Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation of mouse and human cell lines and tissues using E2F4 antibodies

ABSTRACT: Despite being expressed in most tissues, a number of mammalian process-specific transcriptional regulators, such as those involved in cell cycle and immune responses, often have profound tissue-specific phenotypes. The mechanism underlying this effect is poorly understood. We chose to investigate on a genome-wide basis how the cell cycle master regulator E2F4, a key regulator of proliferation and differentiation in G0 cells, controls gene expression in multiple mammalian tissues. We identified potential direct targets of E2F4 in primary mouse and human tissues using chromatin immunoprecipitation. E2F4 binds a core set of genes in most mouse tissues that includes a substantial number of previously identified direct targets, and these common targets are highly enriched in the canonical binding sequence. Comparison of the genes bound in mouse tissues versus those bound in comparable human tissues revealed that, consistent with previous results, a core set of targets was bound in both species, and contains a substantial overrepresentation of cell-cycle genes.

INSTRUMENT(S): Axon GenePix 4000B scanning hardware

ORGANISM(S): Mus musculus

SUBMITTER: Duncan Odom

PROVIDER: E-TABM-272 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin immunoprecipitation using promoter microarrays to identify genes occupied by the transcriptional regulators HNF1a, HNF4a and HNF6, together with RNA polymerase II, in human liver and pancreatic islets

Project description:Here, we use chromatin immunoprecipitation combined with promoter microarrays to identify the genes occupied by the transcriptional regulators HNF1a, HNF4a and HNF6, together with RNA polymerase II, in human liver and pancreatic islets.

2004-07-15 | E-MEXP-68 | biostudies-arrayexpress

Chromatin immunoprecipitation of mouse polycomb group (PcG) proteins in embryonic stem cells

Project description:Polycomb group (PcG) proteins are highly conserved from flies to mammals and many of these factors have essential roles in early embryonic development. PcG proteins comprise two multimeric complexes, the Polycomb Repressive complexes 1 and 2 (PRC1 and 2), which have been shown to repress transcription through epigenetic modification of chromatin structure. To gain insight into the role of Polycomb in early development, we have identified PRC1 and PRC2 target genes in mouse embryonic stem (ES) cells using genome-scale location analysis. We found that PRC2 occupies many genes that encode key regulators of development including those encoding transcription factors and components of signaling pathways. These genes are repressed and contain nucleosomes methylated at lysine 27 on histone H3. The majority of PRC2 bound and methylated target genes are co-occupied by PRC1 indicating that these complexes function at a similar set of genes in ES cells. Lack of PRC1 or PRC2 subunits in ES cells results in derepression of target genes and loss of pluripotency. These results provide insight into how PcG proteins contribute to the maintenance of stem cell identity.

2006-05-09 | E-WMIT-12 | biostudies-arrayexpress

Chromatin immunoprecipitation of liver tissue from humans, wild type mice and a Down syndrome mouse model containing human chromosome 21 to determine where genetic sequence or nuclear environment directs tissue specific-specific transcription factor binding

Project description:Homologous sets of transcription factors direct conserved tissue-specific transcription, yet transcription factor binding events diverge rapidly between closely related species. We used hepatocytes from a Down syndrome mouse model containing human chromosome 21 to determine whether human genetic sequence or mouse nuclear environment primarily determines tissue-specific transcriptional regulation. Virtually all transcription factor binding locations, transcription initiation events and the resulting gene expression observed in human hepatocytes are recapitulated across the entire human chromosome 21 in the mouse nucleus. Thus, in homologous tissues, genetic sequence is largely responsible for directing transcriptional programs, and interspecies differences in epigenetics, cellular environment, and transcription factors themselves play secondary roles.

2008-06-11 | E-TABM-474 | biostudies-arrayexpress

Chromatin immunoprecipitation of Tcf3, Oct4 and nanog in mouse embryonic stem cells

Project description:Embryonic stem cells have a unique regulatory circuitry, largely controlled by the transcription factors Oct4, Sox2 and Nanog, which generates a gene expression program necessary for pluripotency and self-renewal (Boyer et al. 2005; Loh et al. 2006; Chambers et al. 2003; Mitsui et al. 2003; Nichols et al. 1998). How external signals connect to this regulatory circuitry to influence embryonic stem cell fate is not known. We report here that a terminal component of the canonical Wnt pathway in embryonic stem cells, the transcription factor Tcf3, co-occupies promoters throughout the genome in association with the pluripotency regulators Oct4 and Nanog. Thus Tcf3 is an integral component of the core regulatory circuitry of ES cells, which includes an autoregulatory loop involving the pluripotency regulators. Both Tcf3 depletion and Wnt pathway activation cause increased expression of Oct4, Nanog and other pluripotency factors and enhance pluripotency and self-renewal. Our results reveal that the Wnt pathway, through Tcf3, brings developmental signals directly to the core regulatory circuitry of ES cells to influence the balance between pluripotency and differentiation.

