Dissecting the role of histone variant H2A.Z acetylation in transcription regulation

Abstract

Acetylation of the human histone variant H2A.Z occurs at promoter regions and is associated with gene expression, however, the role of H2A.Zac at other regulatory regions, including enhancers is still poorly understood. Moreover, any functional studies beyond correlative studies, in particular concerning a direct role for H2A.Z acetylation in gene transcription, are lacking. My studies presented as part of my PhD thesis have addressed the gap of knowledge in many of these important questions regarding the role of H2A.Zac in regulation of gene expression.

First, I show that H2A.Zac-containing nucleosomes are also found at enhancers of LNCaP and VCaP human prostate cell lines and that a re-distribution of H2A.Zac occurs to form cancer-related enhancers. Notably, H2A.Zac plays an important role in activation of androgen receptor (AR)-enhancers. H2A.Zac nucleosomes mark AR binding sites and upon androgen induction these nucleosomes are rapidly remodelled to form nucleosome-free regions allowing expression of AR-enhancer RNAs.

Next, I identify the histone acetyltransferases responsible for H2A.Zac in humans and a novel molecular mechanism of writer/reader crosstalk between H2A.Z and H4 acetylation. I show p300 acetylates H2A.Z at multiple lysines both in vitro and in cells. Importantly, I found that the interaction between the bromodomain of p300 and H4 acetylation enhances p300-driven H2A.Z acetylation.

Finally, I examine the causal role of H2A.Zac in transcription, at both promoters and enhancers. For this, I generated inducible models in LNCaP cells where I overexpress a non-acetylable H2A.Z mutant or a constant acetylated form. RNAseq analysis reveals that reduced H2A.Zac levels result in a genome-wide increase in intron retention, although global gene expression was not altered. Cells lacking H2A.Zac also show accumulation of paused RNA polymerase II (RNAPII) at both promoters and enhancers, and a decrease of eRNA expression at enhancers. My data suggests that H2A.Zac regulates RNAPII kinetics and subsequently both splicing and enhancer function.

Altogether, in my thesis I have discovered novel mechanisms for H2A.Zac transcriptional regulation, from identification of the H2A.Zac acetyltransferase (writer) to the downstream consequences of H2A.Zac nucleosome occupancy at promoters and enhancer elements.