Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Zrf1 is required to establish and maintain neural progenitor identity (ChIP-Seq)

ABSTRACT: We report ChIP-seq data for Zrf1 and Ring1B occupancy in NPC Examination and comparison of DNA binding profile of Zrf1 and Ring1B in NPC

ORGANISM(S): Mus musculus

SUBMITTER: Luciano Di Croce

PROVIDER: E-GEOD-53540 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Zrf1 is required to establish and maintain neural progenitor identity.

Aloia Luigi L Di Stefano Bruno B Sessa Alessandro A Morey Lluis L Santanach Alexandra A Gutierrez Arantxa A Cozzuto Luca L Benitah Salvador Aznar SA Graf Thomas T Broccoli Vania V Di Croce Luciano L

Genes & development 20140101 2

The molecular mechanisms underlying specification from embryonic stem cells (ESCs) and maintenance of neural progenitor cells (NPCs) are largely unknown. Recently, we reported that the Zuotin-related factor 1 (Zrf1) is necessary for chromatin displacement of the Polycomb-repressive complex 1 (PRC1). We found that Zrf1 is required for NPC specification from ESCs and that it promotes the expression of NPC markers, including the key regulator Pax6. Moreover, Zrf1 is essential to establish and maint ...[more]

PMID: 24449271

Similar Datasets

Zrf1 is required to establish and maintain neural progenitor identity

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

2013-12-21 | E-GEOD-53542 | biostudies-arrayexpress

Zrf1 is required to establish and maintain neural progenitor identity (ChIP-Seq)

Project description:We report ChIP-seq data for Zrf1 and Ring1B occupancy in NPC

2013-12-21 | GSE53540 | GEO

Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)

Project description:Our work aims to characterize the role of Zrf1 in the generation and maintenance of neural progenitor cells (NPCs) Gene expression profile of shCtrl and shZrf1 cells during generation of RGC-like NPC from ESC at day 6 of neural induction. Cells were grown according to this protocol: Bibel et al, Nat Prot., 2007

2013-12-21 | E-GEOD-53541 | biostudies-arrayexpress

Zrf1 is required to establish and maintain neural progenitor identity (mRNA array)

Project description:Our work aims to characterize the role of Zrf1 in the generation and maintenance of neural progenitor cells (NPCs)

2013-12-21 | GSE53541 | GEO

The Polycomb protein Pcgf2/Mel18 regulates mesoderm cell fate-specification of embryonic stem cells through multiple mechanisms

Project description:Polycomb complexes are essential regulators of stem cell identity, yet very little is known about their molecular mechanisms during cell differentiation. Pcgf proteins (Pcgf1/2/3/4/5/6) are core subunits of the Polycomb repressive complex 1 (PRC1). It has been recently proposed that specific Pcgf proteins are associated to particular PRC1 complexes, yet the molecular and biological functions of different Pcgf proteins remains largely elusive. Using specific differentiation protocols, we have elucidated a role for Pcgf2/Mel18 in specifically regulating mesoderm differentiation. Mechanistically, during early cardiac mesoderm differentiation, Pcgf2/Mel18 functions as a classical Polycomb protein by repressing pluripotency, lineage specification, late cardiac differentiation and negative regulators of the BMP pathway, yet Pcgf2/Mel18 also positively regulates the expression of key mesoderm transcription factors, revealing a novel function of Pcgf2/Mel18 in gene activation during cardiac differentiation. Mel18 depletion results in an unbalance of pathways that positively and negatively regulate cardiac differentiation. We propose that Mel18 is a novel epigenetic factor that controls mesoderm differentiation by opposing molecular mechanisms. List of ChIPseq samples: Mel18 in ESCs and MES, Ring1b, RYBP and Cbx2 in MES, IgG in MESs. List of RNAseq experiments: Mel18 KD, Ring1b KO and CTR in ESCs, Mel18 KD and CTR in MES, Mel18 KD and CTR in CMs.

