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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

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data.

Wanqing Shao^1,2, Ting Wang^1,2,3

¹Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

Genome Research

|December 23, 2020

Summary

This summary is machine-generated.

We developed a new method to analyze transposable element (TE) expression in single cells. This tool quantifies TE-containing noncoding RNAs (ncRNAs), revealing their dynamic roles in early mouse development.

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Area of Science:

Genomics
Developmental Biology
RNA Biology

Background:

Transposable elements (TEs) are crucial components of the host transcriptome, with TE-containing noncoding RNAs (ncRNAs) exhibiting tissue specificity and influencing development.
Single-cell RNA sequencing (scRNA-seq) has transformed gene expression analysis, but tools for TE quantification at single-cell resolution are needed.
Understanding TE dynamics is vital for comprehending cellular processes like stem cell maintenance and differentiation.

Purpose of the Study:

To develop and validate a computational pipeline for quantifying transposable element (TE) expression from single-cell RNA sequencing (scRNA-seq) data.
To enable high-resolution analysis of TE-containing noncoding RNA (ncRNA) expression dynamics across diverse cell types and developmental stages.
To investigate the role of TEs in early mouse embryogenesis and tissue-specific gene regulation.

Main Methods:

Established a TE expression quantification pipeline compatible with multiple scRNA-seq platforms.
Constructed TE-containing ncRNA references using bulk RNA sequencing data for improved accuracy.
Quantified TE expression at the transcript level to minimize noise and enhance resolution.

Main Results:

Successfully applied the pipeline to mouse embryonic stem cells, capturing endogenous retroviral expression profiles.
Analyzed scRNA-seq data from early mouse embryogenesis, revealing dynamic TE expression during preimplantation stages.
Identified 146 TE-containing ncRNA transcripts with significant tissue specificity during gastrulation and early organogenesis.

Conclusions:

The developed pipeline effectively quantifies TE expression at single-cell resolution, overcoming previous limitations.
TE-containing ncRNAs exhibit dynamic and tissue-specific expression patterns crucial for early mammalian development.
This approach provides a valuable tool for dissecting the functional roles of TEs in cellular processes and development.