Immunoprecipitation of methylated DNA (MeDIP) and expression profiling with a new high troughput sequencing technique

Coordinator:    Prof. Dr. Hans Lehrach
Institution: Max-Planck Institut für molekulare Genetik
In biology, epigenetics refers to heritable changes of the DNA function without changing the DNA sequence. The greek term “epi” means “above”, so epigenetic can be translated as “above the genetics”. Epigenetic modifications of the DNA are i) DNA-methylation and ii) histone modifications, histones are proteins around which the DNA is wrapped in the nucleus. These modifications lead to a difference in DNA function, i.e. different genes are used (expressed), referred to as differences in gene expression.
Epigenetic changes of the DNA-methylation are a common feature in tumor tissue: a global hypomethylation (overall the DNA is less methylated compared to healthy tissue) and a hypermethylation of specific genes, in particular of tumor suppressor genes, occurs. As a consequence of the increase in DNA-methylation the tumor suppressor genes are less active (expressed) in tumor tissues compared to healthy tissues.
In mammals DNA-methylation occurs predominantly at cytosines. Here, we use the technique of methylated DNA immunoprecipitation  (MeDIP) to identify methylated DNA regions. An antibody that specifically recognizes methylated cytosine is used to enrich regions of methylated DNA which are subsequently analysed by second generation sequencing.
The alterations in DNA-methylation and gene expression that occur in intestinal cancer are still not well known. The same holds true for the individual genetic risk to develop cancer. Using the mouse as a model, the changes in DNA-methylation and gene expression during intestinal tumor formation are analysed. Moreover, genes influencing the individual genetic risk to develop cancer can be identified with the help of inbred mouse strains. Since similar mutations cause intestinal cancer in mice and human, we expect to gain insights on human intestinal cancer formation by analysing the mouse model. 
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