Open Access Research article

Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns

John S Reece-Hoyes1, Jane Shingles1, Denis Dupuy2, Christian A Grove3, Albertha JM Walhout3, Marc Vidal2 and Ian A Hope1*

Author Affiliations

1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK

2 Center for Cancer Systems Biology (CCSB), and Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA

3 Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 364 Plantation Street, Lazare Research Building, Room 605, MA 01605, USA

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BMC Genomics 2007, 8:27  doi:10.1186/1471-2164-8-27

Published: 23 January 2007

Abstract

Background

The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription factors will form the core of any systems biology model of genome control and therefore the promoter activity of Promoterome inserts for C. elegans transcription factor genes was examined, in vivo, with a reporter gene approach.

Results

Transgenic C. elegans strains were generated for 366 transcription factor promoter/gfp reporter gene fusions. GFP distributions were determined, and then summarized with reference to developmental stage and cell type. Reliability of these data was demonstrated by comparison to previously described gene product distributions. A detailed consideration of the results for one C. elegans transcription factor gene family, the Six family, comprising ceh-32, ceh-33, ceh-34 and unc-39 illustrates the value of these analyses. The high proportion of Promoterome reporter fusions that drove GFP expression, compared to previous studies, led to the hypothesis that transcription factor genes might be involved in local gene duplication events less frequently than other genes. Comparison of transcription factor genes of C. elegans and Caenorhabditis briggsae was therefore carried out and revealed very few examples of functional gene duplication since the divergence of these species for most, but not all, transcription factor gene families.

Conclusion

Examining reporter expression patterns for hundreds of promoters informs, and thereby improves, interpretation of this data type. Genes encoding transcription factors involved in intrinsic developmental control processes appear acutely sensitive to changes in gene dosage through local gene duplication, on an evolutionary time scale.