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

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.