Gene expression in eukaryotes is tightly controlled to determine cell identity and function, and to drive complex differentiation and developmental programs. Each step in the gene expression process can be regulated to influence the final outcome and thus, a comprehensive view of gene expression changes at multiple levels is required for full understanding of the regulation of gene expression. To investigate how the cell integrates regulatory mechanisms at multiple levels to achieve precise and coordinated regulation of gene expression, we combined genome-wide techniques and traditional methodologies to obtain key measurements of gene expression and to dissect the contribution of each step in determining gene expression levels. In chapter 2, we focus on how ribosomal deficiencies alter gene expression. We probed the changes of mRNA abundances, translation rates, and protein abundances in a panel of ribosomal protein mutants and observed changes that were both specific to individual ribosomal proteins and dose-dependent with degree of translation deficiency. We also observed strong evidence of compensatory regulation, including at the transcriptional and protein degradation levels, and distinct cellular responses to loss of small and large ribosomal subunit components. Three current models have been proposed to explain the specific phenotypes associated with loss of ribosomal proteins in diseases of ribosome deficiency, or ribosomopathies, and our data revealed evidence to support all of these models, albeit to differing extents. In chapter 3, we describe a novel regulatory mechanism in which the protein levels are determined by identity, instead of levels, of the transcripts. We collected parallel measurements of mRNA, translation, and protein through a timecourse in yeast meiosis and discovered that the toggling between canonical transcript isoforms and long undecoded transcript isoforms regulates the outcome of gene expression for 380 genes. In chapter 4, we study the regulation of ribosome biogenesis (RiBi) genes and show that global inhibition of translation de-represses RiBi mRNA transcription in a condition-dependent manner. In summary, in three different contexts, we report a surprisingly high degree of integration between different levels of gene expression, highlighting the importance of parallel measurements of different gene expression intermediates to interpret the link between gene expression and cellular outcomes.