Sequence-based evaluation of promoter context for prediction of transcription start sites in Arabidopsis and rice.

ABSTRACT: Genes are transcribed from transcription start sites (TSSs), and their position in a genome is strictly controlled to avoid mis-expression of undesired regions. In this study, we designed and developed a methodology for the evaluation of promoter context, which detects proximal promoter regions from - 200 to - 60 bp relative to a TSS, in Arabidopsis and rice genomes. The method positively evaluates spacer sequences and Regulatory Element Groups, but not core promoter elements like TATA boxes, and is able to predict the position of a TSS within a width of 200 bp. An important feature of the evaluation/prediction method is its independence of the core promoter elements, which was demonstrated by successful prediction of all the TATA, GA, and coreless types of promoters without notable differ

SUBMITTER: Hiratsuka T 

PROVIDER: S-EPMC9050755 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature