UCSF

Chromatin architecture has an incredible influence on the transcription state of genes in a cell. Chromatin occurs primarily in two generalized states: transcriptionally active euchromatin, and transcriptionally silent heterochromatin. This distinction of chromatin states can be accomplished by a number of regulatory processes, including post-translational modification by a variety of enzymes, and by the incorporation of histone variants. In the budding yeast Saccharomyces cerevisiae, transcriptional silencing by heterochromatin is dependent on the silent information regulators, or Sir proteins. Here we describe the results of a genome-wide screen designed to identify novel factors that are able to antagonize the encroachment of heterochromatin into actively transcribed regions. This screen identified a number of both known and novel factors that can to antagonize silencing. Among the proteins identified by the screen were several histone acetyl transferases, the histone tail binding proteins Bdf1 and Bdf1, and components of the Swr1 complex, which is responsible for the deposition of histone variant H2A.Z, a known anti-silencer. This was suggestive of a potential mechanism involving histone tail acetylation to specifically target H2A.Z to regions of chromatin to protect from the encroachment of silencing. Indeed, we were able to successful demonstrate that this is a mode of H2A.Z deposition. However, to our surprise, we found H2A.Z has a wide spread deposition throughout the yeast genome. More specifically, H2A.Z is precisely targeted to single nucleosomes on one, or both sides of a nucleosome-free region, which flanks the transcription initiation site for the vast majority of genes. Additionally, we have shown that this deposition can occur in the absence of active, demonstrating that eukaryotic cells possess a mechanism for marking the 5' ends of genes independent of transcription.