Dr. Heinz Himmelbauer
now at Centre for Genomic Regulation
(CRG), Barcelona, Spain
Ultrasequencing Unit
Phone:     +34 93 3160243
Email:    Heinz.Himmelbauer@crg.es

The focus of the group is in technology development (lab methods and data analysis tools) to support the efficient use of next generation sequencing (NGS) technologies. As central research project, we have sequenced and interpreted the genome of sugar beet, a crop plant only distantly related to other species with sequenced genomes. In addition, we pursue technology-driven cooperations in medical genomics, bioinformatics, and genetics in areas where innovative utilization of NGS is a strong asset.

Dr. Zoltán Konthur* (05/02-09/12)
Phone:     +49 (0)30 8413-1586
Fax:     +49 (0)30 8413-1365
Email:    konthur@molgen.mpg.de

Normally, the immune system protects us from foreign substances or pathogens by generating specific antibodies eliciting an immune response. However, in a variety of diseases – especially autoimmune disorders – dysfunction of the immune system occurs leading to self-reactive (auto)antibodies. In some cases, these antibodies can cause severe damage to the body, while in other cases their presence is not understood. Our knowledge about their role in disease progression, whether being of significance or simply a bystander effect, is vague. The scientific focus of the group has shifted since the last evaluation and now centres on (1) the analysis of V(D)J recombination patterns in immunoglobulin repertoires in healthy individuals and autoimmune patients and (2) the elucidation of autoantigenicity pattern in health and disease. The methodological portfolio includes the use of Next Generation Sequencing (NGS), Phage Display as well as Protein Array Technologies.

Priv. Doz. Dr. Bodo M.H. Lange
(05/03-12/11)
Phone:     +49 (0)30 8413-1645
Fax:     +49 (0)30 8413-380
Email:    lange_b@molgen.mpg.de
b.lange@alacris.de

New opportunities are presently available, for the direct investigation of the molecular basis of diseases caused by mutation of genes. The technology in the area of functional genomics has matured and can now be applied to basic questions in the fields of developmental biology, cell biology and molecular medicine. This, in turn, facilitates the study of many parameters in parallel (mRNA and protein pro- files, morphological cellular or subcellular analysis) and their dynamic changes upon modulating cues (e.g. cellular or environmental stress). Such complex data sets require now system models to understand and predict diseases development. In this context, the study of the protein complexes and protein-protein interactions of the components of cellular proliferation and signalling pathways is now an opportunity and highly relevant for our understanding of the molecular basis of development and diseases.

Markus Ralser (12/07-12/11)
now at University of Cambridge, UK
Cambridge Systems Biology Centre
and Dept. of Biochemistry
Phone:    +44 1223-761346
Email:    mr559@cam.ac.uk

We are interested in the regulatory function of the metabolic network and investigate, how metabolic intermediates are implicated in the control of biological systems. An important situation, where the metabolome has regulatory function, is the oxidative stress response. Exposure to a toxic oxidant dose leads to a (temporal) reconfiguration of cellular metabolism. As a result, the concentration of several metabolites is altered; and these - in turn - are implicated in adapting the cell to oxidative conditions. The main biological questions we focus on are:

• How are metabolic transitions regulated, e.g. the change from oxidative to non-oxidative metabolism?
• How flexible are metabolic pathways? How do they interact with the regulation of cellular macromolecules?
• Why do cells age? Which metabolic processes are involved? Can we modulate aging by changing these processes?

