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Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [RNA-Seq1]

ABSTRACT: In this experiment, we sought to analyze how transcriptome of WT and PATZ1 knock-out (KO) cells change in mouse embryonic stem cells (ESCs)

ORGANISM(S): Mus musculus

PROVIDER: GSE230477 | GEO | 2024/08/21

REPOSITORIES: GEO

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Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq1]

Project description:In this experiment, we sought to identify how the distribution of CTCF, MAZ, PATZ1, RAD21 change in WT and PATZ1 KO mouse embryonic stem cells (ESCs).

2024-08-21 | GSE230479 | GEO

Members of an array of zinc finger proteins specify distict Hox chromatin boundaries [Micro-C]

Project description:In this experiment, we sought to identify how genome organization change in WT versus PATZ1 KO cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

2024-08-21 | GSE266849 | GEO

Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [RNA-Seq2]

Project description:In this experiment, we sought to analyze how transcriptome of WT and PATZ1 knock-out (KO) cells change during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs)

2024-08-21 | GSE230478 | GEO

Members of an array of zinc finger proteins specify distict Hox chromatin boundaries [ChIP-seq]

Project description:In this experiment, we sought to identify how the distribution of RAD21 and ZNF263 change in WT, PATZ1 KO, and ZNF263 KO cells during differentiation of mouse embryonic stem cells (ESCs) into cervical motor neurons (MNs).

2024-08-21 | GSE266783 | GEO

Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq2]

Project description:In this experiment, we sought to identify how the distribution of CTCF, MAZ, and RAD21 change in CTCF-degron (no auxin), CTCF-degron (auxin), CTCF-degron MAZ KO (no auxin), and CTCF-degron MAZ KO (auxin) backgrounds in mouse embryonic stem cells (ESCs).

2024-08-21 | GSE230481 | GEO

Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-08-21 | GSE230482 | GEO

Differentially expressed zinc finger proteins during human adipogenesis

Project description:To investigate the collective role of zinc finger proteins in adipogenesis, we induced adipogenesis using human mesenchymal stem cells (MSC) and compared the gene expression profiles using human Illumina beads arrays. We performed three independent experiments of time-series analysis (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d after induction of adipogenesis) in order to comprehensively capture the dynamic profiles of transcriptome during differentiation. Statistical filtering based on Analysis of Variance (ANOVA; p-value < 0.001, FDR 5%) and Gene Ontology classification using the Human Gene Nomenclature Database (HGNC) identified 618 out of 678 zinc finger proteins (ZFPs) that were significantly expressed during adipogenesis. Moreover, 34 out of 618 genes were differentially expressed more than 2-fold up or down regulated. The K-means clustering analysis further revealed four dynamic expression patterns: one gene in early-response, seven genes in transient, twenty genes in progressively-induced and four genes in the down-regulated, demonstrating the dynamic involvement of ZFPs in the process of adipocyte differentiation and maturation. Total RNA obteind from 10 different time points (0h, 1h, 12h, 24h, 2d, 4d, 6d, 9d, 12d, 15d) during adipogenesis from human Mesenchymal stem cell (MSC) to Adipocyte (ADP). Adipogensis was induced by the different cocktail of chemical compunds containing human-insulin, dexamethasone, indomethacin and IBMX.

2012-12-01 | E-GEOD-37836 | biostudies-arrayexpress

Multiparameter functional diversity of human C2H2 zinc finger proteins

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-10-25 | E-GEOD-76496 | biostudies-arrayexpress

Differentially expressed zinc finger proteins during human adipogenesis

2012-12-01 | GSE37836 | GEO

Recognition of polyadenosine RNA by zinc finger proteins.

Project description:Messenger RNA transcripts are coated from cap to tail with a dynamic combination of RNA binding proteins that process, package, and ultimately regulate the fate of mature transcripts. One class of RNA binding proteins essential for multiple aspects of mRNA metabolism consists of the poly(A) binding proteins. Previous studies have concentrated on the canonical RNA recognition motif-containing poly(A) binding proteins as the sole family of poly(A)-specific RNA binding proteins. In this study, we present evidence for a previously uncharacterized poly(A) recognition motif consisting of tandem CCCH zinc fingers. We have probed the nucleic acid binding properties of a yeast protein, Nab2, that contains this zinc finger motif. Results of this study reveal that the seven tandem CCCH zinc fingers of Nab2 specifically bind to polyadenosine RNA with high affinity. Furthermore, we demonstrate that a human protein, ZC3H14, which contains CCCH zinc fingers homologous to those found in Nab2, also specifically binds polyadenosine RNA. Thus, we propose that these proteins are members of an evolutionarily conserved family of poly(A) RNA binding proteins that recognize poly(A) RNA through a fundamentally different mechanism than previously characterized RNA recognition motif-containing poly(A) binding proteins.

| S-EPMC1941466 | biostudies-literature

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