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Updated: May 5, 2026
Use of Alu Element Containing Minigenes to Analyze Circular RNAs
Published on: March 10, 2020
An oligo walk to identify siRNAs against the circular Tau 12->7 RNA
Abstract:
Circular RNAs are associated with numerous diseases and recent evidence shows that they can be translated into proteins after undergoing RNA modification. Circular RNAs differ from their 'linear' mRNA counterparts in their backsplice site, allowing selective targeting using RNA interference, which however limits the options to place the siRNA. We tested all possible siRNAs against the backsplice site of the circTau 12->7 RNA after it was subjected to adenosine to inosine RNA editing, a modification that promotes translation of the circRNA. Most siRNAs reduced the circRNA and protein abundance, which however did not correlate. We identified an siRNA with an IC50 of 750 pmol efficacy on protein expression. This circRNA fulfilled six of the eight criteria for siRNAs targeting mRNAs. Thus, modified circRNAs expressing protein can be targeted with siRNAs, but their optimal sequence needs to be determined empirically.
Insights
Modified circular RNAs (circRNAs) can be translated into proteins and targeted using small interfering RNA (siRNA). Researchers found that while most siRNAs reduced circRNA and protein levels, empirical testing is needed to find effective sequences for targeting modified circRNAs.
Area of Science:
- Molecular Biology
- RNA Biology
- Genetics
Background:
- Circular RNAs (circRNAs) are increasingly recognized for their roles in various diseases.
- Recent findings indicate that circRNAs can be modified and subsequently translated into proteins.
- Unlike linear mRNAs, circRNAs possess a unique backsplice site, presenting specific challenges for RNA interference (RNAi) targeting.
Purpose of the Study:
- To investigate the efficacy of small interfering RNA (siRNA) in targeting modified circular RNAs that are translated into proteins.
- To determine if RNA editing, specifically adenosine to inosine (A-to-I) editing, influences the targeting of circRNAs.
- To identify optimal siRNA sequences for targeting the circTau 12->7 RNA and its protein products.
Main Methods:
- Systematic screening of all possible siRNAs targeting the backsplice site of circTau 12->7 RNA.
- Assessment of circRNA and protein abundance following siRNA treatment.
- Evaluation of siRNA efficacy using IC50 values for protein expression.
- Comparison of targeting criteria between circRNAs and messenger RNAs (mRNAs).
Main Results:
- Most tested siRNAs effectively reduced both circRNA and protein abundance, but these reductions were not consistently correlated.
- A specific siRNA demonstrated significant efficacy, with an IC50 of 750 pmol for protein expression.
- The targeted circRNA met six out of eight established criteria for siRNA targeting of mRNAs.
Conclusions:
- Modified, protein-expressing circRNAs are amenable to targeting via RNA interference using siRNAs.
- The optimal siRNA sequence for targeting modified circRNAs requires empirical determination.
- This study provides a foundation for developing targeted therapies against diseases involving aberrant circRNA expression and translation.
