title: Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags.
abstract: Information about transcription start sites (TSSs) provides baseline data for the analysis of promoter architecture. In this paper we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324 461 promoters that covered 79.7% (21 672/27 206) of protein-coding genes in the Arabidopsis genome. In addition we identified intragenic, antisense and orphan promoters that were not associated with any gene models. Of these, intragenic promoters exhibited unique characteristics regarding dinucleotide sequences at TSSs and core promoter element composition, suggesting that these promoters use different mechanisms of transcriptional initiation. An analysis of base composition with regard to promoter position revealed a low GC content throughout the promoter region and several local strand biases that were evident for TATA-type promoters, but not for Coreless-type promoters. Most observed strand biases coincided with strand biases of single nucleotide polymorphism rate. Our analysis also revealed that transcription of a gene is supported by an average of 2.7 genic promoters, among which one specific promoter, designated as a top promoter, substantially determines the expression level of the gene.
authors.affiliation: United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.
authors.forename: Mutsutomo
authors.initials: M
authors.lastname: Tokizawa
authors.affiliation: United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.
authors.forename: Kazutaka
authors.initials: K
authors.lastname: Kusunoki
authors.affiliation: United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.|Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Koyama
authors.affiliation: RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kurotani
authors.affiliation: RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Sakurai
authors.affiliation: Institute of Medical Science, University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo, 108-8639, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Sakamoto
authors.affiliation: Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayam-cho 8916-5, Ikoma, Nara, 630-0192, Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Kurata
authors.affiliation: United Graduate School of Agriculture, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.|Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu City, Gifu, 501-1193, Japan.|RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.|JST ALCA, Tokyo, Japan.
authors.forename: Yoshiharu Y
authors.initials: YY
authors.lastname: Yamamoto
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D011401:Promoter Regions, Genetic / Q000235:genetics*; D024363:Transcription Initiation Site / Q000502:physiology*
chemical_list: D029681:Arabidopsis Proteins
keywords: 
  Arabidopsis thaliana
  ; TSS-seq; core promoter element; promoter; promoter maturation; transcription start site; transcriptional regulation