Overcoming chromatin restricted dna access
Differential gene expression programs account for the diversity of cell types in our body. They are controlled by intricate networks of sequence-specific transcription factors (TFs) that operate in the context of chromatin. Chromatin is itself an essential component of this process, and is part of the system that selectively restricts DNA access for TFs. As a consequence, most TFs only bind to a small subset of their motif occurrences, in a way we currently do not fully understand. Our inability to predict binding of a TF based on its cognate motif and location in the genome is a serious obstacle towards predictive models of gene regulation.
DNAccess has the ambitious goal to define in vivo the sensitivities of TFs to nucleosomes and their reliance on chromatin remodeling enzymes for binding. Using novel genomics and genome editing tools we will: (a) systematically vary TF motifs, presence of nucleosomes and their modifications at a defined chromosomal locus and quantify resulting TF binding; (b) explore genome-wide the ability of ectopic TFs to engage with a chromatinized genome in the absence of host cofactor engagement; (c) dissect chromatin remodeler dependent TF binding in order to define temporal order and subcomplex function and (d) deconstruct remodeler recruitment by mutating TF interaction domains. 
DNAccess will build a highly integrated setup to comprehensively characterize how nucleosomes, their modifications and mobility restricts genome access. We will characterize existing chromatin barriers and identify how TFs overcome them. This represents a crucial step towards a comprehensive understanding of the role of chromatin in gene regulation, and will advance our understanding of how specificity is generated in large eukaryotic genomes.