Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Mihara, Motohiro, Itoh, Takeshi, Izawa, Takeshi
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566928/
https://www.ncbi.nlm.nih.gov/pubmed/18835840
http://dx.doi.org/10.1093/pcp/pcn129
_version_ 1782159971965730816
author Mihara, Motohiro
Itoh, Takeshi
Izawa, Takeshi
author_facet Mihara, Motohiro
Itoh, Takeshi
Izawa, Takeshi
author_sort Mihara, Motohiro
collection PubMed
description 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.
format Text
id pubmed-2566928
institution National Center for Biotechnology Information
language English
publishDate 2008
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-25669282009-02-25 In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice Mihara, Motohiro Itoh, Takeshi Izawa, Takeshi Plant Cell Physiol Special Issue – Regular Papers 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. Oxford University Press 2008-10 2008-10-10 /pmc/articles/PMC2566928/ /pubmed/18835840 http://dx.doi.org/10.1093/pcp/pcn129 Text en © 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
spellingShingle Special Issue – Regular Papers
Mihara, Motohiro
Itoh, Takeshi
Izawa, Takeshi
In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title_full In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title_fullStr In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title_full_unstemmed In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title_short In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
title_sort in silico identification of short nucleotide sequences associated with gene expression of pollen development in rice
topic Special Issue – Regular Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566928/
https://www.ncbi.nlm.nih.gov/pubmed/18835840
http://dx.doi.org/10.1093/pcp/pcn129
work_keys_str_mv AT miharamotohiro insilicoidentificationofshortnucleotidesequencesassociatedwithgeneexpressionofpollendevelopmentinrice
AT itohtakeshi insilicoidentificationofshortnucleotidesequencesassociatedwithgeneexpressionofpollendevelopmentinrice
AT izawatakeshi insilicoidentificationofshortnucleotidesequencesassociatedwithgeneexpressionofpollendevelopmentinrice