Visualization of RNA structure models within the Integrative Genomics Viewer

Area of Science:

• Genomics
• Structural Biology
• Bioinformatics

Background:

• Understanding RNA structure and function is crucial for genomic studies.
• Existing RNA structure visualization tools are inadequate for long, heterogeneous RNAs.
• Interpreting RNA structure models with other experimental and genomic data is challenging.

Purpose of the Study:

• To develop an enhanced module for the Integrative Genomics Viewer (IGV) for visualizing RNA structure data.
• To enable the analysis of RNA structure models in the context of linear genomic data.
• To facilitate the interpretation of RNA structure probing data alongside gene annotation.

Main Methods:

• Developed an IGV module for visualizing SHAPE-MaP data, including raw reactivities and structural entropies.
• Integrated visualization of data-constrained base-pair secondary structure models.
• Enabled simultaneous viewing of RNA structure data and linear genomic tracks.

Main Results:

• Demonstrated the module's utility in analyzing a large viral RNA genome structure.
• Facilitated comparison of bacterial mRNA structure under different conditions.
• Enabled comparison of SHAPE-derived RNA structures with sequence covariation models.

Conclusions:

• The new IGV module provides a powerful platform for visualizing and analyzing RNA structure data.
• This tool enhances the interpretation of RNA structure in the broader genomic context.
• The module supports diverse applications, from viral RNA genomes to bacterial mRNAs and noncoding RNAs.