Research article
Identification of functional TFAP2A and SP1 binding sites in new TFAP2A-modulated genes
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* Corresponding author: Daniela Taverna daniela.taverna@unito.it
- † Equal contributors
1 Molecular Biotechnology Center (MBC) and Department of Oncological Sciences, University of Torino, Via Nizza, 52, 10126 Torino, Italy
2 National Institute of Nuclear Physics (INFN) and Department of Theoretical Physics, University of Torino, Via Pietro Giuria, 1, 10125, Torino, Italy
3 Molecular Biotechnology Center (MBC) and Department of Genetics, Biology and Biochemistry, University of Torino, Via Nizza, 52, 10126 Torino, Italy
4 Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Via Acc. Albertina, 13, 10023 Torino; Italy
5 Systems Biology Lab, Institute for Cancer Research and Treatment (IRCC), School of Medicine, University of Torino, Str. Prov. 142 Km. 3.95, I-10060 Candiolo, Torino, Italy
6 Cancer Research UK London Research Institute, Lincoln's Inn Fields Laboratories, Vascular Biology Laboratory, 44 Lincoln's Inn Fields, London, WC2A 3PX, UK
BMC Genomics 2010, 11:355 doi:10.1186/1471-2164-11-355
Published: 3 June 2010Abstract
Background
Different 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.
Results
The 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/ webcite. 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.
Conclusions
We 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.