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Updated: Mar 5, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs
Qianqian Ning1,2, Yixue Li1,2,3,4, Zhen Wang3
1Department of Bioinformatics and Biostatistics, School of Life Sciences &Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Long non-coding RNA (lncRNA)-coding gene pairs in the human genome are prioritized during evolution and exhibit complex expression correlations. These overlapping gene pairs may play a role in cancer development.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Long non-coding RNAs (lncRNAs) are increasingly recognized for their regulatory roles.
- Overlapping genes, particularly protein-coding pairs, are well-studied, but lncRNA-coding pairs remain less understood.
- Understanding the interplay between lncRNAs and protein-coding genes in overlapping configurations is crucial.
Purpose of the Study:
- To comprehensively investigate the evolutionary patterns of human lncRNA-coding pairs.
- To analyze the expression characteristics and correlations within lncRNA-coding pairs.
- To explore the potential role of these pairs in tumorigenesis.
Main Methods:
- Bioinformatic analysis of human genome data.
- Comparative genomics to study evolutionary conservation.
- Gene expression correlation analysis in normal and cancer tissues.
Main Results:
- lncRNA-coding pairs are frequently generated by overprinting and prioritized for retention during evolution.
- lncRNA interactions with protein-coding partners can be unilateral (splicing promotion) or bidirectional (gene expression enhancement).
- Expression correlation in lncRNA-coding pairs is influenced by configuration, genomic context, and evolutionary age, with potential implications in cancer.
Conclusions:
- Human lncRNA-coding pairs display unique evolutionary trajectories and expression dynamics.
- The evolutionary age and genomic context significantly modulate the regulatory effects within these pairs.
- Lineage-specific lncRNA-coding pairs, especially those involving ancient protein-coding genes, may contribute to cancer development.
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