Journal Article

Characteristics of Core Promoter Types with respect to Gene Structure and Expression in <i>Arabidopsis thaliana</i>

Yoshiharu Y. Yamamoto, Yohei Yoshioka, Mitsuro Hyakumachi and Junichi Obokata

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 18, issue 5, pages 333-342
Published in print October 2011 | ISSN: 1340-2838
Published online July 2011 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsr020

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It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent transcription. Several transcriptional characteristics are known to be associated with core types, including distribution patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive expression profiles. However, their relationship to gene structure is poorly understood. In this report, we carried a comparative analysis of three Arabidopsis core types, TATA, GA, and Coreless, with regard to gene structure. Our genome-wide investigation was based on the peak TSS positions in promoters that had been identified in a large-scale experimental analysis. This analysis revealed that the types of core promoter are related with the room for promoters that is measured as the distance from the TSS to the end of the upstream gene, the distance from the TSS to the start position of the coding sequence (CDS), and the number and species of the cis-regulatory elements. Of these, it was found that the distance from the TSS to the CDS has a tight, inverse correlation to the expression level, and thus the observed relationship to the core type appears to be indirect. However, promoter length and preference of cis-elements are thought to be a direct reflection of core type-specific transcriptional initiation mechanisms.

Keywords: plant genome; core promoter; environmental response; 5′ UTR

Journal Article.  4881 words.  Illustrated.

Subjects: Genetics and Genomics

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