Computational epigenomics in gene regulation and cancer research

DNA is packaged together with proteins, such as histones, in the nucleus of a cell to form a fiber called chromatin. The nature of this packaging, the "chromatin structure", is essential for proper cell functioning. This is illustrated by the fact that perturbating chromatin can be associated with many diseases. Hence, artificial perturbation of...

3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes

Genomically distal mutations can contribute to the deregulation of cancer genes by engaging in chromatin interactions. To study this, we overlay viral cancer-causing insertions obtained in a murine retroviral insertional mutagenesis screen with genome-wide chromatin conformation capture data. Here we find that insertions tend to cluster in 3D...

Chromatin Landscapes of Retroviral and Transposon Integration Profiles

The ability of retroviruses and transposons to insert their genetic material into host DNA makes them widely used tools in molecular biology, cancer research and gene therapy. However, these systems have biases that may strongly affect research outcomes. To address this issue, we generated very large datasets consisting of to unselected...