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Related Experiment Video

Updated: Jan 11, 2026

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells

Published on: October 28, 2025

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

This summary is machine-generated.

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.

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Last Updated: Jan 11, 2026

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Quantitative Analysis of Protein Expression to Study Lineage Specification in Mouse Preimplantation Embryos

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Published on: February 22, 2016

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.