Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags

Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y. Yamamoto

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)587-605
Number of pages19
JournalPlant Journal
Issue number3
Publication statusPublished - 2017 May
Externally publishedYes


  • Arabidopsis thaliana
  • TSS-seq
  • core promoter element
  • promoter
  • promoter maturation
  • transcription start site
  • transcriptional regulation

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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