Drosophila Functional Genomics

Diabetes, Digestive, Kidney Diseases

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Abstract

Core promoters are critical starting points for the transcription of information encoded in the genome. While there a number of case studies that have identified a few of the sequences that can function at core promoters, we know little about these elements on a global scale and even less about what core promoter subtypes might have to do with deployment of specific genes or classes of genes.[unreadable] [unreadable] We mapped the position of all possible octamers (65,536) in all known Drosophila promoters and in two human promoter data sets. Several hundred of these sequences are preferentially located at precise distances from the transcription start site. These positioned sequences occurred on a single strand or on both strands and showed differing degrees of positional constraint. Interestingly, particular octamers are associated with particular functional classes of genes (based on controlled vocabulary from the Gene Ontology project) and on both temporal and spatial expression patterns. These data suggest that there is greater core promoter diversity than previously recognized (perhaps even a core promoter code). Core promoter elements may be binding sites for proteins that are thematically similar to prokaryotic sigma factors.