Long-range RNA structures in the human transcriptome beyond evolutionarily conserved regions

Area of Science:

• Molecular Biology
• Genomics
• Computational Biology

Background:

• RNA structure is crucial for gene regulation but difficult to predict in eukaryotes due to large, discontinuous genes.
• Existing methods like thermodynamic modeling and comparative genomics have limitations in predicting RNA structures across diverse genomic regions.

Purpose of the Study:

• To develop a computational pipeline (PHRIC) for predicting long-range RNA structures beyond conserved genomic regions.
• To leverage RNA contacts from RNA in situ conformation sequencing (RIC-seq) for structure prediction.
• To analyze the prevalence and characteristics of predicted RNA structures in human cell lines.

Main Methods:

• Developed the PHRIC computational pipeline to extract RNA fragments and predict complementary base pairings based on RNA contact data from RIC-seq.
• Applied PHRIC to RIC-seq experiments across seven human cell lines.
• Analyzed predicted structures for stability (free energy < -15 kcal/mol) and conservation patterns.

Main Results:

• PHRIC predicted approximately 12,000 stable long-range RNA structures, with most located outside conserved vertebrate regions.
• Predicted structures exhibited sequence conservation and compensatory substitutions in other clades.
• Introns showed a higher propensity for forming stable long-range RNA structures, often within the same intron.

Conclusions:

• PHRIC successfully extends RNA structure prediction beyond conserved regions, overcoming limitations of previous methods.
• The findings reveal a significant number of functional RNA structures in non-conserved regions, particularly within introns.
• This work demonstrates the utility of proximity ligation assays for comprehensive RNA structure discovery.