One of the fundamental questions in science is how chromatin transitions from actively transcribed euchromatin to silent heterochromatin, and what factors affect this transition. One area of my research has focused on understanding the differences in the chromatin structure of active and silent regions in the ribosomal DNA locus (rDNA), a heterochromatin region in S. cerevisiae. Secondly, I have focused on understanding a histone methyltransferase Set1, which is involved in both euchromatin and heterochromatin regions. To distinguish actively transcribed open regions of chromatin from silent and closed regions of chromatin, we have expressed a DNA methyltransferase M.CviPI in vivo to utilize its accessibility to GpC sites. We have used this technique to study changes in nucleosome positioning within the NTS2 region of the rDNA in two cases: as a result of a silencing defect caused by the loss of Sir2, a histone deacetylase involved in silencing at the rDNA, and as an indicator of active transcription by RNA Pol I. Using this technique, we observed differences between open and closed chromatin structure by changes in nucleosome positioning within NTS2. Additionally, we have observed the presence of bound factors within the 35S rRNA gene promoter that are unique to actively transcribed genes. The second area of my research focused on the protein methyltransferase Set1 that mono-, di-, and trimethylates lysine 4 of histone H3 (H3K4) utilizing the methyl group from S-adenosyl methionine (SAM). Set1 is part of a multi protein complex called COMPASS (Complex associated with Set1), and is associated with both actively transcribed and silent regions. Thirty mutants of Set1 were made within the SET domain to learn more about the catalytic mechanism of Set1. The crystal structures of human SET domain proteins, as well as sequence alignments and a random mutagenesis of yeast Set1, were used to identify conserved amino acids in the SET domain of Set1. Mutants were analyzed for their effect on histone methylation in vivo, silencing of RNA Pol II transcription within the rDNA, suppression of ipl1-2, and COMPASS complex formation. Our results show that trimethylated H3K4 is required for silencing of RNA Pol II transcription at the rDNA. Overall, we have shown the importance of tyrosine residues in SET domain proteins. To summarize, my research has strived to understand chromatin structure and the factors that affect the transition between euchromatin and heterochromatin.