Ubiquitylated H2A.Z is associated with diverse types of silenced chromatin including methylated CpG islands and homopurine/homopyrimidine sequences

Abstract

H2A.Z monoubiquitylation has been linked to transcriptional repression, but the molecular details involved remain unclear. To address this, we developed a unique ubiquitylation-dependent auto-biotinylation approach, named H2A.Z-UAB, to purify ubiquitylated H2A.Z (H2A.Zub) mononucleosomes for biochemical and genome-wide analyses. We found that H2A.Zub nucleosomes are enriched for the repressive histone post-translational modification H3K27me3 but depleted of H3K4 methylation and other active transcription-associated modifications. ChIP-seq analyses revealed that H2A.Zub-nucleosomes associate with repressive chromatin states and are mostly enriched at genes with low or no expression. Consistent with the biochemical analyses, H2A.Zub ChIP-seq peaks align with regions depleted of H3K4 methylation, H3K27 acetylation, but enriched for H3K27me3. We further observed a strong correlation between high levels of H2A.Zub and DNA methylation, particularly at methylated CpG-rich islands. Finally, we found that a significant proportion of H2A.Zub peaks correspond to homopurine/homopyrimidine sequences that are generally linked to silenced genes and repressive chromatin. Collectively, these findings suggest that H2A.Z ubiquitylation plays an overarching role in global transcriptional silencing through its association with multiple types of repressive mechanisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/759852v3_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@71804eorg.highwire.dtl.DTLVardef@19eb987org.highwire.dtl.DTLVardef@1a67e15org.highwire.dtl.DTLVardef@19fc5c2_HPS_FORMAT_FIGEXP M_FIG C_FIG