Decoding chromatin modification states using chemical biology and proteomic approaches

DNA and histone modifications play central roles in the control of gene expression and errors in their regulation are associated with a multitude of diseases. These modifications form an epigenetic ‘code’ that stores information within chromatin. This information is “read” by epigenetic effector molecules that recognise DNA and histone modifications through specialised binding domains in order to regulate chromatin function and to orchestrate subsequent biological events such as transcription, DNA replication or DNA repair. It has become apparent in recent years that DNA and histone modifications do not act in isolation but form combinatorial modification signatures that define the functional state of the underlying chromatin. Our research aims to unravel how epigenetic effectors can read DNA and histone modification patterns and how they recognise different chromatin modification states. Our goal is to decipher the “epigenetic code” by identifying epigenetic reader molecules that can integrate information from multiple chromatin modifications and to understand how these factors operate at the molecular level. For this we are taking two complementary approaches. Firstly, we are tackling this problem via a large-scale systems level approach in which we combine chemical biology, proteomic and computational methods to identify new factors and complexes that mediate the functions of specific chromatin states (Bartke et al. 2010, Cell 143, 470). In addition, we are interested in understanding the molecular details of how epigenetic effectors ‘read out’ chromatin and we use biochemical, cell biological, and genomic techniques to investigate how these proteins recognise nucleosomal histone and DNA modifications and how this contributes to their function (e.g. Borgel et al. 2017, NAR 45, 1114). I will present the latest results of our investigation of the E3 ubiquitin ligase UHRF1, a replication factor that reads ^meCpG- and H3K9me3 modifications, and our progress with SILAC Nucleosome Affinity Purifications (SNAP) to decode chromatin.