Changes of nucleosome positioning and 3D chromatin organization in cell transitions

The genome of a eukaryotic cell is stored inside the nucleus in a highly condensed form called chromatin. The basic unit of chromatin is the nucleosome. The positioning of nucleosomes on the DNA determines the accessibility of transcription factors (TFs) and other regulatory molecules. Beyond nucleosome positioning, the higher level of 3D chromatin architecture is constituted by relatively large loops of DNA such as topologically associating domains (TADs) which serve to insulate some loci from the rest of the genome. A major determinant of the chromatin domain boundaries is the architectural protein CTCF that binds to thousands of locations in the genome and changes the chromatin configuration during cell differentiation or cancer development. Chapter 1 of this thesis provides an overview of the field of chromatin folding and a premise of the questions that we later address. Chapter 2 is based on our paper [Clarkson et al. (2019) Nucleic Acids Res. 47, 11181-11196] devoted to CTCF-nucleosome interplay at chromatin boundaries. It reports a new effect: the strength of CTCF binding to DNA is inversely proportional to the average distance between nucleosomes near its binding site. We found that a number of CTCF binding sites that remain bound during the differentiation of mouse embryonic stem cells maintain a relatively short distance between the neighbouring nucleosomes. Furthermore, we observed that CTCF binding sites occur in clusters at TAD boundaries, and proposed a new model of chromatin boundary formation through ordered, asymmetric nucleosome arrays. Chapter 3 documents my work on the connection between nucleosome positioning and chromatin state using machine learning. We developed a general methodology for this task and provided a proof of principle that it can work as a diagnostic tool classifying nucleosome positioning patterns to distinguish samples from peripheral blood of healthy individuals and patients with chronic lymphocytic leukaemia.