An epigenomics approach to characterize alterations in disease

Petrini, Cristiano
Epigenetics is the term that describes all the mechanisms that regulate the genomic activities such as transcription, DNA repair, DNA replication, transposon duplication. There is a great variety of epigenetic mechanisms that act at different genomic scales: from a single nucleotide resolution (e.g. DNA modifications) to several megabases (chromatin-lamina interactions). As epigenetics mechanisms are involved in many cellular processes, their alteration could lead to the development of pathologies including genetic diseases and cancer. Thus, considering the importance and variety of epigenetics mechanisms numerous experimental techniques have been developed to study them. Despite the progresses so far, the genome-wide techniques to study epigenetics mechanisms are still affected by several technical biases and most of them are not suitable for investigation of tissue samples, especially in case of biological material scarcity. In this thesis I am presenting a new technique: the Sequential Analysis of Macro-Molecule Accessibility by sequencing (SAMMY-seq). This method is not affected by most common technical biases of epigenomics methods and can be easily performed on as little as 10 thousand cells, as well as in tissue samples. With SAMMY-seq it is possible to extract and separately analyze distinct chromatin regions according to their different biochemical properties. We analyzed different cells, organisms and samples, showing that the technique is highly reproducible and the results in line with known epigenetic profiles. Once applied on two different disease cellular models (progeroid fibroblast and MCF10DICIS cancer cells) SAMMY-seq has been able to detect chromatin alterations where other techniques failed. In addition, thanks to its low starting material requirement, it has been possible to apply SAMMY-seq on prostate biopsies from patients with cancer, thus describing for the first time on tissue an association between epigenomic alterations and patients subgroups. Finally, using SAMMY-seq we developed a data analysis technique to reconstruct chromatin compartments. We have been able to investigate the relationship between chromatin compartments and chromatin fractions separated by solubility. Our results demonstrate that SAMMY-seq is a powerful method to study epigenomics providing new insights over common diseases such as prostate cancer. Furthermore, altering chromatin solubility inside the cell nucleus we observe changes in compartments distribution, we have been able to suggest solubility as a new epigenetic mechanism.
NUI Galway
Publisher DOI
Attribution-NonCommercial-NoDerivs 3.0 Ireland