Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes

Abstract

BackgroundDifferent approaches have been developed to dissect the interplay between transcription factors (TFs) and their cis-acting sequences on DNA in order to identify TF target genes. Here we used a combination of computational and experimental approaches to identify novel direct targets of TFAP2A, a key TF for a variety of physiological and pathological cellular processes. Gene expression profiles of HeLa cells either silenced for TFAP2A by RNA interference or not were previously compared and a set of differentially expressed genes was revealed.ResultsThe regulatory regions of 494 TFAP2A-modulated genes were analyzed for the presence of TFAP2A binding sites, employing the canonical TFAP2A Positional Weight Matrix (PWM) reported in Jaspar http://jaspar.genereg.net/. 264 genes containing at least 2 high score TFAP2A binding sites were identified, showing a central role in "Cellular Movement" and "Cellular Development". In an attempt to identify TFs that could cooperate with TFAP2A, a statistically significant enrichment for SP1 binding sites was found for TFAP2A-activated but not repressed genes. The direct binding of TFAP2A or SP1 to a random subset of TFAP2A-modulated genes was demonstrated by Chromatin ImmunoPrecipitation (ChIP) assay and the TFAP2A-driven regulation of DCBLD2/ESDN/CLCP1 gene studied in details.ConclusionsWe proved that our computational approaches applied to microarray selected genes are valid tools to identify functional TF binding sites in gene regulatory regions as confirmed by experimental validations. In addition, we demonstrated a fine-tuned regulation of DCBLD2/ESDN transcription by TFAP2A.

Expression of AP-2α, AP-2γ and ESDN in primary melanomas: Correlation with histopathological features and potential prognostic value

“…The concomitant loss of AP-2α, AP-2γ and ESDN in primary melanoma supports preliminary evidence about ESDN regulation by the AP-2 family in human melanomas, suggesting a modulation between these genes and thus confirming our previous findings [4] and [5]. The relevance of these alterations in the metastatic pathways is underlined by the skin metastasis pattern expression.…”

“…Loss of the transcription factor activator protein-2α (AP-2α) is an important molecular event in melanoma progression resulting in deregulation of AP-2 target genes involved in tumour growth and metastasis and associated with short Disease-Free-Survival (DFS) [2] and [3]. Our recent investigations on different tumour cells including melanoma [4], [5] and [6] provided evidence that not only AP-2α but also AP-2γ play an essential role in tumorigenesis by modulating specific genes such as Endothelial and Smooth muscle cell Derived Neuropilinlike molecule (ESDN) [7]. So far, no data are available regarding AP-2γ and ESDN expression in primary melanoma lesions.…”

Inhibition of neural crest formation by Kctd15 involves regulation of transcription factor AP-2

“…A large number of target genes have been identified by genomewide approaches, including genes activated and suppressed by AP-2 (26,41,42). It remains to be studied whether Kctd15 inhibits gene regulation by AP-2 in general or only in a certain context.…”

Genetic and Expression Analysis of MET, MACC1, and HGF in Metastatic Colorectal Cancer: Response to Met Inhibition in Patient Xenografts and Pathologic Correlations

“…In accordance with previous work showing that the integrity of a specific SP1 binding site in the Met promoter is required for Met regulation by MACC1 (26), we initially selected genes only for the presence of an SP1 consensus and tested whether this was sufficient to enrich for transcripts coexpressed with MACC1 (28). Geneset enrichment analysis (GSEA) of a public dataset comprising 372 CRC samples (GSE2109; see Supplementary Methods for Tables S4 and S5).…”