Abstract
BackgroundThe 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.ResultsTransgenic 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.ConclusionExamining 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.
Highlights
The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically
C. elegans transcription factor gene promoter/reporter gene fusions A recent comprehensive analysis of the C. elegans genome using a combination of computational and manual interrogation methods compiled a list of 934 putative transcription factor genes, wTF2.0 [15] and this formed the
The translational initiation codon was selected as the downstream end point in the cloned DNA fragment of each promoterome clone, as trans-splicing means the transcriptional start is known for few C. elegans genes
Summary
The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. A primary determinant of the spectrum of gene products in each cell will be the spectrum of sequence specific transcription factors that have driven expression of the genome during that cell's developmental history The scale of this problem, which needs to be addressed to fully understand an animal's development, would be dramatically reduced by using a species in which development, at least down to the level of individual cells, is invariant. These considerations make the free-living soil nematode Caenorhabditis elegans an excellent choice for systems biology approaches [1]. The remarkable conservation of biological processes, at the molecular genetic level, means that findings with this animal are likely to be widely relevant
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