ArticleNucleic acids research2021
Predict long-range enhancer regulation based on protein-protein interactions between transcription factors.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 26 citations in OpenAlex.
- Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- EPIFBMC: A New Model for Enhancer-Promoter Interaction Prediction.International journal of molecular sciences · 2025Article
- Distilling knowledge from graph neural networks trained on cell graphs to non-neural student models.Scientific reports · 2025Article
- Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM.PLoS computational biology · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes.Genome biology · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- GRPhIN: graphlet characterization of regulatory and physical interaction networks.Bioinformatics advances · 2025Article
- Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases.Briefings in bioinformatics · 2024Article
- PancanQTLv2.0: a comprehensive resource for expression quantitative trait loci across human cancers.Nucleic acids research · 2024Article
- IVEA: an integrative variational Bayesian inference method for predicting enhancer-gene regulatory interactions.Bioinformatics advances · 2024Article
- Identifying genetic loci that are associated with changes in gene expression in PTSD in a South African cohort.Journal of neurochemistry · 2023Article
- Transcriptional and post-transcriptional controls for tuning gene expression in plants.Current opinion in plant biology · 2023Review
- MIR retrotransposons link the epigenome and the transcriptome of coding genes in acute myeloid leukemia.Nature communications · 2022Article
- Expression regulation of genes is linked to their CpG density distributions around transcription start sites.Life science alliance · 2022Article
- Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development-New Insights From Technical Advances.Frontiers in cell and developmental biology · 2022Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Long-range regulation by distal enhancers plays critical roles in cell-type specific transcriptional programs. Computational predictions of genome-wide enhancer-promoter interactions are still challenging due to limited accuracy and the lack of knowledge on the molecular mechanisms. Based on recent biological investigations, the protein-protein interactions (PPIs) between transcription factors (TFs) have been found to participate in the regulation of chromatin loops. Therefore, we developed a novel predictive model for cell-type specific enhancer-promoter interactions by leveraging the information of TF PPI signatures. Evaluated by a series of rigorous performance comparisons, the new model achieves superior performance over other methods. The model also identifies specific TF PPIs that may mediate long-range regulatory interactions, revealing new mechanistic understandings of enhancer regulation. The prioritized TF PPIs are associated with genes in distinct biological pathways, and the predicted enhancer-promoter interactions are strongly enriched with cis-eQTLs. Most interestingly, the model discovers enhancer-mediated trans-regulatory links between TFs and genes, which are significantly enriched with trans-eQTLs. The new predictive model, along with the genome-wide analyses, provides a platform to systematically delineate the complex interplay among TFs, enhancers and genes in long-range regulation. The novel predictions also lead to mechanistic interpretations of eQTLs to decode the genetic associations with gene expression.
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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 Socratic graph.