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E-GEOD-66544 - Multiple Overlapping Mammalian Chromatin Remodeling Systems Collaborate Genome-wide at Dynamic Chromatin Transitions [Affymetrix]

Status
Released on 5 March 2015, last updated on 6 March 2015
Organism
Mus musculus
Samples (17)
Array (1)
Protocols (7)
Description
Expression data from 3134 mouse mammary epithelial cell line -/+ Tet-inducible chromatin remodeler mutant variants ATP-dependent chromatin remodeling is an essential process required for the dynamic organization of chromatin structure. Here we describe the genome-wide location and activity of three remodeler proteins with diverse physiological functions in the mouse genome: Brg1, Chd4 and Snf2h. The localization patterns of all three proteins substantially overlap with one another and with regions of accessible chromatin. Furthermore, using inducible mutant variants, we demonstrate that the catalytic activity of these proteins contributes to the remodeling of chromatin genome wide and that each of these remodelers can independently regulate chromatin reorganization at distinct sites. Many regions require the activity of more than one remodeler to regulate accessibility. We also examined effects of mutant remodeler variants on selective gene expression by global analysis of RNA expression patterns and found more than 800 genes are deregulated by these variants. These findings provide a dynamic view of chromatin organization and highlight the differential contributions of remodelers to chromatin maintenance in higher eukaryotes. Flag tagged dominant negative variants of the chromatin remodelers Brg1, Chd4, and Snf2h were each stably integrated into a cell line containg the tetracycline transactivator regulatory system (3134Tet (7110)). The 3134Tet control cells and each of the dominant-negative remodeler cell lines were grown in media with or without tetracycline for 48 hrs to induce expression of the tetracycline transactivator alone (3134Tet cells) or tetracycline transactivator and dominant negative remodeler variant. Following treatment, cells were harvested for RNA extraction and hybridization to Affymetrix Mouse Gene 1.0 ST arrays.
Experiment type
transcription profiling by array 
Contacts
Citation
Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions. Morris SA, Baek S, Sung MH, John S, Wiench M, Johnson TA, Schiltz RL, Hager GL. , PMID:24317492
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-66544.idf.txt
Sample and data relationshipE-GEOD-66544.sdrf.txt
Raw data (1)E-GEOD-66544.raw.1.zip
Processed data (1)E-GEOD-66544.processed.1.zip
Array designA-AFFY-130.adf.txt
Links