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Nucleic Acids Research Advance Access published online on September 12, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm685
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Genomics

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis

Yoshiharu Y. Yamamoto1,*, Hiroyuki Ichida2,3, Tomoko Abe2, Yutaka Suzuki4, Sumio Sugano4 and Junichi Obokata1

1Center for Gene Research, Nagoya University, Nagoya, Aichi 464-8602, 2RIKEN Nishina Center for Accelerator-Based Science, 2-1 Hirosawa, Wako, Saitama 351-0198, 3Graduate School of Science and Technology, Chiba University, 1-33, Yayoi-cho, Inage-ku, Chiba-shi, Chiba 263-8522 and 4Department of Medical Genome Sciences, Graduate School of Frontier Science, Institute of medical Science, University of Tokyo, Shiroganedai 4-6-1, Minato-ku, Tokyo 108-8639, Japan

*To whom correspondence should be addressed. Tel: +81 52 789 3083; Fax: +81 52 789 3083; Email: yyoshi{at}gene.nagoya-u.ac.jp

Received August 1, 2007. Revised August 19, 2007. Accepted August 20, 2007.

Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also found in plant promoters, it is not known if CpG-type promoters exist in plants. Plant promoters contain Y Patches (pyrimidine patches) in the core promoter region, and the ubiquity of these beyond higher plants is not understood as well. Sets of promoter sequences were utilized for the analysis of local distribution of short sequences (LDSS), and approximately one thousand octamer sequences have been identified as promoter constituents from Arabidopsis, rice, human and mouse, respectively. Based on their localization profiles, the identified octamer sequences were classified into several major groups, REG (Regulatory Element Group), TATA box, Inr (Initiator), Kozak, CpG and Y Patch. Comparison of the four species has revealed three categories: (i) shared groups found in both plants and mammals (TATA box), (ii) common groups found in both kingdoms but the utilized sequence is differentiated (REG, Inr and Kozak) and (iii) specific groups found in either plants or mammals (CpG and Y Patch). Our comparative LDSS analysis has identified conservation and differentiation of promoter architectures between higher plants and mammals.


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