Recent technological advancements have paved the way for high throughput genome-scale experiments to infer individual gene functions, gene and protein interactions, and network structures. We decided to apply state of the art techniques in Saccharomyces cerevisiae, a well-characterized eukaryotic model, to unrevealed the mechanism behind gene expression. Gene regulation is a crucial biological process which comprehends cellular interactions of multiple factors allowing an organism to adapt in response to environmental stimuli quickly. The main mechanisms involved in gene regulation are chromatin modifications and DNA methylation. However, non-coding RNAs have been recently described to have a prominent role in controlling gene expression of protein-coding genes. In this PhD thesis, different approaches to gene regulation were studied. First, we employed a genome-scale model of S cerevisiae to predict in silico imbalances of NAD+ production under single mutations and different media. We aimed to identify if the cofactor affected chromatin modification enzymes and thus, gene regulation. Interestingly, NAD+ imbalances were mirrored on transcriptome changes, and this impairment affects telomeric genes significantly. Moreover, through experimental validations, we established Pro3, Gln1 and Lys12 as novel regulators of NAD+ homeostasis. We hypothesised that those metabolic enzymes might be linked to the PHO-pathway, to restore NAD+ cellular levels when media lack primary NAD+ precursors. Secondly, we focused on the impact of ncRNAs deletions on the yeast transcriptome. We described the effect of SUTs and CUTs in modulating coding genes in response to different environmental conditions, acting on essential biological processes such as respiration (SUT125, SUT126, SUT035, SUT532), steroid biosynthesis (CUT494, SUT530, SUT468) and rRNA processing (SUT075 and snr30). Furthermore, we demonstrated that ncRNAs might be acting indirectly through transcription factors, regulating the expression of genes in trans. These results show the function of ncRNAs in the yeast genome and their essential role in modulating the expression of protein-coding and non-coding targets. This study shows valuable to understand alternative pathways of gene regulations, outside of proteincoding genes. These findings corroborate the concept that gene regulation requires a systematic control associated with distinct levels, from transcription to post-transcriptional mechanisms. This genomic control may involve cellular fluctuations of metabolic cofactors and the activity of ncRNAs.