2015-09-04 | E-GEOD-67868 | biostudies-arrayexpress

Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

Project description:Id proteins are dominant negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein Zrf1 plays a crucial role as a chromatin-bound factor in specification of the neural fate from ESCs. Here, we show that Id1 blocks Zrf1 recruitment to chromatin, thus preventing the activation of neural genes during ESC differentiation. Moreover, genetic deletion of Id1 in ESCs caused misexpression of more than 6000 genes. Interestingly, the expression of almost half of those genes was restored upon further depletion of Zrf1. We therefore identified Zrf1 as a transcriptional regulator downstream of Id1 in ESCs. In Id1KO mESCs, Zrf1 expression was depleted by using shRNAs. Four replicates corresponding to four independent biological samples per group were collected.

2014-11-05 | E-GEOD-58627 | biostudies-arrayexpress

CHARACTERIZATION AND DYNAMICS OF MOUSE PERICENTROMERE-ASSOCIATED DOMAINS

Project description:Despite recent progress in genome topology knowledge, the role of repeats, comprising the majority of mammalian genomes, remains elusive. Satellites are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin and aggregate into nuclear chromocenters that are assumed to form a repressive compartment in the nucleus to which genes are recruited for silencing. Here we designed a strategy for genome-wide identification of pericentromere-associated domains (PADs) in different mouse cell types. The ~1000 PADs and non-PADs have similar chromatin states in embryonic stem cells. During lineage commitment however chromocenters progressively overlap with constitutively inactive genomic regions at the nuclear periphery. This suggests that chromocenters do not actively recruit PADs but are themselves attracted to inactive chromatin compartments. However, we also found that experimentally induced proximity of an active locus to chromocenters was sufficient to cause gene repression. Collectively, our data suggests that rather than being a driver of nuclear organization, pericentromeric satellite repeats mostly co-segregate with inactive genomic regions to nuclear compartments where they can contribute to stably maintaining the repressed status of proximal chromosomal regions. We performed satellite 4C (sat4C) on mouse primary thymus tissue, pluripotent mouse embryonic stem cells (ESC) and neural precursor cells (NPC) and terminally differentiated astrocytes (AC) that were sequentially derived from these ESC in vitro

2015-04-01 | E-GEOD-65618 | biostudies-arrayexpress

Genome-wide occupancy of ZRF1 and BRD4 in neuroblastoma cells.

Project description:Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. Through integrated proteomics and validating studies, we discovered that ZRF1 and BRD4 form a complex with p113, a novel protein derived from CUX1 circular RNA. To investigate the mechanisms underlying the oncogenic functions of ZRF1 and BRD4, we employed the Illumina Novaseq 6000 as a discovery platform to analyze the genome-wide occupancy of ZRF1 and BRD4 on target genes in human SH-SY5Y cells, while the results were further analyzed with p113-regulated target genes. The results showed that 46 target genes were regulated by transcriptional trimer complex p113/ZRF1/BRD4, especially those involved in metabolic pathway or complex I biogenesis, including ALDH3A1, NDUFA1, and NDUFAF5. Furthermore, we validated the ChIP-seq results by real-time PCR with high identity. Overall, our results provided fundamental information about the genomic enrichment of ZRF1 and BRD4 in human NB cells, and these findings will help us understand the pathogenesis of NB.

2021-10-06 | GSE182402 | GEO

Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance

Project description:RNAseq analysis upon KD of ZRF1 to prove that depletion of ZRF1 results in the acquisition of metastatic behavior and drug resistance via misregulation of cell death and cell survival related pathways in MCF7 cells.

2019-09-24 | GSE104675 | GEO

ZRF1 knockdown with shRNA in SK-N-BE(2) cells

Project description:ZRF1 was silenced using two different shRNA in SK-N-BE(2) neuroblastoma cell line

2022-03-14 | GSE168939 | GEO