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Updated: Jan 11, 2026
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
Published on: October 28, 2025
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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
Myunggeun Oh1, Seunghwa Jeong1, Seung-Kyoon Kim2
1Department of Convergent Bioscience and Informatics, and Graduate School of Biological Sciences, Chungnam National University (CNU).
Journal of Visualized Experiments : Jove
|November 17, 2025
Summary
We developed a user-friendly computational workflow to analyze enhancer RNAs (eRNAs) from sequencing data. This tool simplifies the detection and quantification of eRNA transcription, even for complex intragenic regions.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Enhancers are crucial cis-regulatory elements controlling gene expression.
- Enhancers produce enhancer RNAs (eRNAs), linked to active chromatin and gene activation.
- Quantifying eRNAs, especially intragenic ones, presents significant technical challenges.
Purpose of the Study:
- To present a standardized, user-friendly computational workflow for analyzing enhancer transcription.
- To enable accurate detection and quantification of eRNAs from nascent RNA sequencing data.
- To facilitate reproducible and scalable studies of enhancer biology.
Main Methods:
- Development of a computational workflow for analyzing nascent RNA sequencing data.
- Includes data preprocessing, read mapping, quality control, and strand-specific eRNA quantification.
- Dedicated modules for analyzing both intergenic and complex intragenic enhancers.
Main Results:
- The workflow provides standardized procedures for eRNA analysis.
- Enables clear visualization of enhancer activity across genomic contexts.
- Offers dedicated solutions for quantifying transcription from intragenic enhancers.
Conclusions:
- The presented workflow simplifies the analysis of enhancer transcription.
- Facilitates reproducible and scalable research in enhancer biology.
- Aims to broaden the application of enhancer studies across diverse biological systems.
