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Functional analysis of transcription factor binding sites in human promoters

Troy W Whitfield1, Jie Wang1, Patrick J Collins2, E Christopher Partridge3, Shelley Force Aldred2, Nathan D Trinklein2, Richard M Myers3 and Zhiping Weng1*

Author affiliations

1 Program in Bioinformatics and Integrative Biology and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA

2 SwitchGear Genomics, Menlo Park, CA 94025, USA

3 HudsonAlpha Institute for Biotechnology, Hunstville, AL 35806, USA

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Citation and License

Genome Biology 2012, 13:R50  doi:10.1186/gb-2012-13-9-r50

Published: 5 September 2012

Abstract

Background

The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out functional tests on these sites in four different immortalized human cell lines using transient transfections with a luciferase reporter assay, primarily for the transcription factors CTCF, GABP, GATA2, E2F, STAT, and YY1.

Results

In each cell line, between 36% and 49% of binding sites made a functional contribution to the promoter activity; the overall rate for observing function in any of the cell lines was 70%. Transcription factor binding resulted in transcriptional repression in more than a third of functional sites. When compared with predicted binding sites whose function was not experimentally verified, the functional binding sites had higher conservation and were located closer to transcriptional start sites (TSSs). Among functional sites, repressive sites tended to be located further from TSSs than were activating sites. Our data provide significant insight into the functional characteristics of YY1 binding sites, most notably the detection of distinct activating and repressing classes of YY1 binding sites. Repressing sites were located closer to, and often overlapped with, translational start sites and presented a distinctive variation on the canonical YY1 binding motif.

Conclusions

The genomic properties that we found to associate with functional TF binding sites on promoters -- conservation, TSS proximity, motifs and their variations -- point the way to improved accuracy in future TFBS predictions.