Bhubaneswar ILS scientists discover direct interaction of circular RNAs with mRNAs in gene expression

In an extremely proud moment for Odisha, a team of researchers at the prestigious Institute of Life Sciences (ILS) in Bhubaneswar has made a groundbreaking discovery that suggests the role of direct interaction of circRNAs with mRNAs in gene expression regulation.

The findings represent a novel method for illuminating the myriad of uncharacterized circRNA-mRNA hybrids that may regulate gene expression. The research undertaken under the guidance of Dr. Amaresh C. Panda was conducted by Suman Singh, Sharmishtha Shyamal, and Arundhati Das.

Although the functional role of circular RNA (circRNA) interaction with microRNAs and proteins has been studied extensively, circRNA interactions with the protein-coding mRNAs in intact cells remain largely unknown.

By employing AMT-mediated proximity ligation of RNA-RNA duplexes followed by circRNA enrichment and deep sequencing, the scientists reported a novel Cross-Linking Poly (A) Pulldown RNase R Sequencing (CLiPPR-seq) technology which identified hundreds of mRNA-interacting cricRNAs in three different cell types.

Furthermore, the scientists performed CLiPP-seq without RNase R treatment to identify the mRNA expression in these cells. BLAST analysis of circRNAs in CLiPPR-seq sample with the mRNAs in CLiPP-seq samples determined their potential complementary sequences for cricRNA-mRNA interaction.

Pulldown of circRNAs and poly (A) RNAs confirmed the direction interaction of circRNAs with target mRNAs. Silencing of mRNA-interacting circRNAs led to the altered expression of target mRNAs in BTC6 cells, suggesting the role of direct interaction of circRNAs with mRNAs in gene expression regulation. CLiPPR-seq thus represents a novel method for illuminating the myriad of characterized circRNA-mRNA hybrids that may regulate gene expression.  

“This is a completely new discovery that no one had ever thought of. No one had ever thought that gene regulation could be done in this way. So, we are extremely proud of our findings. Now we know that circular RNA is directly regulating protein-coding mRNA," said Dr Amaresh Panda, senior scientist at ILS Bhubaneswar.