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A Computational Pipeline for Intergenic/Intragenic Enhancer RNA Quantification in Mouse Embryonic Stem Cells
Published on: October 28, 2025
Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing.
Haitao Luo1, Silong Sun, Ping Li
1Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.
Plos One
|August 17, 2013
Summary
Researchers cataloged 10,571 mouse long noncoding RNAs (lincRNAs), revealing tissue-specific expression and potential roles in development. This comprehensive resource aids future functional studies of these crucial transcripts.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Large intergenic noncoding RNAs (lincRNAs) are abundant but functionally understudied transcripts.
- Incomplete annotation of tissue-specific lincRNAs in model organisms like mice hinders research.
- Understanding lincRNA function is crucial for deciphering complex biological processes.
Purpose of the Study:
- To create a comprehensive catalog of transcribed mouse lincRNAs.
- To analyze the characteristics and expression patterns of mouse lincRNAs.
- To predict the functional roles of tissue-specific lincRNAs.
Main Methods:
- Ab initio assembly of 1.9 billion tissue-specific RNA-sequencing reads from six mouse tissue types.
- Integration of novel and documented lincRNAs into a unified catalog.
- Systematic analysis of lincRNA conservation, expression, genomic signatures, and correlation with neighboring genes.
Main Results:
- Identification and cataloging of 3,965 novel mouse lincRNAs, resulting in a total of 10,571 transcribed lincRNAs.
- Discovery of evolutionarily conserved lincRNAs with striking tissue-specific expression patterns.
- Correlation observed between lincRNA expression levels and neighboring protein-coding transcripts.
- Prediction of functional associations for tissue-specific lincRNAs in cell cycle and development.
Conclusions:
- The comprehensive mouse lincRNA catalog provides a valuable resource for functional genomics.
- Tissue-specific lincRNAs are likely key regulators of tissue development and function.
- This study establishes a framework for lincRNA annotation and functional characterization in model organisms.
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