ArticleNature genetics2016
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.
Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers.
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Who cites it
256 citing papers in PubMed, 496 citations in OpenAlex.
- Review
- Article
- Methylation Mesa define functional regulatory elements for targeted gene activation.Nature communications · 2026Article
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- PlantCTCIP: Chromatin Interaction Prediction Using Convolutional Neural Network and Transformer in Plants.Plant biotechnology journal · 2026Article
- Predicting enhancer-promoter interactions using a stacking-based ensemble strategy.Bioinformatics (Oxford, England) · 2026Article
- UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility.Nucleic acids research · 2026Article
- BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution.BMC genomics · 2026Article
- FUSE: data-driven functional segmentation of DNA methylation data.Bioinformatics (Oxford, England) · 2026Article
- CRM-TI: an enhanced pipeline for computationally assigning the target genes of cis-regulatory modules by considering comprehensive long-range regulation mechanisms.BioData mining · 2026Article
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- UniChrom: a universal deep learning architecture for cross-scale chromatin interaction prediction.BMC genomics · 2026Article
- A compendium of chromatin interaction maps in the Giant Panda genome.Communications biology · 2026Article
- EPINTLM: enhancer-promoter prediction with pretrained k-mer embeddings and residual cross-attention.Briefings in bioinformatics · 2026Article
- The rs713586 risk variant dysregulates ADCY3 rather than DNAJC27, leading to obesity through ZFP42-TET1-mediated DNA methylation.EBioMedicine · 2026Article
- Pyruvate kinase M2 -mediated histone lactylation alters three-dimensional genomic architecture in polycystic ovary syndrome.Signal transduction and targeted therapy · 2025Article
- PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework.Bioinformatics (Oxford, England) · 2025Article
- ETNet: an interpretable transformer framework for enhancer-enhancer interaction prediction with cross-context transferability.Briefings in bioinformatics · 2025Article
- CTCF Mediates the Cis-Regulatory Hubs in Mouse Hearts.International journal of molecular sciences · 2025Article
- EPIFBMC: A New Model for Enhancer-Promoter Interaction Prediction.International journal of molecular sciences · 2025Article
196 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Discriminating the gene target of a distal regulatory element from other nearby transcribed genes is a challenging problem with the potential to illuminate the causal underpinnings of complex diseases. We present TargetFinder, a computational method that reconstructs regulatory landscapes from diverse features along the genome. The resulting models accurately predict individual enhancer-promoter interactions across multiple cell lines with a false discovery rate up to 15 times smaller than that obtained using the closest gene. By evaluating the genomic features driving this accuracy, we uncover interactions between structural proteins, transcription factors, epigenetic modifications, and transcription that together distinguish interacting from non-interacting enhancer-promoter pairs. Most of this signature is not proximal to the enhancers and promoters but instead decorates the looping DNA. We conclude that complex but consistent combinations of marks on the one-dimensional genome encode the three-dimensional structure of fine-scale regulatory interactions.
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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.