10.7554/eLife.00068.017 Figure 7. Validation of ChIP-chip results by directed ChIP experiments using promoter-specific primer pairs.
According to our data, the genes SYK, GDF9, DGKZ, and FBXO22 are direct p53 targets demonstrated by ChIP on chip analysis and realtime RT-PCR analysis, which have not been described before.
Following initial studies using HPV plasmids and cell lines, we evaluated the clinical utility and effectiveness by comparing our assay with direct sequencing and HPV DNA chip analysis of 80 samples from high-risk, HPV-positive patients.
DHS mapping was complemented by RUNX1/ETO and RUNX1 ChIP analysis.
Importantly, Myc knockdown led to an upregulation in expression of approximately 10% of all Miz-1 direct target genes identified by ChIP-chip analysis (76 out of 735 genes) with the majority of them being involved in ES cell differentiation.
Chromatin immunoprecipitation (ChIP) analysis revealed a direct binding of phosphorylated Smad 1,5,8 on ID1 and PHD2 promoter in both sites after BMP2 stimulus, suggesting a direct regulation of PHD2, and consequently HIF-1 α levels mediated by BMP2.
These analyses show that many of the direct AR target genes identified by ChIP-chip analysis have cancer-related functional annotations, are upregulated in clinical PrCa and might therefore have potential as biomarkers or future therapeutic targets.
Traditionally, biologists only focused on the direct targets and discarded indirect targets because direct targets can be explained simply by overlapping the TFPE data with the ChIP analysis, whereas indirect targets had no easy way to be explained at the molecular level.
ChIP analysis by real-time PCR was compared to analysis by densitometry with the ImageJ software.
Chromatin immunoprecipitation (ChIP) analysis showed that these genes are direct targets of the SOX11 protein.
