Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

An "online" version of a paper appeared in Nature Biotechnology. This work of Michal Rabani, a Hebrew University graduate who is now a PhD student in Aviv Regev's lab at MIT. Michal is also a member of our group, spending several months a year here. This work also included Ido Amit, a postdoc at Aviv's lab who is starting a new lab at the Weizmann later this year.

In this work Michal and Ido used a new method to label newly synthesized RNA using a modified version of uridine that can be later used to separate it from the total RNA pool. This way they measured and sequenced "new" RNA. Michal then used these measurements to estimate the production rate of RNA in cells that respond to an external stimuli. Moreover, by contrasting the production rate of RNA and total RNA she could reconstruct what are the degradation rates through the process.

The main takeaway message from the paper is that RNA degradation rate (or stability) differs between different RNA species. However, for most genes, it did not change dramatically during the response. Thus, most of the shape of RNA level was regulated by production. We did find that for some genes changes in degradation rate was important to modulate the response.