Differential gene expression in <i>Arabidopsis</i> monitored using cDNA arrays

Desprez, Thierry; Amselem, Joëlle; Caboche, Michel; Höfte, Monica

doi:10.1046/j.1365-313x.1998.00160.x

Cited by 114 publications

(67 citation statements)

References 25 publications

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“…Weak expression or low specific activity of cDNA probes (Seki et al 2001) could account for differences reported between macroarray results and RNA gel blots (Taniguchi et al 2001) or QRT-PCR (Desprez et al 1998;Kurth et al 2002).…”

Section: Rna Gel Blot Analysismentioning

confidence: 99%

Changes in gene expression in maize kernel in response to water and salt stress

Andjelkovic

Thompson

2005

Plant Cell Rep

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Increasing pressure on limited water resources for agriculture, together with the global temperature increase, highlight the importance of breeding for droughttolerant cultivars. A better understanding of the molecular nature of drought stress can be expected through the use of genomics approaches. Here, a macroarray of ≈2500 maize cDNAs was used for determining transcript changes during water-and salt-stress treatments of developing kernels at 15 days after pollination. Normalization of relative transcript abundances was carried out using a human nebulin control sequence. The proportions of transcripts that changed significantly in abundance upon treatment (>2-fold compared to the control) were determined; 1.5% of the sequences examined were up-regulated by high salinity and 1% by water stress. Both stresses induced 0.8% of the sequences. These include genes involved in various stress responses: abiotic, wounding and pathogen attack (abscisic acid response binding factor, glycine and proline-rich proteins, pathogenesis-related proteins, etc.). The proportion of down-regulated genes was higher than that for up-regulated genes for water stress (3.2%) and lower for salt stress (0.7%), although only eight

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Section: Rna Gel Blot Analysismentioning

confidence: 99%

Changes in gene expression in maize kernel in response to water and salt stress

Andjelkovic

Thompson

2005

Plant Cell Rep

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“…Filter arrays were produced according to a published protocol [21], with minor modifications. A cDNA library (ZAP Express TM , Stratagene, La Jolla, CA) constructed from ovules ((/3 to 15 DPA) of the wild type G. hirsutum cv.…”

Section: Preparation Of Cdna Filter Arraysmentioning

confidence: 99%

Isolation of genes preferentially expressed in cotton fibers by cDNA filter arrays and RT-PCR

Zhu

Meng

et al. 2002

Plant Science

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Cotton fibers are single-cell trichomes derived from the outer integument cells of ovules. Recent studies showed that the rapid elongation of fibers was coordinated with the expression of a subset of fiber-specific genes. Here we report the use of filter arrays of cDNAs to identify genes preferentially expressed in cotton fibers. An array of 1536 clones was hybridized with cDNA probes prepared from wild type (fiber-containing) and fl mutant (naked) ovules at 5 days post-anthesis (DPA), respectively. Subsequent RT-PCR analyses of 14 genes identified ten that were highly transcribed in cotton fibers. Among them, an RD22-like protein (GhRDL ), a putative acyltransferase (GhACY ), a Fiddlehead homolog (GhFDH ), a serine carboxypeptidase-like protein (GhSCP ), two tubulin components (GhTUA6 and GhTUB1 ) and the previously reported gene encoding fiber protein E6, showed a fiberenriched expression pattern. The other three genes, including an actin (GhACT ), a putative cellulose synthase catalytic subunit (GhCesA-5 ) and a putative 24-sterol-C -methyltransferase (GhSMT ), were actively transcribed in fibers during the elongation stage, but their transcripts were also clearly present in other tissues. The possible roles of these proteins in cotton fiber development and growth are discussed. #

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“…The complete sequencing of the Arabidopsis genome (Arabidopsis Genome Initiative [AGI], 2000) and the expansion of functional genomics in this model plant attest to the power of genomic approaches in addressing important questions in plant biology. Large-scale analysis of gene expression in Arabidopsis using cDNA and oligonucleotide arrays has given new insights into photosynthesis (Desprez et al, 1998), biotic and abiotic stresses (Maleck et al, 2000;Schenk et al, 2000;Bohnert et al, 2001;Seki et al, 2001), nitrogen assimilation (Wang et al, 2000), and organ development (Ruan et al, 1998;Girke et al, 2000;Zhu and Wang, 2000). Although Arabidopsis serves as the model system for most plant processes, it suffers from two major weaknesses in consideration of plant-microbe interactions: the absence of symbiotic associations with mycorrhizal fungi and with rhizobia.…”

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confidence: 99%

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

et al. 2002

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The Medicago truncatula expressed sequence tag (EST) database (Gene Index) contains over 140,000 sequences from 30 cDNA libraries. This resource offers the possibility of identifying previously uncharacterized genes and assessing the frequency and tissue specificity of their expression in silico. Because M. truncatula forms symbiotic root nodules, unlike Arabidopsis, this is a particularly important approach in investigating genes specific to nodule development and function in legumes. Our analyses have revealed 340 putative gene products, or tentative consensus sequences (TCs), expressed solely in root nodules. These TCs were represented by two to 379 ESTs. Of these TCs, 3% appear to encode novel proteins, 57% encode proteins with a weak similarity to the GenBank accessions, and 40% encode proteins with strong similarity to the known proteins. Nodule-specific TCs were grouped into nine categories based on the predicted function of their protein products. Besides previously characterized nodulins, other examples of highly abundant nodule-specific transcripts include plantacyanin, agglutinin, embryo-specific protein, and purine permease. Six nodule-specific TCs encode calmodulin-like proteins that possess a unique cleavable transit sequence potentially targeting the protein into the peribacteroid space. Surprisingly, 114 nodule-specific TCs encode small Cys cluster proteins with a cleavable transit peptide. To determine the validity of the in silico analysis, expression of 91 putative nodule-specific TCs was analyzed by macroarray and RNA-blot hybridizations. Nodule-enhanced expression was confirmed experimentally for the TCs composed of five or more ESTs, whereas the results for those TCs containing fewer ESTs were variable. , and organ development (Ruan et al., 1998;Girke et al., 2000; Zhu and Wang, 2000). Although Arabidopsis serves as the model system for most plant processes, it suffers from two major weaknesses in consideration of plant-microbe interactions: the absence of symbiotic associations with mycorrhizal fungi and with rhizobia.In recent years, Medicago truncatula and Lotus japonicus have emerged as model systems for genomic approaches to plant-microbe symbiotic associations (Barker et al., 1990;Handberg and Stougaard, 1992; Cook et al., 1997; Cook, 1999;Oldroyd and Geurts, 2001;Thoquet et al., 2002). Both species possess small genomes, are diploid, have fast generation times, and can be transformed with Agrobacterium tumefaciens and regenerated (Handberg and Stougaard, 1992; Blondon et al., 1994;Handberg et al., 1994; Chabaud et al., 1996;Jiang and Gresshoff, 1997;Stiller et al., 1997;Trinh et al., 1998;Trieu et al., 2000). Currently, both functional and structural genomics approaches are being pursued within each of these species. Covitz et al. (1998) reported the sequencing of about 900 cDNA tags from the M. truncatula root hairs. In addition, hundreds more expressed sequence tags (ESTs) have been isolated and characterized from effective root nodules of L. japonicus and M. truncatula, and a ...

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Differential gene expression in Arabidopsis monitored using cDNA arrays

Cited by 114 publications

References 25 publications

Changes in gene expression in maize kernel in response to water and salt stress

Changes in gene expression in maize kernel in response to water and salt stress

Isolation of genes preferentially expressed in cotton fibers by cDNA filter arrays and RT-PCR

Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula

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