Related Experiment Video
Updated: Jan 9, 2026
06:02
A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
Published on: October 28, 2025
408
scAED: a framework for mapping the enhancer state at single-cell resolution
Avinash Veerappa1, Jai Chand Patel1, Sushil Shakyawar1
1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, S 45th St, Omaha, NE 68198, United States.
Briefings in Bioinformatics
|December 8, 2025
Summary
We developed a novel computational framework to map active enhancers in individual cells, creating the single-cell Active Enhancer Database (scAED). This database captures enhancer dynamics, crucial for understanding cellular heterogeneity and gene regulation in health and disease.
Area of Science:
- Genomics
- Epigenetics
- Computational Biology
Background:
- Cellular heterogeneity arises from dynamic gene expression.
- Enhancers regulate gene expression spatially and temporally.
- Existing enhancer databases obscure cell-specific enhancer dynamics.
Purpose of the Study:
- To develop a computational framework for single-cell enhancer activity analysis.
- To create a comprehensive database of active enhancers at single-cell resolution.
- To address limitations of pooled-cell and clustered single-cell data.
Main Methods:
- Utilized sc-Multiome and matched snATAC-seq/snRNA-seq datasets.
- Developed a novel computational framework to extract enhancer chromatin states per cell.
- Established the single-cell Active Enhancer Database (scAED).
Main Results:
- Catalogued over 2.2 million unique active enhancer regions across diverse cell types.
- scAED provides single-cell resolution of enhancer activity.
- Introduced novel features like bidirectional enhancer characterization and trans-acting element capture.
Conclusions:
- scAED offers unprecedented insights into enhancer dynamics and cellular heterogeneity.
- The database facilitates hypothesis generation for regulatory mechanisms in health and disease.
- scAED is a growing resource for enhancer biology research.
