Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

52 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation analysis of human hepatocyte regulatory circuitry

ABSTRACT: We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that these regulators form a highly interconnected core circuitry, and reveal the local regulatory network motifs created by regulator-gene interactions. Auto-regulation was a prominent theme among these regulators. We found that hepatocyte master regulators tend to bind promoter regions combinatorially and that the number of transcription factors bound to a promoter corresponds with observed gene expression. Our studies reveal portions of the core circuitry of human hepatocytes.

ORGANISM(S): Homo sapiens

SUBMITTER: Elizabeth Herbolsheimer

PROVIDER: E-WMIT-9 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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, Nanog and Suz12 in human and mouse embryonic stem cells to identify promoters for miRNAs

Project description:Understanding the transcriptional regulatory circuitry responsible for pluripotency and self-renewal in embryonic stem (ES) cells is fundamental to understanding human development and realizing the therapeutic potential of these cells. The transcription factor Oct4 and the chromatin-modifying Polycomb complex, key regulators of ES cell pluripotency and self-renewal, contribute to positive and negative control of a known set of protein-coding genes. MicroRNAs (miRNAs), non-coding transcripts that participate in post-transcriptional gene regulation are also important for normal pluripotency and self-renewal in ES cells, but there has been no systematic investigation of how miRNA expression is controlled by transcriptional regulators of ES cell identity. Here we identify promoters for miRNAs in the human and mouse genomes and describe the subset of these genes that are under the control of Oct4 and Polycomb in ES cells. We find that the majority of miRNAs that are uniquely or preferentially expressed in ES cells are bound by and dependent on Oct4. Oct4 also occupies a set of miRNA genes that are co-occupied by the Polycomb Group protein, Suz12. These miRNAs, repressed in ES cells, are later expressed in differentiated cells in a highly tissue-specific fashion, suggesting that they may contribute to cell-fate determinations. These data reveal how the core transcriptional regulatory circuitry of ES cells controls the miRNA expression program that contributes to pluripotency and self-renewal.

2010-12-01 | E-TABM-365 | 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 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 immunopreciptiation of H2AZ in mouse embryonic stem cells and neural precursor cells

Project description:Elucidating how chromatin organization influences gene expression patterns and ultimately cell fate is fundamental to understanding development and disease. Histone variants have emerged as key regulators of genome function by creating specialized chromatin domains. The histone variant H2AZ plays an essential, but poorly understood function during early mammalian development. Genome-wide analysis reveals that H2AZ is enriched at a large class of developmentally important genes that are known targets of Polycomb-mediated repression in embryonic stem (ES) cells. H2AZ displays a highly defined spatial patterning that is remarkably similar to the Polycomb group (PcG) protein Suz12 in ES cells, but not in differentiated cell types. By using RNA interference, we demonstrate that H2AZ is a critical regulatory component at developmental genes in ES cells and show that localization of H2AZ and PcG proteins is interdependent at target promoters. Moreover, similarly to Suz12, H2AZ is required for lineage commitment. This study reveals a connection between H2AZ and PcG proteins in ES cells and suggests that these factors functionally interact to regulate chromatin states necessary for the proper execution of developmental gene expression programs.

2009-01-22 | E-TABM-556 | 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

Chromatin immunoprecipitation of human PolII and SUZ12 proteins in embryonic stem cells

Project description:Polycomb group proteins are essential for early development in metazoans but their contributions to human development are not yet well understood. We have mapped the Polycomb Repressive Complex 2 (PRC2) subunit Suz12 across the entire non-repeat portion of the genome in human embryonic stem (ES) cells. We found that Suz12 is distributed across large portions of over two hundred genes encoding key developmental regulators. These genes are occupied by nucleosomes trimethylated at histone H3K27, are transcriptionally repressed, and contain some of the most highly conserved non-coding elements in the vertebrate genome. We found that preferential activation of PRC2 target genes occurs during differentiation of ES cells into other cell types. The ES cell transcriptional regulators Oct4, Sox2 and Nanog co-occupied a significant subset of these genes, further supporting a link between repression of developmental regulators and stem cell pluripotency. These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation.

2006-06-14 | E-WMIT-7 | biostudies-arrayexpress

Chromatin immunoprecipitation genome wide binding sites of Oct4, Sox2, and Nanog in human

Project description:The transcription factors Oct4, Sox2, and Nanog have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture. To gain insights into transcriptional regulation of human ES cells, we have identified Oct4, Sox2, and Nanog target genes using genome-scale location analysis. We found, surprisingly, that Oct4, Sox2, and Nanog co-occupy a substantial portion of their target genes. These target genes frequently encode transcription factors, many of which are developmentally important homeodomain proteins. Our data also indicates that Oct4, Sox2, and Nanog collaborate to form regulatory circuitry in ES cells consisting of autoregulatory and feedforward loops. These results provide new insights into the transcriptional regulation of stem cells and reveal how Oct4, Sox2, and Nanog contribute to pluripotency and self-renewal.

2005-09-23 | E-WMIT-5 | biostudies-arrayexpress

Chromatin immunoprecipitation of Foxp3 in mouse T-cell hybridoma cells

Project description:The forkhead transcription factor Foxp3 is essential for the development of CD4+CD25+ regulatory T (Treg) cells and prevention of autoimmunity, but how it controls the Treg gene expression program is not understood. We describe here genome-wide location and expression data that identify Foxp3 target genes and report that many Foxp3 target genes are key modulators of T cell activation and function. Remarkably, the predominant effect of Foxp3 binding is to suppress the activation of target genes upon T cell stimulation. Foxp3 suppression of its targets appears to be crucial for the normal function of Treg cells because overactive variants of some target genes are known to be associated with autoimmune disease.

2007-01-27 | E-TABM-154 | 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