Characteristics of Core Promoter Types with respect to Gene Structure and Expression in Arabidopsis thaliana

Abstract

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.

Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures

“…Previous studies (Yamamoto et al, 2009(Yamamoto et al, , 2011 reported that TATA-box and sequence enrichments, such as GA content, were associated heavily with TSS peaks of different patterns. These reports suggest that given a high-resolution data set and a model that uses location-specific enrichments, these features alone could be explanatory.…”

“…However, the overall frequency of functional TF binding events in vivo, the functional combinations with other elements, and the positional preferences within plant gene promoters remain largely unknown. In a popular model, the TATA-box and one of several possible plant-specific forms of the Initiator element may alone form a recognizable core promoter of pol-II transcribed genes in plants (Grasser, 2006;Yamamoto et al, 2011). Yet, some well-studied and highly expressed plant genes do not contain an upstream TATA site (Nakamura et al, 2002), and this combination of short sequence elements is abundant in intergenic regions.…”

“…Since this time, there have been no major changes to views of plant core promoters. More recently, motif discovery-based analyses utilizing thousands of available promoter examples (Yamamoto et al, 2009(Yamamoto et al, , 2011 have included a focus on general sequence enrichments such as Y-Patch, GA, and CA elements, hypothesizing that these enrichments may play a similar role to CpG islands in mammalian promoters. CpG islands are found in the promoters of many mammalian genes (Saxonov et al, 2006), and their presence has been used as a key feature in TSS prediction models (Deaton and Bird, 2011).…”

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

“…While many of these CPEs have been well studied in animals, studies in plants are not as extensive, leaving many elements that have only been identified computationally (Yamamoto et al, 2007a(Yamamoto et al, , 2011Civán and Svec, 2009;Bernard et al, 2010;Zuo and Li, 2011;Kumari and Ware, 2013). This is especially problematic considering that even some of the most well studied and conserved elements such as TATA and Inr show distinct consensus sequence differences in plants compared with their yeast and mammalian counterparts, making plant-specific consensus sequence identification an important priority in accurate promoter identification in plants (Kumari and Ware, 2013).…”

Unexpected Structure of Plant Promoters

“…The structure of plant promoters has been considered to be similar to that of animals, with "core" and "enhancer" regions, defined by positionspecific DNA binding elements such as the TATA box (Kaufmann et al, 2010). Although known to be lacking in some promoters, the TATA box is still thought to be a defining element of many plant promoters (Yamamoto et al, 2011). However, few studies have examined the basic structure of plant promoters on a genome-wide scale with advanced high-resolution sequencing techniques available today.…”