Nucleosome stability mediated by histone variants H3.3 and H2A.Z

Abstract

Nucleosomes containing the histone variant H3.3 tend to be clustered in vivo in the neighborhood of transcriptionally active genes and over regulatory elements. It has not been clear, however, whether H3.3-containing nucleosomes possess unique properties that would affect transcription. We report here that H3.3 nucleosomes isolated from vertebrates, regardless of whether they are partnered with H2A or H2A.Z, are unusually sensitive to salt-dependent disruption, losing H2A/H2B or H2A.Z/H2B dimers. Immunoprecipitation studies of nucleosome core particles (NCPs) show that NCPs that contain both H3.3 and H2A.Z are even less stable than NCPs containing H3.3 and H2A. Intriguingly, NCPs containing H3 and H2A.Z are at least as stable as H3/H2A NCPs. These results establish an hierarchy of stabilities for native nucleosomes carrying different complements of variants, and suggest how H2A.Z could play different roles depending on its partners within the NCP. They also are consistent with the idea that H3.3 plays an active role in maintaining accessible chromatin structures in enhancer regions and transcribed regions. Consistent with this idea, promoters and enhancers at transcriptionally active genes and coding regions at highly expressed genes have nucleosomes that simultaneously carry both H3.3 and H2A.Z, and should therefore be extremely sensitive to disruption.

The double face of the histone variant H3.3

“…Furthermore, these three residues are thought to participate in the regulation of histone-histone interaction stability [25]. Indeed, H3.3 nucleosomes isolated from avian cells stably expressing tagged H3.3 are unusually sensitive to salt-dependent disruption, resulting in loss of their H2A/ H2B dimers [26]. Moreover, a recent study in HeLa cells expressing tagged H3.3 showed that splitting events of H3.3-H4 tetramers could be detected during DNA replication in vivo, a process that could not be observed for H3.1 [27].…”

Epigenetics in the Human Brain

“…In addition to the core histones H2A/H2B/H3/H4, metazoan genomes encode histone variants ,such as H3.3, H2A.Z, and H2A.X (Figure 1), that in contrast to the canonical histones are subject to replication-independent expression and assembly (Woodcock, 2006), with strong effects on nucleosome stability and compaction (Jin and Felsenfeld, 2007). It is generally thought that RNA polymerase and the transcriptional activation and elongation complexes destabilize nucleosomes, promoting nucleosome remodeling, and variant histone incorporation, which then further potentiate or stabilize gene expression (Bintu et al, 2011;Sutcliffe et al, 2009).…”

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

“…In addition to regulated nucleosome assembly and disassembly through the action of histone chaperones and chromatin remodelers, nucleosome stability is influenced by histone modifications, histone variants, DNA features encoded in cis, and competition with DNA-binding factors in trans . A complete picture of the mechanisms governing nucleosome stability is fundamental to understanding how gene expression is dynamically regulated.Nucleosome stability has been studied in vitro using sensitivity to enzymatic digestion or salt concentration (Bloom and Anderson 1978;Burton et al 1978;Li et al 1993;Polach and Widom 1995;Wu and Travers 2004;Jin and Felsenfeld 2007). Genome-wide adaptations of these methods have been used to identify nucleosome position and stability in vivo.…”

“…Nucleosome stability has been studied in vitro using sensitivity to enzymatic digestion or salt concentration (Bloom and Anderson 1978;Burton et al 1978;Li et al 1993;Polach and Widom 1995;Wu and Travers 2004;Jin and Felsenfeld 2007). Genome-wide adaptations of these methods have been used to identify nucleosome position and stability in vivo.…”