E-GEOD-6629 - Transcription profiling of human HED293 cells with GFP constructs at different genomic positions are expressed corresponding to the activity of the domains of integration

Status
Submitted on 3 January 2007, released on 15 June 2008, last updated on 27 March 2012
Organism
Homo sapiens
Samples (2)
Array (1)
Protocols (7)
Description
Transcription factor complexes bind to regulatory sequences of genes, providing a system of individual expression regulation. Targets of distinct transcription factors usually map throughout the genome, without clustering. Nevertheless, highly and weakly expressed genes do cluster in separate chromosomal domains with an average size of 80 to 90 genes. We therefore asked whether, besides transcription factors, an additional level of gene expression regulation exists that acts on chromosomal domains. Here we show that identical green fluorescent protein (GFP) reporter constructs integrated at 90 different chromosomal positions determined by sequencing, obtain expression levels that correspond to the activity of the domains of integration. These domains are about 80 genes long and can exert an effect of up to 8-fold on the expression of integrated genes. 3D-FISH shows that active domains of integration have a more open chromatin structure than integration domains with weak activity. These results reveal a novel domain-wide regulatory mechanism that, together with transcription factors, exerts a dual control over gene transcription. See Gierman et al., 2007, Genome Research (DOI: 10.1101/gr.6276007). Experiment Overall Design: The experiment was performed in duplo, whereby HEK293 cells were grown under standard conditions and RNA was isolated, labelled and hybridized separately. Data from the duplicate arraying experiment were then averaged and further analyzed.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Domain-wide regulation of gene expression in the human genome. Hinco J Gierman, Mireille H G Indemans, Jan Koster, Sandra Goetze, Jurgen Seppen, Dirk Geerts, Roel van Driel, Rogier Versteeg. Genome Res 17(9):1286-95 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-6629.idf.txt
Sample and data relationshipE-GEOD-6629.sdrf.txt
Raw data (1)E-GEOD-6629.raw.1.zip
Processed data (1)E-GEOD-6629.processed.1.zip
Array designA-AFFY-44.adf.txt
R ExpressionSetE-GEOD-6629.eSet.r
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