ArticleNucleic acids research2020
Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning.Nature communications · 2026Article
- Epromoters bind key stress-related transcription factors to regulate clusters of stress response genes.The EMBO journal · 2026Article
- A nextflow pipeline for molecular quantitative trait loci mapping in small sample size datasets with an application in Atlantic salmon.BMC genomics · 2025Article
- The contribution of genetic determinants of blood gene expression and splicing to molecular phenotypes and health outcomes.Nature genetics · 2025Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Genetic variants associated mRNA stability in lung.BMC genomics · 2022Article
- Epromoters function as a hub to recruit key transcription factors required for the inflammatory response.Nature communications · 2021Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
- AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators.Scientific reports · 2021Article
- Genetic effects on liver chromatin accessibility identify disease regulatory variants.American journal of human genetics · 2021Article
- Article
- RNA, Genome Output and Input.Frontiers in genetics · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Identifying DNA cis-regulatory modules (CRMs) that control the expression of specific genes is crucial for deciphering the logic of transcriptional control. Natural genetic variation can point to the possible gene regulatory function of specific sequences through their allelic associations with gene expression. However, comprehensive identification of causal regulatory sequences in brute-force association testing without incorporating prior knowledge is challenging due to limited statistical power and effects of linkage disequilibrium. Sequence variants affecting transcription factor (TF) binding at CRMs have a strong potential to influence gene regulatory function, which provides a motivation for prioritizing such variants in association testing. Here, we generate an atlas of CRMs showing predicted allelic variation in TF binding affinity in human lymphoblastoid cell lines and test their association with the expression of their putative target genes inferred from Promoter Capture Hi-C and immediate linear proximity. We reveal >1300 CRM TF-binding variants associated with target gene expression, the majority of them undetected with standard association testing. A large proportion of CRMs showing associations with the expression of genes they contact in 3D localize to the promoter regions of other genes, supporting the notion of 'epromoters': dual-action CRMs with promoter and distal enhancer activity.
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Registered trials
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.