Promoter Elements in Drosophila melanogaster Revealed by Sequence Analysis

INVESTIGATIONS

Promoter Elements in Drosophila melanogaster Revealed by Sequence Analysis

I. R. Arkhipova
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138

A Drosophila Promoter Database containing 252 independent Drosophila melanogaster promoter entries has been compiled. The database and its subsets have been searched for overrepresented sequences. The analysis reveals that the proximal promoter region displays the most dramatic nucleotide sequence irregularities and exhibits a tripartite structure, consisting of TATA at -25/-30 bp, initiator (Inr) at +/-5 bp and a novel class of downstream elements at +20/+30 bp from the RNA start site. These latter elements are also strand-specific. However, they differ from TATA and Inr in several aspects: (1) they are represented not by a single, but by multiple sequences, (2) they are shorter, (3) their position is less strictly fixed with respect to the RNA start site, (4) they emerge as a characteristic feature of Drosophila promoters and (5) some of them are strongly overrepresented in the TATA-less, but not TATA-containing, subset. About one-half of known Drosophila promoters can be classified as TATA-less. The overall sequence organization of the promoter region is characterized by an extended region with an increase in GC-content and a decrease in A, which contains a number of binding sites for Drosophila transcription factors.

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				T. W. Burke and J. T. Kadonaga The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila Genes & Dev., November 15, 1997; 11(22): 3020 - 3031. [Abstract] [Full Text] [PDF]

				C Merli, D E Bergstrom, J A Cygan, and R K Blackman Promoter specificity mediates the independent regulation of neighboring genes. Genes & Dev., May 15, 1996; 10(10): 1260 - 1270. [Abstract] [PDF]

				T W Burke and J T Kadonaga Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes & Dev., March 15, 1996; 10(6): 711 - 724. [Abstract] [PDF]

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