Every day, the human body makes new cells to promote growth and sustain life. The cell cycle—the process by which cells divide and duplicate over time—ensures the development and survival of eukaryotic organisms. For the process to be successful, hundreds of mRNAs need to synthesize and degrade in a time-specific manner. But measuring those changes is difficult as most techniques used to investigate the process disturb the metabolism of the cell, dramatically changing its transcription behavior.
In 2011, Patrick Cramer, a biochemist at Germany’s Ludwig-Maximilians-Universität München, and colleagues heralded a new technique to measure rates of mRNA synthesis and decay. This technique, dynamic transcriptome analysis (DTA), is a combination of metabolic RNA labeling and kinetic modeling that allows researchers to follow changes to mRNA in yeast cells with high sensitivity and temporal resolution, enabling monitoring of mRNA metabolism and how it is dynamically regulated by gene systems.
“One of the main benefits is that it is a non-perturbing method, which allows you to monitor cellular activities without influencing the cellular system,” said Cramer. After proving the method, Cramer and colleagues used it to perform a genome-scale measurement of mRNA changes in the yeast Saccharomyces cerevisiae to better understand the mechanisms of transcription during the cell cycle. While it had long been known that levels of mRNAs change periodically, Cramer wanted to see to what extent those changes were the result of changes to transcription or RNA degradation. And so, using comparative DTA, the group measured mRNA synthesis and degradation rates every 5 minutes during 3 complete cell cycle periods for the yeast.
With this innovative technique, the group is the first to be able to make these kinds of critical measurements. Using a statistical model to analyze their data, Cramer and his team discovered 479 different genes that show a distinct temporal profile. In each, the group saw time-specific changes in both mRNA synthesis and degradation rates during the cell cycle. They further observed that synthesis and degradation appear to work in a cooperative manner, with peaks of synthesis being quickly followed by peaks in degradation. Finally, while timing was regulated by upstream DNA motifs and their associated transcription factors, Cramer discovered that synthesis rates, instead, appeared to be set by the core promoter.
“We were first surprised that sharp peaks of mRNA expression required not only changes in transcription but also changes in RNA degradation. But a simulation demonstrated nicely that it has to be like that—in the absence of changes in RNA degradation, the expression peaks are broad and less pronounced,” he said. “Prior studies describe gene regulation only at the level of transcription. Surely, transcription changes dominate changes in gene expression. However, changes in RNA degradation can lead to more defined and effective responses, cooperating with transcription changes during gene expression.”
The group plans to follow this work by using comparative DTA to study mRNA synthesis and degradation rates in human cells—which will, Cramer hopes, help elucidate the role of non-coding RNA in human cell division.
Eser P, Demel C, Maier KC, Schwalb B, Pirkl N, Martin DE, Cramer P, Tresch A. Periodic mRNA synthesis and degradation co-operate during cell cycle gene expression. Mol Syst Biol. 2014 Jan 30;10(1):717.