Identification of 3D motifs in Rfam with JAR3D

Area of Science:

• RNA structural biology
• Bioinformatics
• Computational biology

Background:

• Non-protein-coding RNAs (ncRNAs) are increasingly discovered, necessitating understanding their 3D structures for function.
• Recurrent 3D structural motifs, like kink turns and GNRA loops, are found in various ncRNAs.
• Identifying these motifs aids in predicting the function of newly discovered ncRNAs.

Purpose of the Study:

• To introduce JAR3D, a tool for identifying known 3D structural motifs in RNA loops.
• To make these identifications accessible for researchers studying ncRNA structure and function.
• To analyze the prevalence of known 3D loop motifs across RNA families.

Main Methods:

• JAR3D was developed to map RNA loop sequences to known 3D structural motifs.
• The tool was extended to include 3-way and 4-way junction motifs.
• JAR3D was applied to 4,166 Rfam seed alignments (Rfam 15.0), and results were made web-accessible.

Main Results:

• JAR3D successfully identified matching 3D loop motifs in a large set of Rfam alignments.
• Validation using external 3D RNA structures confirmed JAR3D's accuracy.
• A new web page allows searching for specific motif occurrences across all Rfam families.

Conclusions:

• JAR3D provides an accessible method for identifying known 3D RNA loop motifs in sequence alignments.
• The tool facilitates the study of motif distribution and potential functional implications across RNA families.
• Internal loops showed higher match rates to known motifs compared to hairpins and multi-helix junctions.