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Open Access Research article

Promoter analysis of intestinal genes induced during iron-deprivation reveals enrichment of conserved SP1-like binding sites

James F Collins1 and Zihua Hu2

Author Affiliations

1 Department of Exercise and Nutrition Sciences, University at Buffalo, the State University of New York, Buffalo, NY, USA

2 Center for Computational Research, New York State Center of Excellence in Bioinformatics & Life Sciences, and the Department of Biostatistics, University at Buffalo, the State University of New York, Buffalo, NY, USA

BMC Genomics 2007, 8:420  doi:10.1186/1471-2164-8-420

Published: 15 November 2007

Abstract

Background

Iron-deficiency leads to the induction of genes related to intestinal iron absorption and homeostasis. By analyzing a large GeneChip® dataset from the rat intestine, we identified a large cluster of 228 genes that was induced by iron-deprivation. Only 2 of these genes contained 3' iron-response elements, suggesting that other regulation including transcriptional may be involved. We therefore utilized computational methods to test the hypothesis that some of the genes within this large up-regulated cluster are co-ordinately regulated by common transcriptional mechanisms. We thus identified promoters from the up-regulated gene cluster from rat, mouse and human, and performed enrichment analyses with the Clover program and the TRANSFAC database.

Results

Surprisingly, we found a strong statistical enrichment for SP1 binding sites in our experimental promoters as compared to background sequences. As the TRANSFAC database cannot distinguish among SP/KLF family members, many of which bind similar GC-rich DNA sequences, we surmise that SP1 or an SP1-like factor could be involved in this response. In fact, we detected induction of SP6/KLF14 in the GeneChip® studies, and confirmed it by real-time PCR. Additional computational analyses suggested that an SP1-like factor may function synergistically with a FOX TF to regulate a subset of these genes. Furthermore, analysis of promoter sequences identified many genes with multiple, conserved SP1 and FOX binding sites, the relative location of which within orthologous promoters was highly conserved.

Conclusion

SP1 or a closely related factor may play a primary role in the genetic response to iron-deficiency in the mammalian intestine.