Characterization of structure, divergence and regulation patterns of plant promoters

Liu, Yingchun, Yin, Jiaming, Xiao, Meili, Mason, Annaliese S., Gao, Caihua, Liu, Honglei, Li, Jiana and Fu, Donghui (2013) Characterization of structure, divergence and regulation patterns of plant promoters. Journal of Molecular Biology Research, 3 1: 23-36. doi:10.5539/jmbr.v3n1p23

Author Liu, Yingchun
Yin, Jiaming
Xiao, Meili
Mason, Annaliese S.
Gao, Caihua
Liu, Honglei
Li, Jiana
Fu, Donghui
Title Characterization of structure, divergence and regulation patterns of plant promoters
Journal name Journal of Molecular Biology Research   Check publisher's open access policy
ISSN 1925-430X
Publication date 2013-04-27
Year available 2013
Sub-type Article (original research)
DOI 10.5539/jmbr.v3n1p23
Open Access Status DOI
Volume 3
Issue 1
Start page 23
End page 36
Total pages 14
Place of publication Toronto, Canada
Publisher Canadian Center of Science and Education
Collection year 2014
Language eng
Abstract Plant promoters have attracted increasing attention because of their irreplaceable role in modulating the spatio-temporal expression of genes interacting with transcription factors (TFs). Despite their importance, the basic characteristics of plant promoters are not well understood. In order to determine sequence diversity within promoter regions, evolutionary divergence of promoters between plant species, and the general structural characteristics of promoter sequences, we downloaded and analyzed 3922 plant promoter sequences from a wide range of plant species. The average plant promoter GC content was lower in dicotyledons than in monocotyledons, which might suggest different evolutionary pressures for promoter sequences between the twoclades. Approximately 3.3% of plant promoters harbored minisatellite sequences, and 15.4% of plant promoters harbored microsatellite sequences (also called simple sequence repeats). Very few transposable elements were detected within the plant promoters. The most common transcription factor binding site (TFBS) motif was AGAGAGAGA, followed by TTAGGGTTT and then GCCGCC. Transcribed gene regions with promoters containing the corresponding TFBSs were predicted to be most commonly involved in metabolic processes, biological regulation, and stimulus response in plants. These results reveal some basic structural characteristics of plant promoters and clarify the evolutionary forces shaping plant promoters. This data might facilitate cloning of plant promoter sequences and aid in our understanding of gene spatio-temporal expression patterns in plants.
Keyword Transcription factor binding sites
Transposable elements
Functional annotation,
GC content,
Evolutionary forces
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2014 Collection
Version Filter Type
Citation counts: Google Scholar Search Google Scholar
Created: Tue, 02 Jul 2013, 09:36:26 EST by Annaliese Mason on behalf of School of Agriculture and Food Sciences