Acetylation of Vertebrate H2A.Z and Its Effect on the Structure of the Nucleosome

Abstract

Purified histone H2A.Z from chicken erythrocytes and a sodium butyrate-treated chicken erythroleukemic cell line was used as a model system to identify the acetylation sites (K4, K7, K11, K13, and K15) and quantify their distribution in this vertebrate histone variant. To understand the role played by acetylation in the modulation of the H2A.Z nucleosome core particle (NCP) stability and conformation, an extensive analysis was conducted on NCPs reconstituted from acetylated forms of histones, including H2A.Z and recombinant H2A.Z (K/Q) acetylation mimic mutants. Although the overall global acetylation of core histones destabilizes the NCP, we found that H2A.Z stabilizes the NCP regardless of its state of acetylation. Interestingly and quite unexpectedly, we found that the change in NCP conformation induced by global histone acetylation is dependent on H2A/H2A.Z acetylation. This suggests that acetylated H2A variants act synergistically with the acetylated forms of the core histone complement to alter the particle conformation. Furthermore, the simultaneous occurrence of H2A.Z and H2A in heteromorphic NCPs that most likely occurs in vivo slightly destabilizes the NCP, but only in the presence of acetylation.In the nucleus of the living cell, DNA interacts with a set of highly basic proteins called histones to form a nucleoprotein complex, which is called chromatin (1). Histones are grouped into two major types: core histones (H2A, H2B, H3, and H4) and linker histones (histone H1). The former organize the protein core around which approximately 146 bp of DNA is wrapped to produce the basic chromatin subunit, the nucleosome core particle (NCP). 1 Histones of the H1 family bind to the linker DNA regions connecting adjacent nucleosomes. Both core and linker histones consist of nonallelic variants. Some of these are expressed exclusively during S phase, and the mRNAs transcribed from their genes are not polyadenylated (replication-dependent variants). They are also often termed canonical variants. Other variants are expressed throughout the cell cycle; their mRNAs are polyadenylated, and they replace the replicationdependent variants to specify function or supplement their loss during cell cycle turnover (replacement variants).

Nucleosome fragility is associated with future transcriptional response to developmental cues and stress inC. elegans

“…This distinction could be due to a divergence in H2A.Z properties between yeast and C. elegans (Zlatanova and Thakar 2008). It is also possible that the H2A.Z-containing nucleosomes used for analysis in this study (measured by Ho et al 2014) were comprised of the particularly stable, homotypic type of H2A.Z nucleosomes (Ishibashi et al 2009). …”

Pericentric heterochromatin state during the cell cycle controls the histone variant composition of centromeres

“…Previous studies have proposed that H2A.Z functions as a structural component in the heterochromatin context, where the morestable hypoacetylated homotypic (H2A.Z-H2A.Z) nucleosomes might influence the folding of the chromatin fiber and facilitate the formation of secondary structures with increased compaction (Fan et al, 2002;Fan et al, 2004;Ishibashi et al, 2009;Suto et al, 2000). This is supported by a series of observations in yeast, where H2A.Z mostly functions as a negative regulator of transcription in the case of heterochromatic regions (Buchanan et al, 2009;Dhillon and Kamakaka, 2000;Hou et al, 2010).…”

Reconciling the positive and negative roles of histone H2A.Z in gene transcription

“…In vitro studies aimed at investigating the structural impact of the incorporation of H2A.Z on nucleosome dynamics have generated contradictory observations with respect to its stability. 68,69 Differences in the methodologies used in these studies may explain at least part of the discrepancies observed. A number of these studies were conducted with nucleosomes assembled in vitro using bacterially purified recombinant histones.…”

“…A number of these studies were conducted with nucleosomes assembled in vitro using bacterially purified recombinant histones. [68][69][70][71] These artificial nucleosomes were shown to have different characteristics when compared to native nucleosomes. 72 It appears that in vitro assembly of histones does not perfectly mimic the native folding of histones and/or that chaperone-assisted folding of nucleosomes is important for proper nucleosome assembly.…”