Alexey V. Soldatov (06/07-07/12)
Phone:     +49 (0)30 8413-1128
Fax:     +49 (0)30 8413-1380
Email:    soldatov@molgen.mpg.de

Till June 2007, A. Soldatov’s team was within Lehrach’s group and has specialised in the area of SNP genotyping and sequencing. A new SNP-genotyping method was developed, patented (PCT/EP2004/009546) and successfully applied for genotyping of Arabidopsis thaliana and human DNA samples. We have also worked on the development of new sequencing technologies in the frame of the European MolTools project: (i) microbead based sequencing (PCT/EP2006/008535) and (ii) ligation based sequencing in collaboration with U. Lan-degren laboratory (Uppsala University, Uppsala, Sweden).
Since June 2007, our group specializes in technology development and bioinformatics related with second generation sequencing (NGS). Till spring 2010 we were responsible for the NGS service in the department. We have set up the optimized laboratory workflows for both Illumina and ABI SOLiD sequencing platforms. We have developed a NGS bioinformatics pipeline, which brings together the information about the whole sequencing process from sample handling to results analysis. The system enables each authorized user (also external col-laborators) to track processing of samples, check the sequencing quality and view data in the genomic browser.
The group uses NGS platforms for analysis of genome (resequencing) and transcriptome (gene expression profiling, splice junctions search, allele-specific expression, reverse transcription, etc.). We have performed RNA-Seq, ChIP-Seq, MedIP-Seq and genomic DNA sequencing (including sequencing library preparation, sequencing and sometimes data analysis) for several groups within the MPIMG (AG Yaspo, AG Nietfeld, AG Himmelbauer, AG Schweiger, AG Hoehe, AG Lange, AG Krobitsch, AG Ralser, dept. Herrmann) and for external collaborators (Y. Shiloh (U. Tel Aviv), C. Koncz (MPI for Plant Breeding Research, Cologne), J. Klose (Charite, Berlin)).
We have developed, patented and published a convenient method for strand-specific sequencing of cDNA. The method is based on incorporation of uridine bases during first (or second) cDNA strand synthesis and subsequent destruction of this strand before sequencing. Knowledge of transcript orientation is important for transcriptome studies. It allows (i) to annotate novel genes correctly, (ii) to investigate antisense transcription, which plays an important regulatory role in all eukaryotes, (iii) to resolve transcript overlaps, which are abundant in compact genomes of prokaryotes and lower eukaryotes, and (iv) to correctly determine
gene expression levels in the presence of overlapping antisense transcription. The method is licensed by New England Biolabs company. We have developed and patented a method for preservation of information about spatial distribution of nucleic acid molecules transferred from a solid surface to another solid surface or into solution. This method permits to use a power of NGS for studying of two-dimensional distributions of nucleic acid molecules on tissue sections or other biological objects. Biological processes are spatially organized and rely upon the interplay of many different components forming an intricate structure of cells, tissues and organisms. Molecules participating in these processes have a certain spatial distribution. Understanding the biological processes is critically dependent on a detailed knowledge of this distribution.

At present, the group’s activities are focused on NGS-related technology development:

•    early coding for parallel preparation of a number of sequencing libraries;
•    RNA structural analysis;
•    methylation analysis;
•    preparation of NGS libraries from ultra small amounts of starting material;
•    long-run NGS sequencing for haplotyping.

Univ.-Prof. Dr. med. Silke Rickert-
Sperling,
now at Experimental Clinical
Research Center (ECRC), Berlin
Phone:     +49 (0)30 8413-1232
Fax:     +49 (0)30 8413-1699
Email:    sperling@molgen.mpg.de

Most cardiovascular diseases have complex genetic and environmental origins. Our lab studies molecular mechanisms underlying cardiac development and function using molecular biological techniques and bioinformatics expertise. We focus on the transcriptional regulation process, which plays a key role for normal and abnormal cardiogenesis leading in the latter case to congenital heart disease (CHD). A rapidly growing number of factors have been shown to be involved in regulating the pattern and timing of expression of genes responsible for the cardiac lineage determination, heart chamber formation, valvulogenesis and conduction- system development. Spatiotemporal and quantitative regulation of cardiac transcription factors must occur in a precise manner to ensure fine regulation of downstream targets. However, the ability of transcription factor binding to DNA is highly influenced by the chromatin status, and epigenetic mechanisms have an important role in establishing and maintaining transcriptional programs. To understand networks directing gene expression, the interplay between different transcription factors, co-regulatory elements and epigenetic factors has to be considered.