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Protein-RNA networks revealed through covalent RNA mark

1) What was the research project?

A 2015 study published in Nature Methods that proposed a new method to identify global protein-RNA interactions in vivo where the interactions were unambiguous and occurred inside the cell. The method was termed RNA Tagging which would be independent of protein purification, cross-linking, or radioactive-labeling steps seen in other methods such as RIP and CLIP (Lapointe et al., 2015).   

2) Were they testing a hypothesis or doing discovery science?

The study was proposing a new method to the already existing methods such a RIP and ClIP.  The authors did not offer this method as a hypothesis but rather as a new concept that they were trying to create to improve upon existing methods so it is a discovery science.

3) What genomic technology was used in the project?

The researchers fused the desired RNA-binding protein to Caenorhabdtis elegant poly (U) polymerase PUP-2. This enzyme lacks the RNA-binding domains and as a result the protein covalently tags only the RNA where RNA-binding protein binds. The tagged RNAs are identified by high-thoughput sequencing arrays.


4) What was the take home message?

The method of RNA tagging identified the targets of RNA-binding proteins with only the covalent marks left on the RNA. The paper states that the method is simple and easy to replicate so it make this process of RNA biology that had been difficult to examine much easier. RNA tagging can also be used to show the biological roles of RNA-binding proteins.

5) What is your evaluation of the project?

Overall, the project was interesting and provided insight into the expansion of RNA biology. The article was well-written and easy to follow. The data and discussion did well in convincing me that the method that they developed works and could advance this field. Hopefully this projects efforts can cause more advancements of this field of biology thanks to its relatively simple methodology in the analysis of RNA-binding proteins.   

Citations:

Lapointe, Christopher P., Daniel Wilinski, Harriet AJ Saunders, Marivin Wickens. 2015. Protein-RNA networks revealed through covalent RNA marks. Nature Methods 12(12).

Lapointe, Christopher P., Daniel Wilinski, Harriet AJ Saunders, Marivin Wickens. 2015. Protein-RNA networks revealed through covalent RNA marks. [cited 25 Jan 2016]  12(12). Available from: http://www.nature.com/nmeth/journal/v12/n12/full/nmeth.3651.html