How to precisely regulate RNA polymerase?

Scientists have developed a way to analyze and modify phosphorylation sites on the RNA polymerase II enzyme, which is responsible for copying and expressing (turning on) genes.

Our genetic information is actually silent (meaning inactive) and only becomes active via RNA polymerase II — Pol II for short. When Pol II rolls over DNA, it transcribes genetic and epigenetic information. But, to keep the RNA enzyme from working randomly, many sites within the RNA control its activity.

"Phosphorylation makes it possible to influence the activity of the enzyme at 240 different sites," explains Proffessor Dirk Eick, last author on the study and head of the Molecular Epigenetics Research Unit at the German Research Center for Environmental Health in Munich.

A procedure used to identify and measure the tiny molecules making up DNA and RNA is called mass spectrometry. By transforming these molecules into a gas and then electrically charging that gas, molecules (or even smaller fragments) can be accelerated through an electric field and measured for their mass to charge ratio. As each molecule has its own acceleration speed depending on its mass — scientists can then sort the molecules and identify patterns and relationships.

Together with research colleagues from the German Research Center for Environmental Health (Helmholtz Zentrum München), and with colleagues from the Ludwig Maximilian University of Munich (Ludwig-Maximilians-Universität München), Eick's team developed a method for simultaneously examining and identifying all 240 sites on Pol II.

"The trick was a combination of genetic and mass spectrometry methods. By producing genetically modified variants of the regions in question, we examined each individual phosphorylation site with a mass spectrometer."

Roland Schüller PhD, Department of Molecular Epigenetics, Helmholtz Center Munich and Center for Integrated Protein Science Munich (CIPSM), Munich, Germany, and first author

This combination procedure allowed researchers to map exactly how and precisely where certain enzymes influence phosphorylation. The scientists were then able to successfully map the carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) and choose to interrupt CDK9 kinase specifically reducing S2 phosphorylation levels, a phosphorylation event that stimulates mRNA processing.

"The regulation of the transcription of genes by Pol II is an elementary process in life — and gene regulation deviations are the basis for many human disorders.

"Research into the phosphorylation pattern at certain times during the transcription cycle is needed to be able to understand the underlying mechanisms of gene regulation."

Dirk Eick PhD, head of the Molecular Epigenetics Research Unit at the German Research Center for Environmental Health, and study leader.

The published research appears in the journal Molecular Cell.

Abstract Highlights
•CTD variants make the entire CTD sequence accessible to mass spectrometry analysis
•Valid CTD phosphosite mapping is based on a synthetic CTD peptide library
•Predominant phosphorylation signatures prevail within neighboring CTD residues
•Inhibition of CDK9 strongly reduces Ser2-P phosphorylation in the CTD

Summary
The carboxy-terminal domain (CTD) of RNA polymerase II (Pol II) consists of heptad repeats with the consensus motif Y1-S2-P3-T4-S5-P6-S7. Dynamic phosphorylation of the CTD coordinates Pol II progression through the transcription cycle. Here, we use genetic and mass spectrometric approaches to directly detect and map phosphosites along the entire CTD. We confirm phosphorylation of CTD residues Y1, S2, T4, S5, and S7 in mammalian and yeast cells. Although specific phosphorylation signatures dominate, adjacent CTD repeats can be differently phosphorylated, leading to a high variation of coexisting phosphosites in mono- and di-heptad CTD repeats. Inhibition of CDK9 kinase specifically reduces S2 phosphorylation levels within the CTD.

Contact for the media: Department of Communication, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg - Tel. +49 89 3187 2238 - Fax: +49 89 3187 3324 - E-mail: presse@helmholtz-muenchen.de

Scientific contact at Helmholtz Zentrum München: Prof. Dr. Dirk Eick, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Research Unit Molecular Epigenetics, Marchioninistraße 25, 81377 München - Tel. +49 89 3187-1512 - E-mail: eick@helmholtz-muenchen.de

Original publication: Schüller, R. et al. (2015). Heptad-specific Phosphorylation of RNA Polymerase II CTD, Molecular Cell
DOI: 10.1016/j.molcel.2015.12.003
http://www.cell.com/molecular-cell/abstract/S1097-2765%2815%2900937-5

The Helmholtz Zentrum München, the German Research Center for Environmental Health, pursues the goal of developing personalized medical approaches to the prevention and therapy of major common diseases such as diabetes and lung disease. To achieve this, it investigates the interaction of genetics, environmental factors and lifestyle. The Helmholtz Zentrum München has about 2,300 staff members and is headquartered in Neuherberg in the north of Munich. It is a member of the Helmholtz Association, a community of 18 scientific-technical and medical-biological research centers with a total of about 37,000 staff members. The Helmholtz Zentrum München is a partner in the German Center for Diabetes Research.

As one of Europe's leading research universities, LMU Munich is committed to the highest international standards of excellence in research and teaching. Building on its 500-year-tradition of scholarship, LMU covers a broad spectrum of disciplines, ranging from the humanities and cultural studies through law, economics and social studies to medicine and the sciences. 15 percent of LMU's 50,000 students come from abroad, originating from 130 countries worldwide. The know-how and creativity of LMU's academics form the foundation of the University's outstanding research record. This is also reflected in LMU's designation of as a "university of excellence" in the context of the Excellence Initiative, a nationwide competition to promote top-level university research.

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