Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms
- 135 Downloads
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.
KeywordsTiling array Chromatin immunoprecipitation Microarray Yeast
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.
- Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang JY, Gerstein M, Snyder M (2007) Divergence of transcription factor binding sites across related yeast species. Science, in pressGoogle Scholar
- Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, Wheeler R, Wong B, Drenkow J, Yamanaka M, Patel S, Brubaker S, Tammana H, Helt G, Struhl K, Gingeras TR (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499–509PubMedCrossRefGoogle Scholar
- Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, Shannon KW, Lefkowitz SM, Ziman M, Schelter JM, Meyer MR, Kobayashi S, Davis C, Dai H, He YD, Stephaniants SB, Cavet G, Walker WL, West A, Coffey E, Shoemaker DD, Stoughton R, Blanchard AP, Friend SH, Linsley PS (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19:342–347PubMedCrossRefGoogle Scholar
- Nuwaysir EF, Huang W, Albert TJ, Singh J, Nuwaysir K, Pitas A, Richmond T, Gorski T, Berg JP, Ballin J, McCormick M, Norton J, Pollock T, Sumwalt T, Butcher L, Porter D, Molla M, Hall C, Blattner F, Sussman MR, Wallace RL, Cerrina F, Green RD (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res 12:1749–1755PubMedCrossRefGoogle Scholar
- Zhang ZD, Rozowsky JS, Lam HYK, Snyder M, Gerstein MB (2007) Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol, in pressGoogle Scholar