Transcriptomics,Genomics

Dataset Information

42

Global effect of H2A.Z hypervariant knockdown on basal expression of neuronal genes


ABSTRACT: Variant histone H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the process remains perplexing. In vertebrates, H2A.Z has two hypervariants – H2A.Z.1 and H2A.Z.2 – that have almost identical amino-acid sequences excepting three residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated mature cortical neurons, we asked if H2A.Z hypervariants have functional specificity 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 non-overlapping gene-sets, including genes that code for several synaptic proteins. In response to neuronal activity, depletion of H2A.Z hypervariants impairs transcription of our model gene Arc differentially. As part of the +1 nucleosome, H2A.Z.2, not H2A.Z.1, is necessary for rapid immediate-early transcription by facilitating RNA Pol II promoter proximal pausing. In contrast, H2A.Z.1 plays complicated and perhaps indirect roles that affect Arc transcription kinetics context-dependently. Context-dependent roles of H2A.Z hypervariants are also evident amongst several other immediate early genes where their regulatory roles 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. Overall design: Seven-day-old rat dissociated cortical neurons were treated with lentiviruses expressing shRNA against H2A.Z.1 or H2A.Z.2 mRNA (versus scrambled shRNA as control) for seven days and gene expression was tested by microarray.

INSTRUMENT(S): Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Feature Number version)

SUBMITTER: NIEHS Microarray Core  

PROVIDER: GSE96886 | GEO | 2017-09-14

SECONDARY ACCESSION(S): PRJNA379995

REPOSITORIES: GEO

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Publications

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

Dunn Carissa J CJ   Sarkar Pushpita P   Bailey Emma R ER   Farris Shannon S   Zhao Meilan M   Ward James M JM   Dudek Serena M SM   Saha Ramendra N RN  

eNeuro 20170701 4


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 c  ...[more]

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