Hundreds of proteins have been identified as RNA binding proteins (RBPs), including proteins associated with various diseases such as neural degeneration, immune system defects and cancer. Therefore, it is necessary to systematically isolate RNA binding proteins.

Current approaches for systematically characterizing the RBPs are mainly based on the capture of polyadenylated (polyA) RNAs, which fails to capture proteins interacting with non-polyA RNAs.

Miguel Esteban, BAO Xichen, and ZHANG Biliang at Guangzhou Institutes of Biomedicine and Health of Chinese Academy of Sciences, developed a versatile method to capture the interactome of newly transcribed RNAs. The findings were published in Nature Methods.

The researchers combined RNA labeling with characterization of bound proteome. Application of the methodology (RICK: capture of the newly transcribed RNA Interactome using ClicK chemistry) successfully identified hundreds of novel RBPs with extensive binding to the previous neglected non-polyA RNAs. Besides, short labeling of RICK also captured proteins interacting with nascent RNAs, to understand the events coupled with nascent RNA production.

This methodology would not only provide a novel approach for systematically analyzing RNA-protein interaction in cells, but also shed light on the biological functions of genomic ‘dark matter’- long non-coding RNAs.

This work was funded by the National Key Research and Development Program of China, the National Natural Science Foundation of China, the Pearl River Science and Technology Nova Program of Guangzhou, the Youth Innovation Promotion Association of the Chinese Academy of Sciences, etc.