Touched by CTCF: Analysis of a multi-functional zinc finger protein

Multicellular organisms contain a complete set of genes in nearly all of their cells. However most cells are very different to each other and are able to form organs with distinct functions. The identity and survival of the cell is regulated by the activity of specific genes in time and space. Specific sets of genes encoding proteins become activated, whereas others are repressed. CTCF is a protein that mediates distinct processes of gene regulation, including transcription and the structural organization of the genome. The aim of this thesis is to investigate the different functions of CTCF by a combined analysis of CTCF-interacting proteins and by deletion of CTCF in vivo and in vitro. Using these approaches we aimed to improve our understanding of the molecular mechanism underlying its functions. Chapter 1 gives an overview of the information required to understand the foundations of studies presented and discussed in this thesis. It gives an introduction to gene regulation and how this process is influenced by chromatin modifications, nuclear organization and compartmentation. A specific nuclear compartment, the nucleolus, and its involvement in ribosomal RNA synthesis, are highlighted. Furthermore the characteristics of CTCF and its homolog CTCFL are described in detail.