for finding enhancers, but they have high false positive rates unless transcription factor occupancy is also included.
conclusionsOccupancy by key transcription factors such as TAL1, GATA1, SMAD1, and EP300, along with evidence of transcription, improves the accuracy of enhancer predictions based on epigenetic features.
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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.