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Published on: February 1, 2019
Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes
Ping Wang1, Shanye Yin, Zhenguo Zhang
1Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiao Tong University School of Medicine, 225 South Chong Qing Road, Shanghai 200025, PR China. pwang01@sibs.ac.cn
Genome Biology
|December 6, 2008
Summary
Coding RNAs may regulate other coding RNAs through short sense-antisense binding. This study found more such pairs than expected, suggesting a common regulatory mechanism in human cells.
Area of Science:
- Molecular Biology
- Genetics
- Bioinformatics
Background:
- Gene regulation occurs at the RNA level via sense-antisense binding.
- Research often focuses on non-coding RNAs, but most cellular transcripts are coding.
- The potential for coding RNAs to regulate other coding RNAs through sense-antisense pairing is explored.
Purpose of the Study:
- To investigate the prevalence of short, perfect sense-antisense binding sites between human protein-coding messenger RNAs (mRNAs).
- To determine if coding RNAs can potentially regulate other coding RNAs.
Main Methods:
- Compared all human protein-coding mRNA RefSeq sequences against the entire transcriptome.
- Identified potential sense-antisense binding sites of 15-25 base pairs.
- Used randomization to assess the statistical significance of observed pairs.
Main Results:
- Every protein-coding mRNA sequence had at least one potential match in the transcriptome.
- The number of trans short sense-antisense pairs found was higher than predicted by chance.
- Transcripts with more potential partners exhibited lower expression levels.
- Tissue-specific genes showed higher pair density than housekeeping genes.
- Single nucleotide polymorphism density was lower in pairing regions compared to flanking regions.
Conclusions:
- Findings support the hypothesis that short, perfect sense-antisense pairing between transcripts of protein-coding genes is common.
- This suggests a potential widespread mechanism for gene regulation among coding RNAs.
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