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

ABSTRACT: 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).

ORGANISM(S): Mus musculus

PROVIDER: GSE266849 | GEO | 2024/08/21

REPOSITORIES: GEO

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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 [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 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 distinct Hox chromatin boundaries [RNA-Seq1]

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

2024-08-21 | GSE230477 | 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

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

Expression of the zinc-finger gene PLZF at rhombomere boundaries in the vertebrate hindbrain.

Project description:To investigate the potential biological role(s) of the PLZF gene, discovered as a fusion with the RARA locus in a patient with acute promyelocytic leukemia harboring a t(11;17) chromosomal translocation, we have isolated its murine homologue (mPLZF) and studied its patterns of developmental expression. The levels of mPLZF mRNAs increased perinatally in the liver, heart, and kidney, but with the exception of the heart, they were either absent or very low in the adult tissues. In situ analysis of mPLZF expression in mouse embryos between 7.0 and 10.5 days of development revealed that mPLZF mRNAs and proteins were coexpressed in spatially restricted and temporally dynamic patterns in the central nervous system. In the hindbrain region, a segmental pattern of expression correlated with the development of the rhombomeres. From 9.0 days of development, starting first in rhombomeres 3 and 5, there was an ordered down-regulation of expression in the center of each rhombomere, so that 1 day later elevated levels of mPLZF mRNAs and proteins were restricted to cells surrounding the rhombomeric boundaries. The chicken homologue of the PLZF gene, which we have also cloned, demonstrated a similar segmental pattern of expression in the hindbrain. To date, PLZF represents the only example of a transcription factor with elevated expression at rhombomeric boundaries. The high degree of evolutionary conservation between the patterns of PLZF expression during mammalian and avian central nervous system development suggests that it has an important functional role in the regionalization of the vertebrate hindbrain, potentially regulating boundary cell interactions.

| S-EPMC42461 | biostudies-other

PATZ1 is a DNA damage responsive transcription factor that inhibits p53 function

Project description:Insults to cellular health cause p53 protein accumulation and loss of p53 function leads to tumorigenesis. Thus, p53 has to be tightly controlled. Here we report that the BTB/POZ domain transcription factor PATZ1 (MAZR), previously known for its transcriptional suppressor functions in T lymphocytes, is a crucial regulator of p53. The novel inhibitory role of PATZ1 on the p53 protein marks it as a proto-oncogene. PATZ1 deficient cells have reduced proliferative capacity which we assess by RNASeq and real time cell growth rate analysis. PATZ1 modifies the expression of p53 target genes associated with cell proliferation gene ontology terms. Moreover, PATZ1 regulates several genes involved in cellular adhesion and morphogenesis. Significantly, treatment with the DNA damage inducing drug doxorubicin results in the loss of the PATZ1 transcription factor, as p53 accumulates. We find that PATZ1 binds to p53 and inhibits p53 dependent transcription activation. We examine the mechanism of this functional inhibitory interaction and demonstrate that PATZ1 excludes p53 from DNA binding. This study documents PATZ1 as a novel player in the p53 pathway. RNA-seq was used to define differentially expressed genes in wild-type and PATZ1-/- MEFs. Each sample was represented in triplicate.

2015-03-27 | E-GEOD-65864 | biostudies-arrayexpress

The tandem zinc finger RNA binding domain of members of the tristetraprolin protein family.

Project description:Tristetraprolin (TTP), the prototype member of the protein family of the same name, was originally discovered as the product of a rapidly inducible gene in mouse cells. Development of a knockout (KO) mouse established that absence of the protein led to a severe inflammatory syndrome, due in part to elevated levels of tumor necrosis factor (TNF). TTP was found to bind directly and with high affinity to specific AU-rich sequences in the 3'-untranslated region of the TNF mRNA. This initial binding led to promotion of TNF mRNA decay and inhibition of its translation. Many additional TTP target mRNAs have since been identified, some of which are cytokines and chemokines involved in the inflammatory response. There are three other proteins in the mouse with similar activities and domain structures, but whose KO phenotypes are remarkably different. Moreover, proteins with similar domain structures and activities have been found throughout eukaryotes, demonstrating that this protein family arose from an ancient ancestor. The defining characteristic of this protein family is the tandem zinc finger (TZF) domain, a 64 amino acid sequence with many conserved residues that is responsible for the direct RNA binding. We discuss here many aspects of this protein domain that have been elucidated since the original discovery of TTP, including its sequence conservation throughout eukarya; its apparent continued evolution in some lineages; its functional dependence on many key conserved residues; its "interchangeability" among evolutionarily distant species; and the evidence that RNA binding is required for the physiological functions of the proteins. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.

| S-EPMC6570553 | biostudies-literature

CTCF-mediated topological boundaries during development foster appropriate gene regulation

Project description:In this experiment, we performed 5C across a 4Mb region surrounding the HoxA region in WT and Δ5|6:7|9 ESCs and MNs

2017-02-10 | GSE83124 | GEO