E-GEOD-45390 - Protein and histone binding profiles from mouse ES cells during differentiation and after Kdm6a RNAi treatment

Released on 22 March 2013, last updated on 4 May 2014
Mus musculus
Samples (24)
Array (1)
Protocols (12)
Here we show binding and occupancy profiles for KDM6A, H3K27me3 and H3K4me3 to address the epigenetic regulation of a subset of Rhox genes, Rhox6 and 9, in female and male ES cells during differentiation. To further address a functional role for KDM6A in the epigenetic regulation of Rhox6 and 9, binding profiles for female ES cells treated with a control siRNA and siRNA specific for Kdm6a are shown. We report that two members of the Rhox cluster, Rhox6 and 9, are regulated by de-methylation of histone H3 at lysine 27 by KDM6A, a histone demethylase with female-biased expression. Our results are consistent with other homeobox genes in that Rhox6 and 9 are in bivalent domains prior to embryonic stem cell differentiation and thus poised for activation. In female mouse ES cells KDM6A is specifically recruited to Rhox6 and 9 for gene activation, a process inhibited by Kdm6a knockdown. In contrast, KDM6A occupancy at Rhox6 and 9 is low in male ES cells and knockdown has no effect on expression. Our study implicates Kdm6a, a gene that escapes X inactivation, in the regulation of genes important in reproduction, suggesting that KDM6A may play a role in the etiology of developmental and reproduction-related effects of X chromosome anomalies. ChIP-chip was used to analyze the binding profiles of KDM6A, H3K27me3, and H3K4me3 during differentiation in female and male ES cells. Additionally, ChiP-chip of KDM6A binding in control treated and siRNA treated ES cells is presented.
Experiment type
ChIP-chip by tiling array 
Joel Berletch <joelb07@uw.edu>, Christine M Disteche, Di K Nguyen, Joel B Berletch, Xinxian Deng
Investigation descriptionE-GEOD-45390.idf.txt
Sample and data relationshipE-GEOD-45390.sdrf.txt
Raw data (14)Click to browse raw data
Processed data (2)E-GEOD-45390.processed.1.zip, E-GEOD-45390.processed.2.zip
Array designA-GEOD-10129.adf.txt