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Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

ABSTRACT: The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 double knock out (KO) cells in chicken DT40 cells. The expression pattern of H2A.Z-1 and H2A.Z-2 double KO cells was compared with WT cells to characterize the genes regulated by H2A.Z-1 and H2A.Z-2. We used microarrays to analysis the alternation of gene expression between WT and H2A.Z double KO cells and identify classes of up or down regulated gene by H2A.Z-1 and H2A.Z-2.

ORGANISM(S): Gallus gallus

PROVIDER: GSE35430 | GEO | 2015/11/04

SECONDARY ACCESSION(S): PRJNA152767

REPOSITORIES: GEO

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Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

Project description:The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 double knock out (KO) cells in chicken DT40 cells. The expression pattern of H2A.Z-1 and H2A.Z-2 double KO cells was compared with WT cells to characterize the genes regulated by H2A.Z-1 and H2A.Z-2. We used microarrays to analysis the alternation of gene expression between WT and H2A.Z double KO cells and identify classes of up or down regulated gene by H2A.Z-1 and H2A.Z-2. In H2A.Z-1 and H2A.Z-2 double KO cells, H2A.Z-2 is knocked out constitutively, but H2A.Z-1 conditionally by tetracycline. The expression of H2A.Z-1 transgene is suppressed completely when H2A.Z-1 and H2A.Z-2 double KO cells culture with tetracycline for three days. For this reason, we prepared the total RNA of WT cells and H2A.Z-1and H2A.Z-2 double KO cells treated with tetracycline for three days and hybridization on Affymetrix microarrays.

2015-11-04 | E-GEOD-35430 | biostudies-arrayexpress

Expression data from H2A.Z isoforms single KO cells

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Genetic complementation analysis revealed distinct contributions of the N-terminal tail of H2A.Z to epigenetic regulations

Project description:The histone variant H2A.Z is one of the most evolutionally conserved histone variants. In vertebrates, two isoforms, H2A.Z.1 and H2A.Z.2, are identified and are involved in multiple epigenetic regulations. However, the role of H2A.Z in epigenetic regulations largely remains unknown especially in vertebrate. Previously, we derived tetracycline-inducible H2A.Z isofmrs double knockout (DKO) cells by using DT40 cells. With this cell, we showed that H2A.Z DKO leads to defects in mitotic progression and gene expression. To elucidate the function of H2A.Z further, we established genetic complementation system and confirmed that introducing exogenous H2A.Z complemented phenotypes of H2A.Z DKO cells. Given that acetylation of the N-terminal tail of H2A.Z reportedly contributes to significant roles in H2A.Z functions, we introduced two types of H2A.Z mutants, non-acetylable H2A.Z (5KR-H2A.Z) and chimeric H2A.Z in which its N-terminal tail is replaced with that of canonical H2A (H2A-H2A.Z), into H2A.Z DKO cells. These H2A.Z mutants complemented defects in mitotic progression. However, significant transcriptional dysregulation was observed in H2A.Z DKO cells stably expressing 5KR-H2A.Z and H2A-H2A.Z. These results suggest that the core domain and the N-terminal tail of the vertebrate H2A.Z contribute individually to mitotic progression and transcription regulation, respectively.

2017-08-21 | GSE70182 | GEO

Effect of modified H2A.Z protein to gene expression in DT40 cells.

Project description:H2A.Z-nucleosomes participate in both euchromatin and heterochromatin and it has proven difficult to reveal how the disparate roles and stability features imparted by H2A.Z are connected. Using an in situ assay of nucleosome stability in nuclei of DT40 cells expressing engineered forms of the variant we show that H2A.Z is released from nucleosomes of peripheral heterochromatin at unusually high salt concentrations, compared to cells expressing C-terminally truncated H2A.Z. Binding of the tail-peptide (C9) to reconstituted nucleosomes, DNA and the nuclear lamina were detected. Upon treatment of HeLa nuclei with C9, the H2A.Z-nucleosomes assumed canonical stability, the peripheral heterochromatin became dispersed and overall nuclease sensitivity increased, recapitulating tail-dependent differences in DT40. When introduced into live cells, C9 elicited chromatin reorganization and transcriptional down-regulation of ~600 genes. Thus, large-scale epigenetic modulation can be achieved by targeting or making advantage of molecular interactions involving the C-terminal tail of H2A.Z.

