Deciphering regulation in eukaryotic cell: from sequence to function

TL;DR

This paper develops computational methods to analyze DNA sequences, focusing on transcriptional regulation and genome structure in cancer, revealing mechanisms like transcription factor binding and phenomena such as chromothripsis.

Contribution

Introduces new sequence analysis methodologies for identifying transcription factor binding sites, gene targets, and genomic rearrangements, advancing understanding of regulation in normal and cancer cells.

Findings

Identification of transcription factor binding sites and histone positioning.

Analysis of oncogenic transcription factors in cancer cell regulation.

Discovery of chromothripsis in tumor genomes.

Abstract

A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in normal and cancer cells. This topic connects together the projects presented in this thesis. Two chapters of the thesis represent major areas of my research interests: (1) methods for deciphering transcriptional regulation and their application to answer specific biological questions, and (2) methods to study the genome structure and their application in cancer studies. The first chapter predominantly focuses on transcriptional regulation. Here I describe my contribution to the development of methodology for the discovery of transcription factor binding sites and the positioning of histone proteins. I also explain how sequence analysis, in combination with gene expression data, can allow the identification of direct target genes of a transcription factor under study, as well as the physical mechanisms of its action. As two examples, I provide the results of my study of transcriptional regulation by (i) oncogenic protein EWS-FLI1 in Ewing sarcoma and (ii) oncogenic transcription factor Spi-1/PU.1 in erythroleukemia. In the second chapter, I describe the sequence analysis methods aimed at the identification of the genomic rearrangements in species with existing reference genome. I explain how the developed methodology can be applied to detect the structure of cancer genomes. I provide an example of how such an analysis of tumor genomes can result in a discovery of a new phenomenon: chromothripsis, when hundreds of rearrangements occur in a single cellular catastrophe. The thesis is concluded by listing the major challenges in high-throughput sequencing analysis. I also discuss the current top questions demanding the integration of sequencing data.