UMass Chan Medical School Faculty Publications


High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection

UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Program in Molecular Medicine; Graduate School of Biomedical Sciences

Publication Date


Document Type



Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Genetics and Genomics | Molecular Biology


Eukaryotic gene expression regulation involves thousands of distal regulatory elements. Understanding the quantitative contribution of individual enhancers to gene expression is critical for assessing the role of disease-associated genetic risk variants. Yet, we lack the ability to accurately link genes with their distal regulatory elements. To address this, we used 3D enhancer-promoter (E-P) associations identified using split-pool recognition of interactions by tag extension (SPRITE) to build a predictive model of gene expression. Our model dramatically outperforms models using genomic proximity and can be used to determine the quantitative impact of enhancer loss on gene expression in different genetic backgrounds. We show that genes that form stable E-P hubs have less cell-to-cell variability in gene expression. Finally, we identified transcription factors that regulate stimulation-dependent E-P interactions. Together, our results provide a framework for understanding quantitative contributions of E-P interactions and associated genetic variants to gene expression.


chromosome conformation, cis-regulatory elements, dendritic cells, enhancers, genetic variation, innate immunity, machine learning, multiway promoter interactions, single cell, single molecule

DOI of Published Version



Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M. High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection. Mol Cell. 2020 Oct 15;80(2):359-373.e8. doi: 10.1016/j.molcel.2020.09.005. Epub 2020 Sep 28. PMID: 32991830; PMCID: PMC7572724. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Molecular cell

PubMed ID