Development and validation of novel technology for high throughput epigenome mapping

The recent advances in epigenomics are founded on the combination of novel experimental protocols and advanced measurement devices. Continued improvement in both aspects will further catalyze progress in this field. BLUEPRINT will focus on a) developing novel devices and protocols to perform reproducible chromatin-IP with small amounts of cells and b) developing and validating novel chemistries and devices for specific detection of different forms of cytosine methylation. The robustness of current ChIP protocols depends on the number of cells, which are limited in primary material. To reduce this bottleneck, the SME Diagenode will develop a liquid handling robotics unit for automatized chromatin-IP on small volumes. A further substantial reduction in reaction volumes for Chromatin-IP will be attempted by the SME Sigolis, which will apply its proprietary technology to develop a ChIP tailored microfluidic device.
Whole-genome bisulfite genomic sequencing (BS-seq) as it will be performed for the BLUEPRINT references set is the current gold standard for DNA methylation detection as it provides single molecule basepair resolution. Yet it is read and cost intensive and cannot discriminate between 5-methylcytosine (5mC) and the recently identified 5-hydroxymethylcytosine (5hmC). To overcome these limitations BLUEPRINT will develop and validate direct sequencing approaches together with the SME Oxford Nanopore Technologies and the Sanger Institute. The proposed approaches promise substantially higher read number at lower costs and, furthermore, have the potential for directly distinguishing 5mC and 5hmc without the need of chemical conversion. In addition, BLUEPRINT will also develop novel nucleotide chemistry and immunocapturing approaches able to distinguish between the two methylation states. Each of the generated technologies will be implemented into the BLUEPRINT epigenome pipelines whenever proven to be superior to current technologies.

Research Area Leader: Dirk Schübeler
Technology development for profiling of cytosine (hydroxy)methylation    Leader: Wolf Reik 
Technology optimization for microscale application                                 Leader: Eileen Furlong