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Published online 19 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 1798-1807
Oxford University Press

Calculating the statistical significance of physical clusters of co-regulated genes in the genome: the role of chromatin in domain-wide gene regulation

Cheng-Fu Chang, Ka-Man Wai1 and Hugh G. Patterton*

Department of Molecular and Cell Biology and Institute for Infectious Diseases and Molecular Medicine and 1 Department of Computer Science, University of Cape Town, University Private Bag, Rondebosch 7701, South Africa

*To whom correspondence should be addressed at: Department of Molecular and Cell Biology, University of Cape Town, University Private Bag, Rondebosch 7701, South Africa. Tel: +27 21 650 3267; Fax: +27 21 650 5188; Email: patterh{at}science.uct.ac.za

Received December 25, 2003; Revised January 23, 2004; Accepted March 5, 2004

Physical clusters of co-regulated, but apparently functionally unrelated, genes are present in many genomes. Despite the important implication that the genomic environment contributes appreciably to the regulation of gene expression, no simple statistical method has been described to identify physical clusters of co-regulated genes. Here we report the development of a model that allows the direct calculation of the significance of such clusters. We have implemented the derived statistical relation in a software program, Pyxis, and have analyzed a selection of Saccharomyces cerevisiae gene expression microarray data sets. We have identified many gene clusters where constituent genes exhibited a regulatory dependence on proteins previously implicated in chromatin structure. Specifically, we found that Tup1p-dependent gene domains were enriched close to telomeres, which suggested a new role for Tup1p in telomere silencing. In addition, we identified Sir2p-, Sir3p- and Sir4p-dependent clusters, which suggested the presence of Sir-mediated heterochromatin in previously unidentified regions of the yeast genome. We also showed the presence of Sir4p-dependent gene clusters bordering the HMRa heterothallic locus, which suggested leaky termination of the heterochromatin by the boundary elements. These results demonstrate the utility of Pyxis in identifying possible higher order genomic features that may contribute to gene regulation in extended domains.


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