Discovering functional transcription-factor combinations in the human cell cycle

Abstract

With the completion of full genome sequences and advancement in high-throughput technologies, in silico methods have been successfully used to integrate diverse data sources toward unraveling the combinatorial nature of transcriptional regulation. So far, almost all of these studies are restricted to lower eukaryotes such as budding yeast. We describe here a computational search for functional transcription-factor (TF) combinations using phylogenetically conserved sequences and microarray-based expression data. Taking into account both orientational and positional constraints, we investigated the overrepresentation of binding sites in the vicinity of one another and whether these combinations result in more coherent expression profiles. Without any prior biological knowledge, the search led to the discovery of several experimentally established TF associations, as well as some novel ones. In particular, we identified a regulatory module controlling cell cycle-dependent transcription of G2-M genes and expanded its functional generality. We also detected many homotypic combinations, supporting the importance of binding-site density in transcriptional regulation of higher eukaryotes.

Figure 1.

Strategy used to discover functional combinations for any motif of interest.

Figure 2.

Distribution of all and human-mouse conserved E2F-binding sites relative to transcription start site (as estimated by the start of mRNA sequence).

Figure 3.

A functional combination discovered from our analysis involving NF-Y binding site and a significantly enriched neighbor motif within 50 bp downstream. (A) Sequence logo of the neighbor motif, produced by the World Wide Web service at http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi. The height of each letter is proportional to its frequency of occurrence in the binding-site matrix, times the information content at each position. (B) The expression profiles of genes containing the NF-Y neighbor-motif combination. The blue lines represent expression profiles of individual genes, and the red line represents mean expression profile of the group. (C) The expression profiles of genes containing NF-Y motif, but without neighbor motif within 50 bp downstream. (D) The expression profile of genes containing the neighbor motif, but without NF-Y within 50 bp upstream.

Figure 3.

A functional combination discovered from our analysis involving NF-Y binding site and a significantly enriched neighbor motif within 50 bp downstream. (A) Sequence logo of the neighbor motif, produced by the World Wide Web service at http://www.bio.cam.ac.uk/cgi-bin/seqlogo/logo.cgi. The height of each letter is proportional to its frequency of occurrence in the binding-site matrix, times the information content at each position. (B) The expression profiles of genes containing the NF-Y neighbor-motif combination. The blue lines represent expression profiles of individual genes, and the red line represents mean expression profile of the group. (C) The expression profiles of genes containing NF-Y motif, but without neighbor motif within 50 bp downstream. (D) The expression profile of genes containing the neighbor motif, but without NF-Y within 50 bp upstream.