A new paper from the Wierzbicki lab reveals some insights into the mysterious world of non-coding RNAs.  Gudrun Böhmdorfer, a postdoctoral fellow and co-authors, took advantage of a unique feature of a model plant organism Arabidopsis thaliana  to discover how these RNAs may help maintain genome integrity.

In each cell, genetic information for the production of proteins is stored in deoxyribonucleic acid (DNA.) A closely related nucleic acid, ribonucleic acid (RNA) transfers the genetic information from the DNA to the protein production sites in the cell. But RNA turns out to live a secretive double life, says Andrzej Wierzbicki, an associate professor in MCDB.  In addition to its role in protein coding, RNA performs a multitude of additional functions.

Böhmdorfer and colleagues used Arabidopsis thaliana because this plant contains a specialized enzyme that produces a class of non-coding RNAs. The presence of this enzyme, known as RNA Polymerase V, allows the scientists to overcome two important barriers to making progress in studying RNAs in other organisms –- identification of non-coding from coding RNA and specific experimental elimination of an entire class of non-coding RNA. Arabidopsis  thus provides a "genetic toolset" for unprecedented insight into the mysterious world of non-coding RNAs, says Wierzbicki.

The researchers' study of the specific class of non-coding RNAs revealed that their production is controlled by a mechanism completely different than those known for other RNAs. This non-coding RNA provides binding sites for an important protein in DNA methylation, which silences genes, and this binding occurs during production of the non-coding RNA.

Importantly, this non-coding RNA production targets edges of potentially harmful DNA regions known as transposable elements or transposons. This assures that the transposons are silenced while allowing the neighboring genes to be active.

This work not only revealed several mysteries of RNA but also opened the door for future studies of other intriguing properties of these important nucleic acids, says Wierzbicki.

eLife: "Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin"
Gudrun Böhmdorfer, Shriya Sethuraman, M. Jordan Rowley, Michal Krzyszton, M. Hafiz Rothi, Lilia Bouzit, and Andrzej T. Wierzbicki