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Functional & Integrative Genomics

, Volume 7, Issue 4, pp 335–345 | Cite as

Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms

  • Anthony R. Borneman
  • Zhengdong D. Zhang
  • Joel Rozowsky
  • Michael R. Seringhaus
  • Mark Gerstein
  • Michael Snyder
Original Paper

Abstract

In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.

Keywords

Tiling array Chromatin immunoprecipitation Microarray Yeast 

Notes

Acknowledgments

We would like to thank Elsa Eysteinsdottir and Chloe Lepar for expert technical assistance and Dan Gelperin for critical reading of this manuscript. This work was supported by Burroughs Wellcome and NIH grants to M.S. and M.G.

Supplementary material

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Anthony R. Borneman
    • 1
  • Zhengdong D. Zhang
    • 2
  • Joel Rozowsky
    • 2
  • Michael R. Seringhaus
    • 2
  • Mark Gerstein
    • 2
  • Michael Snyder
    • 1
    • 2
  1. 1.Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenUSA
  2. 2.Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUSA

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