2008-02-28 | E-TABM-409 | biostudies-arrayexpress

Chromatin immunoprecipitation of Oct4 and nanog in mouse embryonic stem cells to enable comparison of regulatory networks obtained by ChIP-Chip and ChIP-PET

Project description:Genome-wide approaches have begun to elucidate the transcriptional and epigenetic regulatory networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip), or by DNA sequencing (ChIP-PET), has identified the genomic-binding targets of the ES cell transcription factors Oct4 and Nanog in humans and mice, respectively. A central issue that remains to be resolved is the concordance of the data obtained by these methods, given the differences between the two techniques. Here, we report the identification of the Oct4 and Nanog genomic targets in mouse ES cells by ChIP-Chip and have compared the data with binding data identified previously by ChIP-PET. Binding data have also been combined with Oct4 and Nanog RNAi knockdown expression profiling data in ES cells. Surprisingly, we find a substantial difference between the regions that identified exclusively by one of the two techniques. In both studies, however, targets identified by either technique contain a number of genes that are differentially expressed on Oct4 or Nanog knockdown, and have been implicated in cell-fate determination events. This study provides a comparison between the data obtained by different genomic platform, and offers a more comprehensive picture of the stem cell transcriptional network.

2008-11-04 | E-TABM-410 | biostudies-arrayexpress

Chromatin immunoprecipitation of human cells after lipopolysaccharide stimulation, to identify binding of NF-KappaB family members

Project description:The NF-KappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-kappaB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a significant number of gene promoters. p50 occupied genes together with RNA polymerase II and defined a set of genes to which other NF-kappaB proteins bound after LPS induction. In stimulated cells, genes bound by multiple NF-kappaB subunits exhibited the greatest increases in RNA polymerase II occupancy and gene expression. This study identifies novel NF-kappaB target genes, reveals how the different NF-kappaB proteins coordinate their activity and maps transcriptional regulatory networks that underlie the host response to infection.

2006-05-09 | E-WMIT-6 | biostudies-arrayexpress

Chromatin immunoprecipitation of human cell lines to identify cAMP-response element binding protein (CREB) binding sites.

Project description:Hormones and nutrients often induce genetic programs via signaling pathways that interface with gene-specific activators. Activation of the cAMP pathway, for example, stimulates cellular gene expression by means of the PKA-mediated phosphorylation of cAMP-response element binding protein (CREB) at Ser-133. Here, we use genome-wide approaches to characterize target genes that are regulated by CREB in different cellular contexts. CREB was found to occupy approximately 4,000 promoter sites in vivo, depending on the presence and methylation state of consensus cAMP response elements near the promoter. The profiles for CREB occupancy were very similar in different human tissues, and exposure to a cAMP agonist stimulated CREB phosphorylation over a majority of these sites. Only a small proportion of CREB target genes was induced by cAMP in any cell type, however, due in part to the preferential recruitment of the coactivator CREB-binding protein to those promoters. These results indicate that CREB phosphorylation alone is not a reliable predictor of target gene activation and that additional CREB regulatory partners are required for recruitment of the transcriptional apparatus to the promoter.

2006-05-09 | E-WMIT-11 | biostudies-arrayexpress

Chromatin immunoprecipitation of human HNF3b and E2F4, and mouse NeuroD1, for THEME analysis

Project description:Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the discovered motifs often do not agree with the binding specificity of the protein, when it is known. RESULTS: We present a powerful approach to analyzing ChIP-chip data, called THEME, that tests hypotheses concerning the sequence specificity of a protein. Hypotheses are refined using constrained local optimization. Cross-validation provides a principled standard for selecting the optimal weighting of the hypothesis and the ChIP-chip data and for choosing the best refined hypothesis. We demonstrate how to derive hypotheses for proteins from 36 domain families. Using THEME together with these hypotheses, we analyze ChIP-chip datasets for 14 human and mouse proteins. In all the cases the identified motifs are consistent with the published data with regard to the binding specificity of the proteins.

2006-05-09 | E-WMIT-8 | biostudies-arrayexpress

Chromatin immunoprecipitation of human MLL1 to understand its role in cell type specification

Project description:An experiment was performed to understand its role in cell type specification, we have determined the human genomic binding sites of MLL1. MLL1 localizes with Pol II to the 5' end of actively transcribed genes, where histone H3 lysine 4 (H3-K4) trimethylation occurs. The ability of MLL1 to serve as a start site-specific global transcriptional regulator and to participate in larger chromatin domains at the Hox genes reveals the dual roles MLL1 plays in maintenance of cellular identity.

2005-06-03 | E-WMIT-4 | biostudies-arrayexpress

Chromatin immunopreciptiation of mouse hepatocytes to validate deep-sequencing libraries

Project description:Chromatin immunoprecipitation followed by ultra-high throughput (UHTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide, and the primary limitation of its broad application at present is the often-limited access to sequencers. Here, we report a protocol, Mab-Seq, to generate preliminary quality evaluations and single-chromosome data for deep-sequencing libraries. We show that commercially available genomic microarrays can be used to maximize the efficiency of library creation, quickly generate preliminary data on a chromosomal scale, and help establish the depth to which novel libraries will require deep sequencing.

2008-06-11 | E-TABM-485 | 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