Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

Ohtsu, K., Smith, M. B., Emrich, S. J., Borsuk, L. A., Zhou, R. L., Chen, T. L., Zhang, X. L., Timmermans, M. C. P., Beck, J., Buckner, B., Janick-Buckner, D., Nettleton, D., Scanlon, M. J., Schnable, P. S. (November 2007) Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant Journal, 52 (3). pp. 391-404. ISSN 0960-7412

URL: https://www.ncbi.nlm.nih.gov/pubmed/17764504
DOI: 10.1111/j.1365-313X.2007.03244.x

Abstract

All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.

Item Type: Paper
Uncontrolled Keywords: shoot apical meristem global gene expression laser capture microdissection 454 sequencing development retrotransposon expression LASER-CAPTURE MICRODISSECTION DNA METHYLATION RNA-POLYMERASE TRANSPOSABLE ELEMENTS ARABIDOPSIS-THALIANA LEAF DEVELOPMENT AUXIN TRANSPORT TISSUE-CULTURE HOMEOBOX GENES ROUGH SHEATH2
Subjects: organism description > plant > maize
organs, tissues, organelles, cell types and functions > tissues types and functions > apical meristem
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > cDNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Timmermans lab
Depositing User: CSHL Librarian
Date: November 2007
Date Deposited: 07 Nov 2011 19:50
Last Modified: 17 Feb 2017 16:32
PMCID: PMC2156186
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23111

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