Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• Gene creation traditionally involves modifying existing genes.
• Recent discoveries show new protein-coding genes can arise de novo from non-coding DNA.
• The origins of de novo genes remain largely unexplored.

Purpose of the Study:

• To identify and characterize hominoid-specific de novo protein-coding genes.
• To determine the origination timing of these genes within vertebrate phylogeny.
• To investigate the evolutionary trajectory from non-coding to protein-coding genes.

Main Methods:

• Strand-specific RNA-Sequencing (RNA-Seq) in multiple rhesus macaque tissues.
• Integration of RNA-Seq data with public transcriptome data from humans, chimpanzees, and rhesus macaques.
• Comparative analysis of RNA expression profiles across species to infer evolutionary steps.

Main Results:

• Identified 24 hominoid-specific de novo protein-coding genes with defined origination times.
• Observed that most of these genes encoded non-coding RNAs in macaques and chimpanzees, with similar structures and expression patterns.
• Found that genes acquired regulated transcript structure and expression profiles prior to coding potential.

Conclusions:

• Long non-coding RNAs with active, regulated transcription may act as a reservoir for new protein-coding genes.
• The acquisition of regulatory elements precedes the development of coding capacity in de novo gene evolution.
• Human protein-coding genes often exhibit higher expression levels than their non-coding precursors in other species.