Elucidation of regulatory mechanisms revealed by human promoter sequence analysis of genes co-expressed in forskolin-treated theca cells in PCOS.

PURPOSE: Polycystic ovary syndrome (PCOS) is a reproductive endocrinopathy and is the most common cause of anovulatory infertility in women of reproductive age group. In PCOS research, there have been several reports which have shown the differential expression of genes from various tissue and cell types. However, little information can be gained about the regulation of these genes from the microarray data itself. Therefore, with the assumption that co-expression can also imply co-regulation in high-throughput gene expression studies, we investigated the role of various transcription factors by elucidating their binding sites (TFBSs) in these genes. METHODS: For this purpose, a group of 40 genes altered in a forskolin-treated PCOS gene expression study in theca cells were analyzed using in silico tools. 2,000 bp of the upstream region were extracted from all these genes, and the PAINT suite of programs was used to identify over-represented TFBSs in these genes. RESULTS: We identified three different TFBSs which were over-represented as compared with a human promoter background model. These three transcription factors (TFs) are Oct, HFH, and neuron-restrictive silencing factor. Each of these three TFs and their compatible members can be implicated in the pathogenesis of PCOS, as described in detail in this article. CONCLUSIONS: These factors might reveal a new insight into the complex pathogenesis of PCOS especially with respect to cAMP pathway.

Deciphering the cis-regulatory elements of co-expressed genes in PCOS by in silico analysis.

In recent times, the focus of research in polycystic ovary syndrome (PCOS) has shifted from candidate gene(s) approach to whole genome analysis for deciphering its molecular pathophysiology. In this regard, several microarray studies have been published, showing differential expression of genes between normal and PCOS states. Co-expression of genes as obtained in microarray experiments can also imply co-regulation at the transcriptional level by various transcription factors. In order to identify such transcription factors, the in silico elucidation of Transcription Factor Binding Sites (TFBS) is emerging as an important tool. With this hypothesis, we looked for TFBS over-representation in a PCOS microarray gene set (n=130) using in silico tools. We extracted 1000 bps upstream and 200 bps downstream regions from all these genes and identified 4 different TFBS, which were over-represented as compared to a human promoter background model. These four transcription factors are Staf, E47, CCAAT and CRE-BP1/c-jun. The role of these transcription factors and their compatible members in PCOS pathophysiology is described in details in the text. The factors might provide a novel insight into the pathophysiology of PCOS.