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Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements.

The TATA box is one of the best characterized transcription factor binding sites. However, it is not a ubiquitous element of core promoters, and other sequence motifs such as Y Patches seem to play a major role in plants. Here, we present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice (Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only approximately 19% of rice genes possess the TATA box, but approximately 50% contain one or more Y Patches in their core promoters. By computational processing of identified elements, we generated extended TATA box and Y Patch nucleotide frequency matrices capable of predicting these motifs in plants with a high degree of confidence.