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Expression analysis of WT and Zbtb4 -/- mouse primary fibroblasts

ABSTRACT: ZBTB4 is a mammalian transcription factor with Zinc fingers and a BTB/POZ domain, which can bind methylated CpGs, as well as certain unmethylated consensus sequences. ZBTB4 is frequently downregulated in human cancers, but it is unclear whether this is a cause or consequence of transformation. To investigate the role of ZBTB4 in normal and pathological conditions, we generated Zbtb4-/- mice

ORGANISM(S): Mus musculus

PROVIDER: GSE77816 | GEO | 2016/11/10

SECONDARY ACCESSION(S): PRJNA311631

REPOSITORIES: GEO

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ChIP-seq with anti-ZBTB17 antibody in HeLa cells to find target genes

Project description:ZBTB17 belongs to the ZBTB (zinc finger and BTB domain protein family) family, which contains a BTB domain at the N-terminus and multiple zinc fingers at the C-terminus. In this dataset, ChIP-seq experiment was performed with anti-ZBTB17 antibody.

2024-08-20 | GSE239778 | GEO

ZBTB2 as a novel reader for unmethylated DNA

Project description:In this study, we investigated the dynamics during differentiation of the in vivo binding sites of ZBTB2, a putative reader for unmethylated DNA. We performed DNA pull-downs followed by mass spectrometry, using a genomic sequence containing either unmethylated or methylated CpGs, to study the influence of DNA methylation on ZBTB2 binding. Additionally, we performed interaction proteomics to identify ZBTB2 interaction partners. We found that ZBTB2 recruits a zinc finger module of three proteins to unmethylated DNA.

2018-01-29 | PXD007099 | Pride

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

Project description:Cys2-His2 zinc finger proteins (ZFPs) are the largest group of transcription factors in higher metazoans. A complete characterization of these ZFPs and their associated target sequences is pivotal to fully annotate transcriptional regulatory networks in metazoan genomes. As a first step in this process, we have characterized the DNA-binding specificities of 130 Zinc finger sets from Drosophila melanogaster using a bacterial one-hybrid system. This data set contains the DNA-binding specificities for at least one encoded ZFP from 71 unique genes and 22 alternate splice isoforms. This represents the largest block of characterized ZFPs from any organism described to date. These recognition motifs can be used to predict genomic binding sites and potential regulatory targets for these factors within the fruit fly genome. We have characterized subsets of fingers from these ZFPs to define the correct orientation and register of the zinc fingers on their defined binding sites. By correlating individual fingers with motif subsites, we can assign finger specificity throughout each ZFP. This reveals the diversity of recognition potential within the naturally-occurring zinc fingers of a single organism, where the characterized fingers can specify 47 of the 64 possible DNA triplets. To confirm the utility of our finger recognition models, we have employed subsets of Drosophila fingers in combination with an existing archive of zinc finger modules to create ZFPs with novel DNA-binding specificity. These finger combinations can be used to create novel functional Zinc Finger Nucleases for editing vertebrate genomes. Illumina sequencing of Barcoded Binding sites obtained after B1H selection of Cys2-His2 zinc finger proteins cloned as a C-terminal fusions to the omega subunit of E. coli RNA polymerase in the B1H system.

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Truncated PARP1 promotes RNA Polymerase III during apoptosis

Project description:The N-terminal three zinc finger motifs of PARP1 are evolutionarily conserved in multicellular organism。However, during apoptosis, human PARP1 is mainly cleaved by caspase 3 at D214. As a result, the truncated PARP1 loses two N-terminal zinc finger motifs and only contains the third zinc finger motif, the BRCT domain, the WGR domain and the C-terminal catalytic domain. Interestingly, when we explored the domain architecture of PARP1 in other organisms, we found that similar to human tPARP1, PARP1 orthologs in several lower organisms do not have the N-terminal two zinc fingers or even they lack the third zinc finger motif. It indicates that even without the first two zinc finger motifs, tPARP1 may still catalyze ADP-ribosylation and play an important role in certain biological processes. To reveal the biological function of tPARP1, we performed tandem affinity purification and searched for the possible substrates.

