The role of Set2, transcription factor residence, and nucleosome spacing in the dynamic access of genomic information

DNA is a heteropolymer that serves as a mutable form of storage for genomic information. Nucleosomes condense genomes by wrapping 147 bp of negatively charged DNA around a positively charged histone core. Histone modifications and selective placement of nucleosomes expand and allow for regulated access of the information content in DNA. Understanding and predicting the placement and organization of nucleosomes, as well as the dynamics of genome utilization, is therefore critical for expanding our knowledge of life. A complex set of machinery regulates RNA polymerase II passage through a nucleosomal template. Loss of the histone H3K36 methyltransferase, SET2, leads to aberrant (cryptic) transcription initiation from within the coding region of genes due to an inability to regulate chromatin reassembly following transcription. We used whole genome microarrays to map and identify sites of aberrant transcription initiation in set2Δ. We developed a statistically principled algorithm to show there is no evidence that cryptic initiation occurs more frequently in long or infrequently transcribed genes. I adapted an assay to study the residence dynamics of the S. cerevisiae transcription factor, Rap1, genome-wide. Rap1 binds with a long residence at highly transcribed genes promoters. These sites typically have a high Rap1 affinity motif and low in vitro affinity for the formation of nucleosomes. In contrast, we find that sites with short Rap1 binding typically have high nucleosome occupancy and fast histone turnover. We propose that an active regulated competition between transcription factors and nucleosomes can regulate transcription factor residence and function. The HMGB class of proteins is known to influence the dynamics of nucleosomes and transcription factors. We mapped the distribution of the major nuclear HMGB containing proteins by ChIP-seq, genome accessibility using FAIRE-seq, and mapped nucleosomes using MNase-seq in an HMGB mutant. We identified linker length differences between several strains. This linker length change allowed us to identify invariant nucleosome boundaries and test the underlying principles of nucleosome positioning in S. cerevisiae. Collectively, these studies provide a richer picture of how DNA access is regulated by complex nucleosome-mediated mechanisms