ReviewComputational and structural biotechnology journal2020
Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- SEgene identifies links between super enhancers and gene expression across cell types.NPJ systems biology and applications · 2025Article
- Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.BMC genomics · 2025Article
- RAEPI: Predicting Enhancer-Promoter Interactions Based on Restricted Attention Mechanism.Interdisciplinary sciences, computational life sciences · 2025Article
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- GATv2EPI: Predicting Enhancer-Promoter Interactions with a Dynamic Graph Attention Network.Genes · 2024Article
- Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets.Briefings in bioinformatics · 2024Review
- Article
- A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health.BMC medicine · 2023Article
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.Bioinformatics (Oxford, England) · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- Computational methods for identifying enhancer-promoter interactions.Quantitative biology (Beijing, China) · 2023Review
- 3D genome perspective on cell fate determination, organ regeneration, and diseases.Cell proliferation · 2023Review
- MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.Genome biology · 2022Article
- A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.Genome biology · 2022Article
- StackEPI: identification of cell line-specific enhancer-promoter interactions based on stacking ensemble learning.BMC bioinformatics · 2022Article
- EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions.Nucleic acids research · 2022Article
- The Impact of Space and Time on the Functional Output of the Genome.Cold Spring Harbor perspectives in biology · 2022Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.
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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.