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Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment

Nature Methods volume 2, pages 47–53 (2005)Cite this article

Abstract

Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets of transcription factors in vivo. STAGE is based on high-throughput sequencing of concatemerized tags derived from target DNA enriched by chromatin immunoprecipitation. We first used STAGE in yeast to confirm that RNA polymerase III genes are the most prominent targets of the TATA-box binding protein. We optimized the STAGE protocol and developed analysis methods to allow the identification of transcription factor targets in human cells. We used STAGE to identify several previously unknown binding targets of human transcription factor E2F4 that we independently validated by promoter-specific PCR and microarray hybridization. STAGE provides a means of identifying the chromosomal targets of DNA-associated proteins in any sequenced genome.

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Figure 1: The STAGE strategy.
Figure 2: Correlation between yeast targets predicted by STAGE and ChIP-chip.
Figure 3: ChIP of E2F4 targets and validation of STAGE targets by ChIP-PCR.
Figure 4: Validation by ChIP-chip of E2F4 targets predicted by STAGE.

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Acknowledgements

We thank K. Struhl for the HA-tagged TBP strain, P. Killion for assistance with the microarray database and T. Hart and members of the Iyer lab for assistance with microarray production. This work was supported in part by a grant from the Texas State Higher Education Coordinating Board, a US Department of Defense Breast Cancer Idea Award and a National Science Foundation Information Technology Research (ITR) grant.

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  1. Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology & Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, 78712-0159, Texas, USA

    Jonghwan Kim, Akshay A Bhinge, Xochitl C Morgan & Vishwanath R Iyer

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  1. Jonghwan Kim
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  2. Akshay A Bhinge
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Correspondence to Vishwanath R Iyer.

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Supplementary information

Supplementary Table 1

Summary of STAGE tags sequenced (PDF 12 kb)

Supplementary Table 2

Gene scores from E2F4 STAGE and SubSTAGE (PDF 114 kb)

Supplementary Table 3

Human E2F4 targets predicted by STAGE (between 10 kb and 6 kb upstream of transcription start site) (PDF 92 kb)

Supplementary Table 4

Human E2F4 targets predicted by STAGE (between 6 kb and 2 kb upstream of transcription start site) (PDF 80 kb)

Supplementary Table 5

Human E2F4 targets predicted by STAGE (1st intron) (PDF 63 kb)

Supplementary Table 6

Primer pairs for ChIP-PCR verification (PDF 92 kb)

Supplementary Methods (PDF 28 kb)

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Kim, J., Bhinge, A., Morgan, X. et al. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat Methods 2, 47–53 (2005). https://doi.org/10.1038/nmeth726

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