Collaborative Research Centre/Transregional 81: Chromatin Changes in Differentiation and Malignancy

Humans and other higher organisms possess a multitude of various cell types that differ greatly in appearance and function.  Although the cells of an organism have largely identical genes, a heart muscle cell, for example, uses different genes than those of a blood cell.  Thus, the activity pattern of a muscle precursor cell's genes must be transferred and modified onto further (muscle) daughter cells. Since necessary genes in varying groups in the genome are present simultaneously, there are numerous inactive genes scattered between groups of active genes.
Inactivity is frequently transmitted via changes in the DNA (DNA methylation) and via chemical modification of the DNA-packing histone (chromatin).  These modifications are the cause of epigenetics, the passing on of the activity condition onto daughter cells, and this is what is under investigation by the CRC/TRR 81.
At JLU, participating institutes include not only the Institute of Genetics (Faculty 08 - Biology and Chemistry), but also the Biochemical Institute and the Rudolf Buchheim Institute for Pharmacology (both Faculty 11 - Medicine).

Establishment of this CRC with the participation of German and Dutch work groups, enables research to address highly topical questions of epigenetics at an international level.  Furthermore, the option of international exchanges is offered to doctoral students during their education, a valuable experience that opens up future career opportunities.

Next generation sequencing (NGS) based methods have become state-of-the-art in studying multiple facets of chromatin dependent processes. Recent NGS technologies generate hundreds of millions of sequencing reads enabling the analysis of transcription factor binding sites, transcriptomes and other data sets on a genome-wide scale. These methods produce tremendous amounts of data within a short time. During the last years it has become clear that the appropriate analysis and integrative interpretation of the resulting data is particularly demanding and crucial to gaining maximal insight into the underlying biological processes.

This central project will assure that all CRC groups have access to next generation sequencing (NGS) based analysis methods on three levels: First, the service project will advise individual projects in the experimental design. Second, it will prepare sequencing libraries for the CRC groups, or alternatively teach library preparation to the individual groups. Third, and most importantly it will perform the standardized analysis and interpretation of the resulting data. The major focus is on the sequencing of chromatin-immunoprecipitated (ChIP) DNA in order to map the binding events of transcription factors, specific histone modifications or other chromatin-associated proteins on a genome-wide scale (ChIPseq).

Furthermore, some groups substitute classical gene expression studies using microarrays with NGS based sequencing of cDNA (RNA-seq). These two techniques present the core methods relevant for many of the groups within the CRC. Nonetheless, some of the groups apply alternative NGSbased methods that require specific analysis workflows and pipelines. Additionally, this central project provides expertise in the analysis of other high-throughput data sets such as gene expression and DNA methylation microarrays or ChIP-chip data.