Coding Genes Helped the Origination and Diversification of Intragenic MicroRNAs

Area of Science:

• Evolutionary genomics
• Molecular biology
• Developmental biology

Background:

• Noncoding microRNAs (miRNAs) frequently originate within introns of coding genes, leveraging host gene transcription.
• The intragenic location is vital for miRNA expression, evolution, and functional synergy with host genes.
• Understanding intragenic miRNA evolution offers insights into genetic and phenotypic evolution but remains understudied.

Purpose of the Study:

• To investigate the evolutionary origins and diversification of intragenic microRNAs across metazoan species.
• To elucidate the role of host genes and genomic events, such as whole-genome duplications, in shaping miRNA evolution.
• To explore the connection between intragenic miRNAs, neural gene regulation, and the emergence of vertebrate-specific features.

Main Methods:

• Genomic analysis of microRNA families in 34 metazoan species.
• Comparative genomics to trace the origin and evolution of intragenic miRNAs.
• Analysis of gene regulatory networks and the impact of whole-genome duplication events.

Main Results:

• A majority of miRNA families (630/1,154) originated from introns of coding genes, acquiring transcriptional capacity.
• Significant expansion of intragenic miRNAs occurred at the vertebrate advent, with 21 families emerging from neural genes, influencing neural crest development and feeding strategies.
• Whole-genome duplications accelerated miRNA independence and diversification, with retained intragenic status in jawed vertebrates contrasting with jawless cyclostomes.

Conclusions:

• Coding genes serve as crucial facilitators for the origin of new microRNAs.
• Genomic events, particularly whole-genome duplications, promote microRNA diversification by enabling host gene loss and subsequent miRNA adaptation.
• Intragenic miRNAs played a key role in vertebrate evolution, particularly in the development of neural crest cells and complex traits.