Using RNA inverse folding to identify IRES-like structural subdomains.

Area of Science:

• Molecular Biology
• RNA Biology
• Bioinformatics

Background:

• Internal ribosome entry site (IRES) elements facilitate cap-independent translation initiation in messenger RNAs (mRNAs), crucial under cellular stress.
• Picornavirus IRES elements are modular cis-acting sequences that recruit ribosomes to internal mRNA sites for translation.
• Understanding the structural basis of IRES function is key to deciphering alternative translation mechanisms.

Purpose of the Study:

• To identify short RNA sequences capable of adopting conserved RNA folding patterns similar to IRES structural subdomains.
• To explore the potential of these RNA motifs to function as novel internal ribosome entry site (IRES)-like elements.
• To investigate the translational capacity of a specific IRES-like RNA motif found in a cellular gene.

Main Methods:

• Utilized RNAiFold, an inverse folding algorithm, to predict sequences with minimum free energy structures matching IRES structural domains.
• Clustered predicted sequences and employed BLAST analysis to identify homologous viral and cellular RNA sequences.
• Analyzed a coding region from Drosophila melanogaster TAF6 for IRES-like structural motifs and translational activity.

Main Results:

• RNAiFold successfully generated RNA sequences with structures mimicking IRES subdomains.
• BLAST searches identified conserved viral and cellular RNA sequences within the predicted clusters.
• The analyzed TAF6 RNA region exhibited biased codon usage, conserved IRES structural motifs, and conferred internal translation initiation in cell culture.

Conclusions:

• Short RNA sequences can be computationally designed to fold into structures resembling functional IRES elements.
• The identified IRES-like motif in the TAF6 gene demonstrates the presence of such regulatory elements in cellular coding regions.
• These findings suggest a broader role for IRES-like structures in regulating protein synthesis beyond viral contexts.