Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain

Area of Science:

• Neuroscience
• Molecular Biology
• Genetics

Background:

• Post-transcriptional gene regulation relies on untranslated regions (UTRs) of messenger RNAs (mRNAs) interacting with proteins and RNAs.
• Stable RNA secondary structures within UTRs and long noncoding RNAs (lncRNAs) have significant functional implications.
• While lncRNAs are recognized for their role in brain development and function, systematic investigation of RNA structure in brain transcripts is lacking.

Purpose of the Study:

• To systematically analyze the potential for RNA structure in brain-expressed transcripts.
• To investigate the functional implications of RNA structures in the adult mouse brain.

Main Methods:

• Comprehensive spatial expression analysis using in situ hybridization data from the Allen Mouse Brain Atlas.
• In silico prediction of structured RNA probes.
• Analysis of gene ontology categories and RNA binding protein interaction sites.

Main Results:

• Transcripts with predicted structured probes were significantly enriched across most brain regions.
• mRNAs with predicted structures in their UTRs were enriched in binding, transport, and localization gene ontology categories.
• Observed agreement between RNA binding protein interaction sites and correlated expression patterns near 3' UTR structures.

Conclusions:

• RNA structures are potentially utilized in both coding and noncoding transcripts in the adult mouse brain.
• Structured RNAs are involved in intracellular signaling pathways and regulatory networks.
• Hypothesize that RNA structure broadly influences transcriptional and translational regulation, impacting overall brain function.