Genome binding/occupancy profiling by high throughput sequencing
Summary
We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription. We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.
Overall design
KDM3A was knocked out in HCT116 and the gene expression profile was studied by RNA sequencing Please note that [1] in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours. [2] each processed data file was generated from two replicate samples together and linked to the first replicate (REP1_*) of the corresponding samples.^SERIES = GSE108920 Examination of H3K4me3, H3K27me3, and pol II modifications in HCT116 wildtype cells, and detection H3K9me2, H3K27ac and TEAD1 distribution in HCT116 wildtype and KDM3A knockout cells Please note that [1] in the sample titles, M represents Mock, which means cell cultureed in normal state. S represents Starvation, which mens cells growed up in normal culture in a due time, then change the nomal culture into no-serum culture. S+F means addition of FBS into the no-serum culture after cell-starved for for 24 hours. [2] each processed data file was generated from two replicate samples together and linked to the first replicate (REP1_*) of the corresponding samples.
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