Z1 Mass spectrometry of proteins  | A. Bruckmann,  R. Deutzmann
The aim of service project Z1 is to provide mass spectrometry based tools and techniques that are required for the various research projects of the CRC, and to implement new, state-of the art methods. The most important applications are qualitative and quantitative analysis of protein complexes and their regulation by phosphorylation. Quantification is done by SRM-methods and iTRAQ. Recently SILAC has been added and we plan to establish further methods, such as label free quantification, and determination of the topology of constituent proteins in a complex by cross-linking.

Z2a Second generation sequencing and sequence bioinformatics  | J. Engelmann
Project Z2a will provide high-throughput sequencing with the Illumina HiSeq 1000 platform and bioinformatic analyses of short read sequence data. In collaboration with projects A6, B4, B5, B6, B9 and B10, we will characterize gene expression, alternative splicing and in particular retained intron events, as well as small RNA expression and RNAs bound to specific proteins with functions in RNA processing and translation. Experimental protocols and computational algorithms will be customized to the needs of the individual research project.

Z2b Computational analysis of sequence and 3D-structure for a deeper understanding of chromatin structure and gene silencing pathways | R. Merkl
To support projects A4 and B2, we will improve statistical tests that allow us to study alterations of chromatin density due to different experimental conditions. Moreover, we will adapt these tests to make possible a comparison of different regions of the chromosomes in order to predict structural changes related to multicopy genes. To support projects A6, B3, B4 and B6, we will characterize proteins based on multiple sequence alignments, homology models, and molecular dynamics simulations and try to detail their function.

Z3 Central Tasks | H. Tschochner