Genome regulation – Patrick Cramer

We try to understand how eukaryotic cells express their genome and how transcription of the genome is regulated. Gene transcription is the first step in the expression of the genetic information and a focal point for cellular regulation.

Functional genomics and computational biology

Our goal is to understand the molecular mechanisms of gene transcription and the principles of genomic regulation in eukaryotic cells. We develop functional genomics methods and computational approaches to unravel the cellular mechanisms of genomic regulation. Our aim is to understand the functional genome as a regulatory network based on the underlying molecular mechanisms.

Our main laboratory is located at the Max Planck Institute for biophysical Chemistry in Goettingen, Germany ( We combine integrated structural biology (electron microscopy, X-ray crystallography, mass spectrometry) and functional genomics to investigate the molecular basis and the systemic principles of gene transcription and genomic regulation. Our past efforts led to a first molecular movie of transcription and provided insights into gene-regulatory cellular networks. We use integrated structural biology and complementary functional studies to unravel the three-dimensional and functional architecture of large macromolecular complexes involved in transcription. Together, these efforts shape the emerging fields of genome biology and molecular systems biology.

New research team at Karolinska Institutet

Starting in 2015, we establish a new satellite research team at the Karolinska Institutet. Here we will systematically investigate how the genome is expressed and regulated in vivo, often in collaborative projects with other laboratories in Stockholm. We study transcription and RNA regulation in the context of living cells on a systems level. Recent advances in functional genomics now allow us to (a) monitor all transcription activity in cells by next-generation sequencing of newly synthesized RNA (4tU-seq), to (b) map the bindings sites of regulatory protein factors over the genome (ChIP-seq), and to (c) map the location of regulatory RNA-binding factors over the transcriptome (PAR-CLIP). By combining these techniques and evaluating the obtained systemic data with a computational biology approach, often in close collaboration with other groups, we uncover principles of genome transcription and its regulation.

Our recent achievements in this area of research include the mapping of transcription factors over the yeast genome (Mayer, Lidschreiber, Siebert et al., NSMB 2010), the development of "dynamic transcriptome analysis" to measure both mRNA synthesis and degradation rates genome-wide (Miller, Schwalb, Maier et al., Mol. Syst. Biol. 2011), an analysis of global mRNA degradation to investigate how cells buffer the levels of their mRNA transcripts (Sun, Schwalb et al. Mol. Cell 2013), and the global analysis of transcriptome surveillance by selective termination of non-coding RNA synthesis (Schulz, Schwalb et al. Cell 2013).

Mapping of an RNA-binding factor over the transcriptome

Join the team

We are looking for researchers with a background in bioinformatics, computational biology, functional genomics, or structural biology, in particular electron microscopy. If you are interested in joining the group, please send an Email to Patrick Cramer ( with a single pdf-file attachment containing one page of motivation letter, a short CV with list of publications and other achievements, and the names and Email addresses of 2-3 mentors who agreed to provide a short letter of recommendation on your behalf.

Team members

Visiting professor

Patrick Cramer

Organizational unit: Cramer


Lisa Anna Jung

Phone: +46-(0)8-524 811 27
Organizational unit: Cramer


Link to our main laboratory at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany: