Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ATAC-seq)

ABSTRACT: Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ATAC-seq)

PROVIDER: PRJNA644001 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12144064_1.fastq.gz	Fastqsanger.gz
	SRR12144064_2.fastq.gz	Fastqsanger.gz
	SRR12144065_1.fastq.gz	Fastqsanger.gz
	SRR12144065_2.fastq.gz	Fastqsanger.gz
	SRR12144066_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

Project description:Transcription factor binding to DNA is a central mechanism regulating cellular gene expression. Thus, thorough characterization of this process is essential for understanding cellular biology in both health and disease. In this study, we combined data from three sequencing-based methods to unravel the DNA binding function of the novel zinc finger protein ZNF414 in cells representing two tumor types. ChIP-exo served to map protein binding sites in the genome, ATAC-seq allowed identification of open chromatin, and RNA-seq examined the transcriptome.

2020-07-06 | GSE153776 | GEO

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ATAC-seq)

2020-07-06 | GSE153769 | GEO

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

2020-07-06 | GSE153772 | GEO

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (ChIP-exo)

| PRJNA644010 | ENA

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data

| PRJNA644005 | ENA

Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

Project description:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. We have determined the binding sites and motifs of 119 C2H2 zinc finger proteins and the expression pattern of 80 cell lines overexpressing C2H2 zinc finger proteins in order to study the role of C2H2 zinc finger proteins in gene regulation. We expressed GFP-tagged C2H2-ZF proteins in stable transgenic HEK293 cells. Total RNA was isolated using Trizol and sequencing libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold or TruSeq RNA Library Preparation Kit v2.

2016-10-25 | E-GEOD-76495 | biostudies-arrayexpress

Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

Project description:Characterization of novel zinc finger protein ZNF414 DNA binding and gene regulatory activity by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data (RNA-seq)

| PRJNA644004 | ENA

Multiparameter functional diversity of human C2H2 zinc finger proteins [RNA-Seq]

2016-10-25 | GSE76495 | GEO

The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation

Project description:Recognition of post-translational modifications on histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Compared to the large number of readers that recognize histone methylation, only a few acetyllysine readers have been identified, including bromodomain, YEATS, and double plant homeodomain zinc finger (DPF). Here, we report the identification of a novel reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-Two-A Containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique histone-binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain. Importantly, acetylation on Lysine 4 of H3 (H3K4ac) enhances the binding, and in cells, ZZZ3 colocalizes with H3K4ac across the genome. The recognition of histone acetylation by ZZ is essential for chromatin occupancy of ZZZ3 and functions of the ATAC complex. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC dependent promoter histone H3K9 acetylation and the expression of ribosomal protein encoding genes. Overall, our study identifies the ZZ domain of ZZZ3 as a novel epigenetic reader that links the GCN5/ATAC complex to histone acetylation.

2018-09-14 | GSE100009 | GEO

Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [ATAC-seq]

Project description:Neural zinc finger protein Myt1 drives oligodendrocyte differentiation via repressing HDAC1-mediated histone deacetylation [ATAC-seq]

| PRJNA1065891 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data