Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Natural antisense transcripts regulate gene expression.
• Cis-sense/antisense pairs (cis-SAs) are well-studied, but trans-sense/antisense pairs (trans-SAs) in animals remain poorly understood.

Purpose of the Study:

• To identify and characterize long trans-SAs in humans and other animal species.
• To investigate the potential regulatory functions and evolutionary origins of trans-SAs.

Main Methods:

• Utilized expressed sequence tags (ESTs) to identify trans-SAs across multiple species.
• Analyzed sequence complementarity, RNA hybridization patterns, and gene ontology enrichment.
• Examined expression patterns and conservation across species.

Main Results:

• Identified numerous long trans-SAs in human and nine other animal genomes, significantly increasing coverage.
• Found that 4.13% of transcriptional units (TUs) are involved in trans-SAs, with 2.89% of human TUs implicated.
• Observed sophisticated RNA-RNA pairing, enrichment in specific functional pathways, concordant/reciprocal expression, and conservation in mice, suggesting regulatory roles.

Conclusions:

• Trans-SAs play significant regulatory roles in gene expression, particularly involving noncoding RNAs.
• Identified potential mechanisms for trans-SA evolution, linking them to cis-SAs via paralogues.