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Stage- and cell type-specific requirements of ikzf1 during hematopoietic differentiation in zebrafish [it325]

Project description:The characterisation of two zebrafish ikzf1 mutant lines missing the two C-terminal zinc fingers only and both part of the DNA binding domain plus the C-terminal zinc fingers respectively gives insight into the specific roles of these elements during zebrafish hematopoiesis

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Stage- and cell type-specific requirements of ikzf1 during hematopoietic differentiation in zebrafish [ikaros]

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Gene expression in mature CD4 and CD8 from WT mice and mature CD4 from DBTBLZ or Mta2-DBTBLZ retrogenic mice

Project description:T cell precursors develop into cytotoxic CD8 and helper CD4+ T cells in thymus. Thpok, a BTB/POZ family transcription factor, enforces commitment to the CD4 lineage and suppresses cytotoxic gene expression. However, it is still not fully understood how Thpok directs CD4 T cell development. Here, using mass-spectrometry, we identify nucleosome remodeling and deacetylase (NuRD) complex as a novel Thpok cofactor. We demonstrate that the Thpok BTB domain is essential for NuRD recruitment. Reconstituting NuRD binding to a BTB-less version of Thpok (which cannot bind NuRD) restored CD4 T cell in vivo. RNA sequencing showed that CD4 T cells expressing the reconstituted protein express a transcriptome similar to that of CD4 T cells expressing Thpok. Thus, our results demonstrate that NuRD recruitment is both necessary and sufficient for the function of the Thpok BTB domain in CD4 T cell development.

2022-06-10 | GSE171610 | GEO

Stage- and cell type-specific requirements of ikzf1 during haematopoietic differentiation in zebrafish

Project description:The zinc finger transcription factor Ikaros1 (Ikzf1) is required for lymphoid development in mammals. It is characterized by the presence of four zinc fingers in its DNA binding domain and two zinc fingers in the C-terminal protein interaction module. Here, we describe the phenotypes of zebrafish homozygous for two distinct mutant ikzf1 alleles. The IT325 variant lacks the C-terminal two zinc fingers, whereas the fr105 variant retains only the first zinc finger of the DNA binding domain. Our results indicate that an intact ikzf1 gene is required for larval T cell development, whereas low levels of adult lymphoid development recover in the mutants. By contrast, the mutants exhibit a signature of increased myelopoiesis at larval and adult stages. Of note, both mutants stimulate erythroid differentiation in larvae, indicating that the C-terminal zinc fingers negatively regulate the extent of red blood cell production. An unexpected differential effect of the two mutants on adult erythropoiesis suggests a direct requirement of an intact DNA binding domain for entry of progenitors into the red blood cell lineage. Collectively, our results reinforce the biological differences between larval and adult haematopoiesis, indicate a stage-specific function of ikzf1 in regulating the hierarchical bifurcations of differentiation, and assign distinct functions to the DNA binding domain and the C-terminal zinc fingers.

2022-12-09 | GSE200756 | GEO

Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants.

2012-12-06 | GSE42709 | GEO

NuRD complex recruitment to Thpok mediates CD4+ T cell lineage differentiation

Project description:Although BTB-zinc finger (BTB-ZF) transcription factors control the differentiation of multiple hematopoietic and immune lineages, how they function is poorly understood. The BTB-ZF factor Thpok controls intrathymic CD4+ T cell development and expression of most CD4+- and CD8+-lineage genes. Here, we identify the nucleosome remodeling and deacetylase (NuRD) complex as a novel Thpok cofactor. We locate three amino-acid residues within the Thpok BTB domain that are required for both NuRD binding and Thpok functions, and show that NuRD recruitment recapitulates the functions of the Thpok BTB domain. NuRD mediates Thpok repression of CD8+-lineage genes, including the transcription factor Runx3, but is dispensable for Cd4 expression. We show that these functions cannot be performed by the BTB domain of the Thpok-related factor Bcl6, which fails to bind NuRD. Thus, cofactor binding critically contributes to the functional specificity of BTB-zinc finger factors, which control the differentiation of most hematopoietic subsets.

2022-06-10 | GSE199739 | GEO

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