Gene dysregulation by histone variant H2A.Z in bladder cancer

Kyunghwan Kim,Jongkyu Choi,Woojin An,Jin-Man Kim,Vasu Punj,Kyu Heo,Peter W Laird

doi:10.1186/1756-8935-6-34

Abstract

BackgroundThe incorporation of histone variants into nucleosomes is one of the main strategies that the cell uses to regulate the structure and function of chromatin. Histone H2A.Z is an evolutionarily conserved histone H2A variant that is preferentially localized within nucleosomes at the transcriptional start site (TSS). H2A.Z reorganizes the local chromatin structure and recruits the transcriptional machinery for gene activation. High expression of H2A.Z has been reported in several types of cancers and is causally linked to genomic instability and tumorigenesis. However, it is not entirely clear how H2A.Z overexpression in cancer cells establishes aberrant chromatin states and promotes gene expression.ResultsThrough integration of genome-wide H2A.Z ChIP-seq data with microarray data, we demonstrate that H2A.Z is enriched around the TSS of cell cycle regulatory genes in bladder cancer cells, and this enrichment is correlated with the elevated expression of cancer-promoting genes. RNAi-mediated knockdown of H2A.Z in the cancer cells causes transcriptional suppression of multiple cell cycle regulatory genes with a distinct decrease in cell proliferation. H2A.Z nucleosomes around the TSS have higher levels of H3K4me2/me3, which coincides with the recruitment of two chromatin factors, WDR5 and BPTF. The observed recruitment is functional, as the active states of H2A.Z target genes are largely erased by suppressing the expression of WDR5 or BPTF, effects resembling H2A.Z knockdown.ConclusionsWe conclude that H2A.Z is overexpressed in bladder cancer cells and contributes to cancer-related transcription pathways. We also provide evidence in support of the engagement of H3K4me2/me3 and WDR5/BPTF in H2A.Z-induced cancer pathogenesis. Further studies are warranted to understand how H2A.Z overexpression contributes to the recruitment of the full repertoire of transcription machinery to target genes in bladder cancer cells.

Highlights

The incorporation of histone variants into nucleosomes is one of the main strategies that the cell uses to regulate the structure and function of chromatin
These findings were further corroborated by the results showing that the ectopic expression of H2A.Z led to a significant increase in the growth of UROtsa cells (Figure 1E and Additional file 1: Figure S1)
H2A.Z is essential for H3K4me and WDR5/BPTF recruitment To check whether the cooperative functions of WDR5 and BPTF in H2A.Z-activated genes reflect their targeted recruitment, we investigated their localization at H2A.Z target genes by chromatin immunoprecipitation (ChIP) assays

Summary

Introduction

The incorporation of histone variants into nucleosomes is one of the main strategies that the cell uses to regulate the structure and function of chromatin. Since H2A.Z-containing nucleosomes wrap DNA more weakly than canonical H2A nucleosomes, they are more susceptible to nuclease digestion and salt-induced destabilization [16,17] This structural instability is most likely driven by amino acid substitutions at the interface between H2A.Z and H3/H4 [18]. Consistent with its effects on gene transcription, the presence of H2A.Z correlates with active histone modifications and RNA Pol II occupancy at gene promoters, which in turn influence transcriptional output [7,13,19] These observations are in agreement with the concept that H2A.Z creates an active transcription environment by altering DNA accessibility in chromatin and facilitating the recruitment of transcription regulators.

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