In eukaryotes, the organization of DNA into a highly compact chromatin structure presents an obstacle for RNA polymerase during transcription. Consequently, organisms have evolved molecular machines that alter the chromatin template through a variety of mechanisms. This machinery includes the conserved Polymerase-Associated Factor 1 Complex (Paf1C), which associates with RNA polymerase II, promotes specific chromatin modifications, and regulates expression of certain genes. Past work has shown that Paf1 plays an important role in mediating transcription of genes across diverse pathways of cellular biology; however, its effects on transcription of noncoding DNA have not been thoroughly investigated. Genome-wide studies have revealed extensive noncoding DNA transcription across the yeast genome. Some of this noncoding transcription impacts the expression of neighboring genes, while giving rise to unstable transcripts that face rapid degradation by the TRAMP complex and its poly-A polymerase subunit, Trf4. To investigate the impact of the Paf1C on the greater transcriptome, whole genome tiling array studies were performed on RNA prepared from paf1Δ, trf4Δ, paf1Δtrf4Δ, and wild-type strains. Using differential expression analysis, we have identified classes of protein-coding genes whose expression is strongly dependent on Paf1. Notably, we observed decreased expression of phosphate signaling genes and increased expression of iron transport genes in paf1Δ cells, as validated by northern blot analysis and reverse transcription quantitative polymerase chain reaction (RT-qPCR). We have also confirmed previous findings that paf1Δ cells have severe transcription termination defects at snoRNA genes, which encode a class of noncoding RNAs involved in ribosome assembly. Finally, preliminary analysis of paf1Δtrf4Δ and trf4Δ cells has provided new insights on transcription of other noncoding RNAs, including CUTs, and antisense transcription. These findings confirm that Paf1 is a major participant in regulation of the global transcriptome. Moving forward, we aim to identify the specific mechanisms by which Paf1 regulates these diverse gene classes and further elucidate the impact of these defects in the cell.