Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Abstract

Background: The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes.

Results: We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters.

Conclusion: The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

Figure 1

Schematic representation of the PEAKS method. Detection of positional bias of two hypothetical motifs in a promoter sequence dataset is shown. After motif scanning, a profile of motif frequency is obtained. The horizontal line delineates the region above a given p-value cut-off. Significant regions are plotted into a single integrated representation.

Figure 2

Integrated representation of motifs with significant positional bias in mouse promoters. The results were obtained by the program PEAKS, using different motif libaries. A. TRANSFAC PSWMs. B. JASPAR CORE PSWMs. C. JASPAR phyloFACTS. D. oligomers of size 6 (6mers). Motifs that belong to the same motif cluster are shown with the same color. A region from -200 to +100 with respect to the TSS is shown. The width of the ovals is the significant region of each motif (p-value <= 10^-5). The height of the ovals, the relative motif signal (RMS), is the number of sequences that contain a motif located at the position with the maximum score divided by the minimum number of sequences containing that motif that would be required to pass the p-value cut-off.

Figure 3

Promoter motif profiles in mouse genes with different expression width. ALL: complete promoter dataset; HK: housekeeping genes; RT: genes with restricted expression. Profiles were obtained with the program PEAKS using window size 31. Profiles with no significant sequence ranges (NA) did not accomplish p-value <= 10^-5. Left-most cells contain the TRANSFAC matrix (or JASPAR for TBP) used for motif prediction and the significant regions in the different datasets. Background color indicates score value grading, from intense red (highest) to pale yellow (lowest). 'score' is the positional footprinting score; '%seq' percentage of sequences at maximum peak; 'pos.', position of the maximum peak; 'ranges' sequence interval significant above the p-value cut-off.

Figure 4

Promoter motif profiles in mouse genes expressed in particular tissues. Selection of motifs that were significant in genes expressed in a particular tissue but not in the housekeeping (HK) dataset. See also Legend to Figure 3.