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ABSTRACT: EPIGENETIC MODULATION USING A PEPTIDE OF THE C-TERMINAL UNSTRUCTURED TAIL OF H2A.Z.

PROVIDER: PRJNA853352 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19870491_1.fastq.gz	Fastqsanger.gz
	SRR19870491_2.fastq.gz	Fastqsanger.gz
	SRR19870492_1.fastq.gz	Fastqsanger.gz
	SRR19870492_2.fastq.gz	Fastqsanger.gz
	SRR19870493_1.fastq.gz	Fastqsanger.gz

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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

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

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (ChIP-Seq)

Project description:To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84 % of misexpressed genes. Finally, our hypothesis that the N-terminal tail of Arabidopsis H2A.Z is not crucial for its overall function was supported by the ability of N-terminal end truncations of Arabidopsis HTA11 to largely rescue the defects of h2a.z mutants.

2024-05-13 | GSE263312 | GEO

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z + HsH2A.Z. RNA-Seq)

2024-05-13 | GSE263311 | GEO

2024-05-13 | GSE263310 | GEO

Gallus gallus

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

| PRJNA287820 | ENA

The Histone Variant H2A.Z C-terminal Domain Has Locus- Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization

Project description:The incorporation of histone variant H2A.Z, a conserved H2A variant, into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, including transcription. H2A.Z-containing nucleosomes may poise gene regulatory regions for transcription, but mechanistic details are lacking. In Saccharomyces cerevisiae, the diverging H2A.Z C-terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C-terminus genome wide, we made use of derivatives where the C-terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide, with the idea of regenerating the H2A.Z-dependent regulation globally. An assessment of the genome-wide distribution of these H2A.Z derivatives shows that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of the targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency vs nucleosome positioning varies enormously, depending on loci analyzed. For the ZA protein, positioning changes most importantly near origins of replication and snoRNA gene promoters, while incorporation is affected on all other sites. Furthermore, the role of H2A.Z in global transcription regulation also depends on its C-terminal region. Remarkably however, the latter mostly involves genes without a H2A.Z nucleosome in the promoter.

2022-08-18 | GSE156492 | GEO

H2A.Z.1 mono-ubiquitylation antagonizes BRD2 to maintain poised chromatin in ESCs [ChIP-seq]

Project description:Histone variant H2A.Z occupies the promoters of active and poised, bivalent genes in ESCs to regulate developmental programs, yet how it contributes to these contrasting states is poorly understood. Here, we investigate the function of H2A.Z.1 mono-ubiquitylation (H2A.Z.1ub) by mutation of the PRC1 target residues (H2A.Z.1K3R3). We show that H2A.Z.1K3R3 is properly incorporated at target promoters in murine ESCs (mESCs), however, loss of mono-ubiquitylation leads to de-repression of bivalent genes, loss of Polycomb binding, and to faulty lineage commitment. Using quantitative proteomics, we find that tandem bromodomain proteins, including the BET family member Brd2, are enriched in H2A.Z.1 chromatin. We further show that Brd2 is gained at de-repressed promoters in H2A.Z.1K3R3 mESCs whereas Brd2 inhibition restores gene silencing at these sites. Together, our study reveals an antagonistic relationship between H2A.Z.1ub and Brd2 to regulate the transcriptional balance at bivalent genes to enable proper execution of developmental programs. ChIP-Seq analysis on mouse embryonic stem cells harboring H2A.Z or H2A.Z.K3R3 (3 C-terminal lysines mutated to arginines) tagged with YFP, in the presence of a knockdown hairpin targeting the endogenous H2A.Z transcript.

2016-01-21 | E-GEOD-53206 | biostudies-arrayexpress

Reactivity of commercial antibodies targeting human histone H2B N-terminal tail on the Intel array platform

Project description:The aim of the study was to test the Intel array platform and map the H2B epitopes bound by commercial antibody reagents. We also tested the ability of SET7 PKMT to methylate Intel array peptides. We diluted antibody reagents 1:1000 and incubated dilutions on the silicon-based Intel array platorm. We mapped antibody binding epitopes and SET7 PKMT methylation target peptides using a novel, silicon-based array platform with 8820 individual peptide features comprising every possible contiguous peptide from 1-21 a.a. in length within the 21-mer N-terminal tail of human histone H2B.

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A negatively-charged region within C-terminal domain maintains proper CTCF DNA binding (ATAC-Seq)

Project description:As an essential regulator of higher-order chromatin structures, CTCF is a highly conserved DNA binding protein with a central DNA-binding domain of 11 tandem zinc fingers, which are flanked by N- and C-terminal domains of intrinsically disordered regions. The N-terminal domain interacts with cohesin complex and the central ZF domains recognize a large range of diverse genomic sites. However, the function of C-terminal unstructured domain remains less understood. Here, we found that deletion of C-terminal fragment of 116 amino acid increases CTCF-DNA binding. By genetic dissection of this fragment, we uncovered a negatively-charged region responsible for repressing CTCF binding to DNA. Thus, the unstructured C-terminal domain play an important role in maintaining proper CTCF-DNA interactions.

2024-11-30 | GSE261213 | GEO

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