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UBC Theses and Dissertations

Targeting of histone acetylation to transcribed chromatin Martin, Benjamin John Elwood


The enrichment of histone acetylation within transcribed chromatin was first observed in the 1960s, and how specific histones are acetylated has been a central question of chromatin biology ever since. One mechanism for specificity is through the targeted recruitment of histone acetyltransferases (HATs) to transcribed chromatin, and we first focused on recruitment of the NuA3 HAT complex in S. cerevisiae. NuA3 is known to bind to cotranscriptional histone methylation through two domains: the PHD finger in Yng1 and the PWWP domain in Pdp3, which in vitro bind to H3K4 and H3K36 methylation, respectively. While the in vitro binding has been well characterized, the relative in vivo contributions of these histone methylation marks in targeting NuA3 is unknown. Here, through genome-wide colocalization and mutational interrogation, we demonstrate that the PHD finger of Yng1 and the PWWP domain of Pdp3 independently target NuA3 to H3K4 and H3K36 methylated chromatin, respectively. Interestingly however, the simple presence of NuA3 is insufficient to ensure the acetylation of associated nucleosomes, suggesting a secondary level of regulation that does not involve control of HAT-nucleosome interactions. Next we studied targeting of histone acetylation itself, focusing on the causality of the relationship between histone acetylation and RNAPII transcription. Through genome-wide analysis of mammalian cell culture and budding yeast, we reveal that the preponderance of histone acetylation is tightly linked with RNAPII occupancy, and, in S. cerevisiae, chemically or genetically altering RNAPII localization results in a corresponding change in histone acetylation. These findings show that histone acetylation is primarily targeted through RNAPII as a consequence of transcription. Importantly, several lines of evidence suggest that RNAPII does not promote acetylation by simple HAT targeting. First, we show that HAT occupancy is a poor predictor of histone acetylation. Second, NuA4 recruitment to upstream activation sequences of either Taf1 (TFIID) enriched or depleted promoters does not result in acetylation in the absence of transcription. Collectively, these data suggest that the activity of HATs is regulated post-recruitment by a mechanism that is dependent on RNAPII.

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