2023-02-23 | GSE225680 | GEO

Anp32e is a histone chaperone that removes H2A.Z from chromatin

Project description:We report a genome wide enrichment, redistribution and accumulation of H2A.Z at specific chromatin control regions, in particular at enhancers and insulators, in mouse embryonic fibroblasts depleted for Anp32e (MEFs Anp32e-/-). H2A.Z ChIP-seq in MEFs WT (+/+) or KO (-/-) for Anp32e.

2014-01-22 | E-GEOD-51579 | biostudies-arrayexpress

Effect of modified H2A.Z protein to gene expression in DT40 cells.

Project description:Effect of modified H2A.Z protein to gene expression in DT40 cells.

| PRJNA936993 | ENA

Project description:In eukaryotes, DNA wraps around histones to form nucleosomes, which are compacted into chromatin. DNA-templated processes, including transcription, require chromatin disassembly and reassembly mediated by histone chaperones. Additionally, distinct histone variants can replace core histones to regulate chromatin structure and function. Although replacement of H2A with the evolutionarily conserved H2A.Z via the SWR1 histone chaperone complex has been extensively studied, in plants little is known about how a reduction of H2A.Z levels can be achieved. Here, we show that NRP proteins cause a decrease of H2A.Z-containing nucleosomes in Arabidopsis under standard growing conditions. nrp1-1 nrp2-2 double mutants show an over-accumulation of H2A.Z genome-wide, especially at heterochromatic regions normally H2A.Z-depleted in wild-type plants. Our work suggests that NRP proteins regulate gene expression by counteracting SWR1, thereby preventing excessive accumulation of H2A.Z.

2020-05-18 | PXD019248 | Pride

Histone variant H2A.Z.2 mediates proliferation and drug sensitivity of malignant melanoma [native ChIP-seq]

Project description:Here we report a novel role for H2A.Z.2 (H2AFV) as a mediator of cell proliferation and sensitivity to targeted therapies in malignant melanoma. While both H2A.Z.1 and H2A.Z.2 are highly expressed in metastatic melanoma and correlate with decreased patient survival, only H2A.Z.2 deficiency results in impaired cellular proliferation of melanoma cells, which occurs via a G1/S arrest. Integrated gene expression and ChIP-seq analyses revealed that H2A.Z.2 positively regulates E2F target genes, and that such genes acquire a distinct H2A.Z occupancy signature over the promoter and gene body in metastatic melanoma cells. We further identified the BET family member BRD2 as an H2A.Z-interacting protein in melanoma cells, and demonstrate that H2A.Z.2 silencing cooperates with BET inhibition to induce cell death. Mononucleosomes from SK-mel147 (wt and stably expressing eGFP-H2A. eGFP-H2A.Z.1 and eGFP-H2A.Z.2) and melanocytes were isolated for ChIP with H2A.Z antibody or GFP trap beads (Chromotek).

2015-07-01 | E-GEOD-68222 | biostudies-arrayexpress

Gallus gallus

Project description:Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

| PRJNA152767 | ENA

Gene expression profiles of Tet1 knockout (T1KO), Tet2 knockout (T2KO) and Tet1/Tet2 double knockout (DKO) mouse embryonic stem cells.

Project description:Global gene expression profile of single and double mutant mouse ES cells were compared to wt ES cells. Two male Tet1 KO, one male Tet2 KO, two male double KO, two female double KO, two male WT and two female WT mouse ES cells were compared.

2013-02-01 | GSE42991 | GEO

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