Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Small self-cleaving RNAs, like Hammerhead ribozymes (HHRs), are increasingly found in genomes across all life forms.
• Penelope-like elements (PLEs) are ancient eukaryotic retrotransposons with unique features, including telomerase-like retrotranscriptases and spliceosomal introns.

Purpose of the Study:

• To investigate the presence and characteristics of HHR variants within Penelope-like elements (PLEs).
• To determine the distribution and potential function of these HHRs in eukaryotic genomes, particularly in metazoans.

Main Methods:

• Bioinformatic analysis to identify HHR motifs within PLE sequences.
• Comparative genomics to assess the prevalence of HHRs in metazoan, plant, fungal, and protist genomes.
• In vitro assays to evaluate the self-cleavage activity of identified ribozymes.

Main Results:

• Minimalist HHR variants were identified in the flanking repeats of PLEs.
• These HHRs are massively and widely distributed in metazoan genomes.
• PLE-associated HHRs in plants are canonical, while those in fungi and protists exist as stable monomers.
• In vitro self-cleavage activity was low, suggesting a need for other factors in vivo.

Conclusions:

• Self-cleaving RNAs are linked to eukaryotic retroelements.
• HHR motifs represent a significant portion of encoded information in eukaryotic genomes.
• PLEs harbor diverse HHR variants with distinct architectures and potential regulatory mechanisms across different eukaryotic lineages.