Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

Qianqian Zhu,Marc S Halfon

doi:10.1186/1471-2164-10-9

Abstract

BackgroundThe promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating temporal and spatial aspects of gene expression through differential binding of transcription factors and selective interaction with distal enhancers. Although many genes have multiple promoters, little attention has been focused on how these relate to one another; nor has much study been directed at relationships between promoters of adjacent genes.ResultsWe have undertaken a systematic investigation of Drosophila promoters. We divided promoters into three groups: unique promoters, first alternative promoters (the most 5' of a gene's multiple promoters), and downstream alternative promoters (the remaining alternative promoters 3' to the first). We observed distinct nucleotide distribution and sequence motif preferences among these three classes. We also investigated the promoters of neighboring genes and found that a greater than expected number of adjacent genes have similar sequence motif profiles, which may allow the genes to be regulated in a coordinated fashion. Consistent with this, there is a positive correlation between similar promoter motifs and related gene expression profiles for these genes.ConclusionsOur results suggest that different regulatory mechanisms may apply to each of the three promoter classes, and provide a mechanism for "gene expression neighborhoods," local clusters of co-expressed genes. As a whole, our data reveal an unexpected complexity of genomic organization at the promoter level with respect to both alternative and neighboring promoters.

Highlights

The promoter is a critical necessary transcriptional cis-regulatory element
Consistent with the trends we observed in the distribution plots, we found that the GC content differs significantly among all three classes of promoters with downstream alternative promoters (DAPs) > first alternative promoters (FAPs) > unique promoters (UPs) (DAP versus UP: mean 0.413 (standard deviation (SD) 0.060) versus 0.379 (0.062), Kolmogorov-Smirnov test P ≈ 0; DAP versus FAP: 0.413 (0.060) versus 0.397 (0.065), Kolmogorov-Smirnov test P ≈ 7.46e-11; FAP versus UP: 0.397 (0.065) versus 0.379 (0.062), Kolmogorov-Smirnov test P ≈ 4.44e-16)
For each of the 15 motifs, we looked at their relative distributions in UPs, FAPs, and DAPs; 13 of them show a significant occurrence bias among the three promoter classes (Table 1)

Summary

Introduction

In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating temporal and spatial aspects of gene expression through differential binding of transcription factors and selective interaction with distal enhancers. Coordinated regulation of gene expression is a fundamental process that depends on the binding of transcription factors to a gene's cis-regulatory sequences. Various tissue-specific members of the TATA box-binding protein (TBP) family, such as the TBP-related factors (TRFs), bind preferentially to certain core promoters [4]. There is substantial evidence for preferred or specific promoter-enhancer interactions, whereby a distal cis-regulatory module (CRM, or "enhancer") can stimulate activity from one promoter, but not another [9,10]

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Discussion

Conclusion