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Plant and Cell Physiology Advance Access originally published online on October 3, 2008
Plant and Cell Physiology 2008 49(10):1451-1464; doi:10.1093/pcp/pcn129
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and the Japanese Society of Plant Physiologists are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Special Issue - Regular Paper

In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice

Motohiro Mihara1, Takeshi Itoh2 and Takeshi Izawa1,*

1Plant Genomics Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Japan
2Bioinformatics Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, 305-8602 Japan

*Corresponding author: E-mail, tizawa{at}nias.affrc.go.jp


  Abstract

Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells at various stages of development. Having joined the LM-microarray analysis project, we utilized such genome-wide gene expression data from developing rice pollen cells to identify candidates for cis-regulatory elements for specific gene expression in these cells. We first found a few clusters of gene expression patterns based on the data from LM-microarrays. On one gene cluster in which the members were specifically expressed at the bicellular and mature pollen mitotic stages, we identified gene cluster fingerprints (GCFs), each of which consists of a short nucleotide representing the gene cluster. We expected that these GCFs would contain cis-regulatory elements for stage- and tissue-specific gene expression, and we further identified groups of GCFs with common core sequences. Some criteria, such as frequency of occurrence in the gene cluster in contrast to the total tested gene set, flanking sequence preference and distribution of combined GCF sets in the gene regions, allowed us to limit candidates for cis-regulatory sequences for specific gene expression in rice pollen cells to at least 20 sets of combined GCFs. This approach should provide a general purpose algorithm for identifying short nucleotides associated with specific gene expression.

Keywords: Cis-regulatory elements - Microarray - Pollen development - Rice - Transcription factor-binding site (TFBS) - Transcription start site (TSS)

Abbreviations: GCF, gene cluster fingerprint; EST, expressed sequence tag; GA20ox, gibberellin 20-oxidase; GA3βox, gibberellin 3β-oxidase; GRSF, germline-restrictive silencing factor; LDSS, local distribution of short sequences; LM, laser microdissection; RAP, Rice Annotation Project; TFBS, transcription factor-binding site; TSS, transcription start site

(Received July 31, 2008; Accepted August 29, 2008)
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