Fingers in action! Chromatin Organization and Transcriptional Regulation by CTCF and CTCFL

Abstract

Chromatin is hierarchically folded and wrapped in order to compact DNA. It is accessible to specific proteins to allow regulation of various cellular processes. Although chromatin is organized into higher-order structures it is highly dynamic and it can influence genome configuration and transcription via interactions with various subnuclear compartments. CTCF is the most important factor involved in chromatin structure regulation, in particular the spatial organization of higher-order chromatin configurations. CTCF-like (CTCFL) is a testis specific paralogue of CTCF, whose function has been characterized to a lesser extent. The aim of this thesis is to obtain more insight in the biological roles of CTCF and CTCFL. A general introduction to the field of nuclear organization and transcription regulation is provided in chapter 1. This chapter also provides an overview of the process of spermatogenesis during which both CTCF and CTCFL are thought to perform important functions. Finally this chapter also summarizes already known aspects of CTCF, CTCFL and their functional interaction partners. The role of CTCF and CTCFL in the regulation of ribosomal repeat DNA is the main focus of chapter 2. CTCF and CTCFL interact with the key regulator of RNA polymerase I, UBF. Furthermore, CTCF regulates the spacer promoter by recruiting RNA polymerase I, H2A.Z and UBF to rDNA. In chapter 3 the focus shifts towards the study of CTCF binding motifs and the binding of CTCF zinc fingers to DNA. Using a genome-wide binding analysis on CTCF zinc finger mutants we propose a model for DNA binding by CTCF. Chapter 4 and 5 examine the functional relationship between CTCF and CTCFL extensively in mouse embryonic stem cells and testis by examining genome-wide binding and transcription profiles. Finally, chapter 6 provides a general discussion elaborating on the findings in this thesis. Furthermore, the findings are positioned in perspective with current literature and provide recommendations for further experiments on this topic.