Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanisms of PU.1 binding site selection in-vivo

ABSTRACT: The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome. ChIP-seq of CTCF in human monocytes and human monocyte-derived macrophages as well as MCIp-seq in human monocytes

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Rehli

PROVIDER: E-GEOD-43098 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.

Pham Thu-Hang TH Minderjahn Julia J Schmidl Christian C Hoffmeister Helen H Schmidhofer Sandra S Chen Wei W Längst Gernot G Benner Christopher C Rehli Michael M

Nucleic acids research 20130508 13

The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well ...[more]

PMID: 23658224

Similar Datasets

Mechanisms of PU.1 binding site selection in-vivo

Project description:The majority of sequence-specific transcription factors bind genomic DNA only at a fraction of their potential binding sites and the ‘rules’ for binding or not-binding are only partially understood. Here, we studied the binding properties of the myeloid and B-cell specific transcription factor PU.1 in-vivo and in-vitro to unveil basic features of occupied vs. non-occupied consensus sites. In addition to published PU.1 ChIP-seq data we mapped CTCF binding sites in monocytes and macrophages to determine chromatin domain boundaries and performed MCIp-seq in monocytes to reveal DNA methylation patterns across the genome.

2013-05-15 | GSE43098 | GEO

Global, comparative analysis of tissue-specific promoter CpG methylation.

Project description:Understanding cell-type-specific epigenetic codes on a global level is a major challenge after the sequencing of the human genome has been completed. Here we applied methyl-CpG immunoprecipitation (MCIp) to obtain comparative methylation profiles of coding and noncoding genes in three human tissues, testis, brain, and monocytes. Forty-four mainly testis-specific promoters were independently validated using bisulfite sequencing or single-gene MCIp, confirming the results obtained by the MCIp microarray approach. We demonstrate the previously unknown somatic hypermethylation at many CpG-rich, testis-specific gene promoters, in particular in ampliconic areas of the Y chromosome. We also identify a number of miRNA genes showing tissue-specific methylation patterns. The comparison of the obtained tissue methylation profiles with corresponding gene expression data indicates a significant association between tissue-specific promoter methylation and gene expression, not only in CpG-rich promoters. In summary, our study highlights the exceptional epigenetic status of germ-line cells in testis and provides a global insight into tissue-specific DNA methylation patterns. Keywords: MCIp-on-Chip The promoter hypomethylation profiles of the two somatic tissues (monocytes and brain) were compared to human testis (reference). The set includes two hybridisations with independent testis samples for each comparison. Each comparison uses a set of two microarrays.

2007-08-07 | E-GEOD-5548 | biostudies-arrayexpress

Detection of aberrant DNA methylation in AML cell lines compared to normal human monocytes

Project description:To globally define methylation-âproneâ and -âprotectedâ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in two acute leukemia cell lines as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. Keywords: MCIp-on-Chip; comparative genomic hybridization CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia cell lines was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.

2010-06-05 | E-GEOD-17455 | biostudies-arrayexpress

Dynamic epigenetic enhancer signatures are predictive for key transcriptional regulators associated with cellular differentiation states

Project description:Cellular differentiation is orchestrated by lineage-specific transcription factors and associates with cell type-specific epigenetic signatures. Here, we utilized stage-specific, epigenetic "fingerprints" to deduce key transcriptional regulators of a cellular differentiation process. In the model of human macrophage differentiation, we globally mapped the distribution of epigenetic enhancer marks (histone H3 lysine 4 monomethylation, histone H3 lysine 27 acetylation, and the histone variant H2AZ) and show that cell type-specific epigenetic "fingerprints" correlate with specific, de novo derived motif signatures at all differentiation stages studied (hematopoietic progenitor cell, monocyte, macrophage). We validated the novel, de novo derived, macrophage-specific enhancer signature which included ETS, CEBP, bZIP, EGR, E-Box and NFkB motifs by ChIP-sequencing for a subset of motif corresponding transcription factors (PU.1, C/EBPbeta, and EGR2) which confirmed their predicted association with differentiation-associated epigenetic changes. This study highlights the power of genome-wide epigenetic profiling studies to reveal novel functional insights. It describes the dynamic enhancer landscape of human macrophage differentiation and provides a unique resource for macrophage biologists. ChIP-seq of 3 histone marks and 3 transcription factors in human blood monocytes and macrophages

2012-05-02 | E-GEOD-31621 | biostudies-arrayexpress

CTCF binding in B cells and Plasmablasts

Project description:The mammalian CCCTC-binding factor (CTCF) regulates gene expression through the formation of higher order chromatin structures. Recent evidence has implicated a role for CTCF in regulating gene expression in the human MHCII locus. To investigate the role of CTCF in murine MHCII gene expression we mapped CTCF binding sites in B cells (MHCII+ cells) and Plasmablasts which are differentiated B cells that have silenced MHCII gene expression. These observations lead to the identification of differential CTCF binding during differentiation in these cell types and suggest mechanims of MHCII gene regulation. Comparison of CTCF binding in B cells and Plasmablasts in mice using ChIP-seq

2014-02-05 | E-GEOD-44637 | biostudies-arrayexpress

Detection of aberrant DNA methylation in acute leukemia samples compared to normal human monocytes

Project description:To globally define methylation-âproneâ and -âprotectedâ CpG islands in leukemia, we analyzed the methylation status of 23,000 CpG islands of the human genome in eight acute leukemia samples as well as normal blood monocytes using our previously described methyl-CpG immunoprecipitation (MCIp) technique (Gebhard et al. 2006; Schilling and Rehli 2007). This method enriches for highly CpG methylated DNA that can be directly applied to fluorescent labeling and oligonucleotide microarray hybridization without an additional amplification step. Keywords: MCIp-on-Chip; comparative genomic hybridization CpG-methylated genomic DNA was enriched using methyl-CpG immunoprecipitation (MCIp). On each microarray, the enriched material from leukemia samples was compared to the enriched material from normal blood monocytes to identify aberrantly methylated regions. Three biological replicates were analysed for each cell line.

2010-06-05 | E-GEOD-17510 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

ChIP-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of ChIP-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. ChIP-sequencing was done for H3K27, RAD21 and CTCF. In total, the data set includes 120 samples.

2022-06-24 | E-MTAB-10849 | biostudies-arrayexpress

Extensive remodeling of DC function by rapid maturation-induced epigenetic gene silencing

Project description:Dendritic-cell (DC) maturation involves substantial remodeling of their gene-expression program. Most research has focused on inducible gene-expression networks promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC-function by inducing gene silencing remain poorly understood. Here we describe a novel primary epigenetic-silencing response that makes major contributions to the DC-maturation process. The repressed genes function in pivotal processes - including antigen-presentation, extracellular-signal detection, signal-transduction and lipid-mediator biosynthesis - underscoring the central contribution of the silencing mechanism to rapid reshaping of DC-function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this transcription factor in marking genes poised for inducible repression Analysis of PU.1 binding sites in mo-DC

2015-01-01 | E-GEOD-58864 | biostudies-arrayexpress

Methylation in breast cancer vs. normal tissue

Project description:We applied a combination of Methyl-CpG Immunoprecipitation (MCIp) and Human CpG Island microarrays to identify aberrant DNA methylation in eight low-grade breast invasive carcinomas and two pre-invasive breast tumors against ten normal breast tissues. 10 breast tumor samples (8 invasive, 2 pre-invasive) and 10 normal breast tissues, paired randomly (except Array 10: matched pair)

2012-09-14 | E-GEOD-35263 | biostudies-arrayexpress

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