Deutsches Epigenom Programm (DEEP)

The German Federal Ministry of Education and Research (BMBF) represented by the Project Management Agency within the German Aerospace Center (PT-DLR) launched the German Epigenome Program “DEEP” on 1 September 2012. DEEP receives an overall funding of approx. 16 Mio EUR and will run for 5 years.

Overall project goal

DEEP creates an interdisciplinary research platform of 17 subprojects linking 21 epigenomic mapping and functional analysis groups across Germany. As the German contribution to IHEC, the ‘International Human Epigenome Consortium’, DEEP will produce und functionally interpret 70 reference epigenomes of selected human (and some murine) cells and tissues using high-throughput technologies and state of the art bioinformatics analysis.


DEEP will focus on cell-types connected to the following complex diseases with high socio-economic impact: metabolic diseases such as i) steatosis (hepatocytes, kupffer-cells) and ii) adipositas (adipocytes (small/large, visceral/subcutaneous), monocytes, macrophages), as well as inflammatory diseases such as iii) morbus crohn (Mucosa, Macrophages, T-memory/effector cells) and iv) rheumatic arthritis (fibroblasts, Macrophages, T-memory/effector cells). The profiling and interpretation of epigenetic signatures or epigenetic (dys)regulation shall contribute to the understanding of the diseases being analyzed and in combination with functional studies lead to the identification of intra- and intercellular networks. These could be starting points for the development of novel diagnostic and therapeutic strategies and biomarkers.

To reach this goal, DEEP will generate for each cell-type genome-wide epigenome maps, including: i) DNA methylation (whole genome bisulfite sequencing), ii) chromatin accessibility (sequencing of DNAse hypersensitive sites), iii) 6 core histone modifications (ChIP-Seq), iv) transcriptome (RNA-seq) v) standard genotyping (SNP-array). On the bioinformatics level new strategies, concepts and tools for the visualization,  integration and interpretation of epigenomic high-througput data shall be established.

Scientific Platforms

Deep is assembled on three interacting scientific platforms: production of epigenomic mapping-data, bioinformatics analysis and method-development and functional analysis with disease-orientation (see Figure 1, Table 1). The disease-oriented platform will contribute expertise to isolate highly purified cell types/tissues for epigenomic mapping and will analyse cell type-/ tissue-associated aspects of the complex diseases. The epigenomic sequencing units will generate primary epigenomic mapping-data that will be submitted to a central data collection unit and interpreted in close collaboration with central bioinformatics units responsible for high quality public data deposition and deep functional interpretation. A programme coordination and communcation platform will monitor the quality controlled data generation and foster interactions between bioinformatics and experimental analysis groups across platforms. DEEP will further coordinate its activities with IHEC and other epigenetic initiatives to establish unified standards for epigenomic data and for scientific exchange. Along this line DEEP will support IHEC in its dissemination activities through a DEEP associated coordination office.

DEEP Structure

Overview of the DEEP-network structure of subprojects organized in four platforms: i) functional analysis with disease-orientation, ii) production of epigenomic mapping-data, iii) bioinformatics analysis and method development and iv) programme coordination and communication. The figure shows the placement of subprojects in the platforms and their interactions (arrows). DNAseI-seq: DNAseI sequencing, WGBS: whole genome bisulfite sequencing, ChIP-seq: ChIP sequencing, RNA-seq: RNA sequencing, DCC: Data Collection Center, DAC: Data Analysis Center.