Circular RNA sequencing (circRNA-seq)

What is circRNA-seq?

Circular RNAs (circRNA) are covalently closed RNA molecules. Studies in recent years have highlighted their functions such as microRNA sponges and RNA-binding protein (RBP) decoys, and their involvement in many biological and clinical contexts including cancer, immunology, and neuroscience.

Starting from a tissue or cell line of interest, RNA is extracted and enriched for circRNA before amplification, size selection, and library prep. Sequenced reads are then quantified for relative abundance and compared across samples.

Applications

Despite their low abundance in cells, some circRNA molecules are found to be even more highly expressed relative to their linear counterpart. This expression is very cell-type specific, making them promising biomarkers for both basic research and diagnosis. We recently developed a highly sensitive method (manuscript in prep) that significantly improves the sensitivity and lowers the input requirement as compared to pre-existing circRNA sequencing methods. Our center provides end-to-end service or collaboration to help identify novel circRNA biomarkers in different biological and clinical contexts and study their functional roles.

CircRNAs also hold a bright future as a therapeutic vector for RNA therapies over mRNAs because they are more stable and less immunogenic than linear mRNAs. Deepening our knowledge of circRNA lifecycle, specifically the regulation by trans factors including RBPs, is critical for designing better circRNA vectors to make them more stable and highly translated. Our center actively develops new technologies to study RBP-circRNA interactions and generate insights into novel circRNA therapeutic vector designs.

Project Workflow

Project Initiation:

Contact the RNA Center at RNAcenter@ucsd.edu.
Discuss experimental designs and goals.
Discuss cost estimates, expectations, and potential outcomes.

Sample Preparation:

Prepare samples according to circRNA sample preparation guidelines for either tissue or dissociated cells.
We accept extracted RNA or cell/tissue lysate in Trizol (additional charge for RNA extraction).

Sample Submission:

Download, fill, and submit Sample Manifest.
Drop off or ship samples.

Sample Processing:

The RNA Center will process the samples according to our SOP.
RNA quality will be assessed before starting circRNA library prep.
Quality-controlled libraries will be sent for sequencing.

Data Transfer:

Generate and transfer raw sequencing data.
Data processing and analysis service is also available (with standardized pipeline).
In depth analysis is available through collaboration upon negotiation.