This PhD thesis can be divided into three distinct sections with the common objective of understanding how and to which extent antisense transcription influences gene expression within the yeast S. cerevisiae genome. The first part of this project aimed to assess the role of antisense transcription in sense transcription genome-wide by deleting the nuclear subunit of the exosome Rrp6. The second part intended to validate a genetic screen set up by a previous PhD student using PHO84 as a model gene with the aim to identify new factors involved in antisense-mediated gene silencing. The goal of the third and final part was to provide molecular insights on how antisense transcription might induce gene silencing. To address this fundamental question we used both single gene and genome-wide approaches examining key chromatin features, including nucleosome occupancy, post-translational modification (PTMs) and histone turnover in relation to antisense transcription.