A systematic analysis of circRNAs in subnuclear compartments

Area of Science:

• Molecular Biology
• Genomics
• RNA Biology

Background:

• Circular RNAs (circRNAs) are crucial regulatory molecules in human cells, impacting physiology and disease.
• Understanding circRNA biogenesis and localization is key to deciphering their functions.
• Analyzing circRNAs from RNA sequencing data presents significant challenges.

Purpose of the Study:

• To introduce Calcifer, a versatile computational workflow for circRNA annotation.
• To investigate the subcellular distribution of circRNAs using APEX-Seq data.
• To explore the functional potential, including translation, of detected circRNAs.

Main Methods:

• Development of Calcifer, a novel workflow for circRNA identification and analysis.
• Application of Calcifer to APEX-Seq data from whole cells, nuclei, and subnuclear compartments.
• Comparative analysis of circRNA abundance across different cellular locations.

Main Results:

• Calcifer effectively annotates circRNAs from sequencing data.
• CircRNAs are predominantly found in the cytoplasm, with notable exceptions like circCANX(9) enriched in the nucleus.
• CircRNAs are depleted from nuclear speckles, suggesting splicing factor interference with back-splicing.
• A significant proportion of circRNAs possess open reading frames, indicating potential for translation.

Conclusions:

• Calcifer is a user-friendly and robust tool for circRNA research.
• New insights into circRNA subnuclear distribution and potential translation are provided.
• This work expands the toolkit for circRNA analysis and understanding their roles in biological processes.