Over the last years the deep-sequencing field has moved quickly. In addition to determining the genome and the DNA methylome, many additional methods have been developed that use a deep-sequencing readout for genome-wide mapping studies. These include ChIPseq for histone modifications and transcription factor binding as well as advanced methods for RNA analysis or spatial genome organization. Thus, a continuously increasing repertoire of methods becomes available that provides deep insight on how the (epi)genome is organized, linked to the transcriptome and how the deregulation of the underlying epigenetic networks is associated with the cancer disease state.
Within HIPO, the CHromatin And RNA Methods Lab (CHARM Lab) establishes, further develops and applies genome-wide chromatin and RNA methods for the analysis of primary tumor samples. At this stage, ChIP-seq of histone modifications, MNase-seq, RIP-seq and ATAC-seq have already been successfully applied within the HIPO program. A collection of validated antibodies for histone modifications and certain chromatin interacting proteins are available.
In addition, we also apply single-cell transcriptomics and epigenomics to address tumor heterogeneity in a clinical context.