Histone Hypervariants H2A.Z.1 and H2A.Z.2 Play Independent and Context-Specific Roles in Neuronal Activity-Induced Transcription ofArc/Arg3.1and Other Immediate Early Genes

Abstract

The histone variant H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the transcriptional process remains perplexing. In vertebrates, H2A.Z has two hypervariants, H2A.Z.1 and H2A.Z.2, that have almost identical sequences except for three amino acid residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated rat cortical neurons, we asked if H2A.Z hypervariants have distinct functions in regulating basal and activity-induced gene transcription. Hypervariant-specific RNAi and microarray analyses revealed that H2A.Z.1 and H2A.Z.2 regulate basal expression of largely nonoverlapping gene sets, including genes that code for several synaptic proteins. In response to neuronal activity, rapid transcription of our model gene Arc is impaired by depletion of H2A.Z.2, but not H2A.Z.1. This impairment is partially rescued by codepletion of the H2A.Z chaperone, ANP32E. In contrast, under a different context (after 48 h of tetrodotoxin, TTX), rapid transcription of Arc is impaired by depletion of either hypervariant. Such context-dependent roles of H2A.Z hypervariants, as revealed by our multiplexed gene expression assays, are also evident with several other immediate early genes, where regulatory roles of these hypervariants vary from gene to gene under different conditions. Together, our data suggest that H2A.Z hypervariants have context-specific roles that complement each other to mediate activity-induced neuronal gene transcription.

Learning and Age-Related Changes in Genome-wide H2A.Z Binding in the Mouse Hippocampus

“…H2A.Z accumulated primarily in exons and 5’UTR regions, with minimal changes occurring in introns, intergenic regions, and non-coding RNA (Figure 2b). A GO enrichment analysis revealed H2A.Z accumulation in categories that include positive and negative regulators of transcription, as well as ubiquitin protein ligase activity (Figure 2e), consistent with a recent study demonstrating H2A.Z-mediated regulation of the ubiquitin proteasome system (Dunn et al, 2017). Combined with evidence for age-related accumulation of H3.3 (Maze et al, 2015), our data suggest that the composition of histone subtypes that make up nucleosomes is subject to age-related changes, which may influence the overall chromatin landscape in aged mice.…”

“…Consistent with those findings, we now show that Arc (Virus × Training interaction: F 1,15 = 7.39, p = 0.02) expression is also elevated 1h after fear conditioning in H2A.Z-depleted mice. Such bidirectional effects of H2A.Z depletion were previously reported (Dunn et al, 2017, Weber et al, 2014), and suggest that H2A.Z can promote or repress learning-induced gene expression, while producing minimal effects on basal transcription.…”

“…We previously showed that learning-induced eviction of H2A.Z from nucleosomes immediately downstream of the TSS is positively associated with the expression of memory-related genes, whereas H2A.Z depletion resulted in both up- and down-regulation of gene expression under basal conditions (Zovkic et al, 2014). Moreover, H2A.Z depletion produced context-specific effects on transcription in rat primary cortical neurons (Dunn et al, 2017), reinforcing a complex regulatory function of H2A.Z in the brain.…”

“…Although DNA methylation and post-translational modifications of histones have well-established roles in memory (Day and Sweatt 2011), a role for histone variants was only recently identified (Dunn et al, 2017, Michod et al, 2012, Zovkic et al, 2014, Maze et al, 2015). H2A.Z, a variant of histone H2A, is actively exchanged in response to learning and H2A.Z depletion in the hippocampus or the medial prefrontal cortex enhances memory, suggesting that H2A.Z is a memory suppressor (Zovkic et al, 2014).…”

Non-redundant functions of H2A.Z.1 and H2A.Z.2 in chromosome segregation and cell cycle progression

“…In DT40 chicken cells, knock-out of H2A.Z.2 results in a slower cell proliferation rate compared to the wild type and H2A.Z.1 knock-out cells 26 , while in humans, Floating-Harbor syndrome 27 and malignant melanoma 28 have been specifically linked to H2A.Z.2 27 . In addition, both variants seem to play independent roles in the transcription of some genes involved in the response to neuronal activity 29 . Moreover, very recently, it was shown that the differences between H2A.Z.1 and H2A.Z.2 on transcription regulation seems to depend more on the relative level of the two paralogues rather than on their chromatin localisation 30 .…”