SmithRNAs: A Common Feature among Metazoa

Area of Science:

• Molecular Biology
• Genomics
• Evolutionary Biology

Background:

• SmithRNAs are novel small noncoding RNAs encoded in mitochondrial genomes.
• Their function in regulating nuclear transcripts was recently confirmed in the Manila clam.
• The evolutionary conservation and broader distribution of smithRNAs across Metazoa remained largely unknown.

Purpose of the Study:

• To investigate the presence and biological features of smithRNAs across a wide range of Metazoan species.
• To determine if smithRNAs are a conserved feature of Metazoa or unique to specific species.
• To propose a transcriptional mechanism for smithRNA biogenesis and identify their potential nuclear targets.

Main Methods:

• Selection of 14 species representing major metazoan lineages.
• Collection and de novo sequencing/assembly of small RNAseq data, transcriptomes, and genomes.
• Analysis using the SmithHunter pipeline for smithRNA identification and target prediction.

Main Results:

• Candidate smithRNAs were identified in all 14 species studied, indicating they are a common feature across Metazoa.
• SmithRNAs are typically encoded within other genes, preferably on mitochondrial rRNAs and tRNAs.
• A transcription model suggests smithRNAs are cleaved from primary mitochondrial transcripts; nuclear targets show variability, often related to regulation, mitochondrial function, and reproduction.

Conclusions:

• SmithRNAs are a conserved feature across Metazoa, not unique to bivalves.
• A proposed biogenesis mechanism involves post-transcriptional processing of mitochondrial gene transcripts.
• SmithRNAs likely play diverse regulatory roles, impacting nuclear gene expression, mitochondrial activity, and reproductive processes.