Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level

Kryvych, Sergiy; Nikiforova, Victoria J.; Herzog, Michel; Perazza, Daniel; Fisahn, Joachim

doi:10.1016/j.plaphy.2007.11.001

Cited by 38 publications

(37 citation statements)

References 42 publications

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“…Our engineered red cells led to an enrichment of differential gene expression profiles, which can precisely reflect the impact of the PAP1 overexpression at the cellular level. This observation can be indirectly validated by several reports on the enrichment of transcriptomic and metabolic profiles in single plant cells that have a specific cellular physiology (Brandt 2005;Ebert et al 2010;Kehr 2003;Kryvych et al 2008).…”

Section: Discussionsupporting

confidence: 57%

Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells

Shi

Xie

2011

Planta

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We report metabolic engineering of Arabidopsis red cells and genome-wide gene expression analysis associated with anthocyanin biosynthesis and other metabolic pathways between red cells and wild-type (WT) cells. Red cells of A. thaliana were engineered for the first time from the leaves of production of anthocyanin pigment 1-Dominant (pap1-D). These red cells produced seven anthocyanin molecules including a new one that was characterized by LC-MS analysis. Wild-type cells established as a control did not produce anthocyanins. A genome-wide microarray analysis revealed that nearly 66 and 65% of genes in the genome were expressed in the red cells and wild-type cells, respectively. In comparison with the WT cells, 3.2% of expressed genes in the red cells were differentially expressed. The expression levels of 14 genes involved in the biosynthetic pathway of anthocyanin were significantly higher in the red cells than in the WT cells. Microarray and RT-PCR analyses demonstrated that the TTG1-GL3/TT8-PAP1 complex regulated the biosynthesis of anthocyanins. Furthermore, most of the genes with significant differential expression levels in the red cells versus the WT cells were characterized with diverse biochemical functions, many of which were mapped to different metabolic pathways (e.g., ribosomal protein biosynthesis, photosynthesis, glycolysis, glyoxylate metabolism, and plant secondary metabolisms) or organelles (e.g., chloroplast). We suggest that the difference in gene expression profiles between the two cell lines likely results from cell types, the overexpression of PAP1, and the high metabolic flux toward anthocyanins.

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Section: Discussionsupporting

confidence: 57%

Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells

Shi

Xie

2011

Planta

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“…An additional analysis of the genes expressed in the cork oak transcriptome studied in this work revealed the presence of genes that were previously associated with bud burst, bud dormancy, bud sprouting, and flower development in other species, such as the sessile oak (Quercus petraea) [8,9,[75][76][77]. In the two studies involving the Quercus species, the set of genes for which differential expression was found encompassed genes that were also expressed in our study.…”

Section: Common Sets Of Genes Used By Different Species In the Regulasupporting

confidence: 49%

“…Moreover, genes involved in the regulation of bud sprouting and flower development in Arabidopsis thaliana, such as FRIGIDA, SOC1, and SVP [75,76], as well as genes implicated in the transition from endodormancy to ecodormancy of leaf buds in Pyrus pyrifolia such as expansin, cellulose synthase, polygalacturonase, arabinogalactan (all of them related with the plant cell wall) and germin-like protein [77], were also expressed in the cork oak transcriptome analyzed in this study. These results highlight a set of genes whose expression during bud development and sprouting is common in different species of the Quercus genus, and likewise in Arabidopsis thaliana and Pyrus pyrifolia, despite the pattern of differential expression not being detected in this work, which could be due to biological and/or technical limitations.…”

Section: Common Sets Of Genes Used By Different Species In the Regulamentioning

confidence: 65%

Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting

Usié

Simões

Barbosa

et al. 2017

Forests

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Cork oaks show a high capacity of bud sprouting as a response to injury, which is important for species survival when dealing with external factors, such as drought or fires. The characterization of the cork oak transcriptome involved in the different stages of bud sprouting is essential to understanding the mechanisms involved in these processes. In this study, the transcriptional profile of different stages of bud sprouting, namely (1) dormant bud and (2) bud swollen, vs. (3) red bud and (4) open bud, was analyzed in trees growing under natural conditions. The transcriptome analysis indicated the involvement of genes related with energy production (linking the TCA (tricarboxylic acid) cycle and the electron transport system), hormonal regulation, water status, and synthesis of polysaccharides. These results pinpoint the different mechanisms involved in the early and later stages of bud sprouting. Furthermore, some genes, which are involved in bud development and conserved between species, were also identified at the transcriptional level. This study provides the first set of results that will be useful for the discovery of genes related with the mechanisms regulating bud sprouting in cork oak.

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“…To that end, we isolated 2000 FCC and 4000 RCC for each mRNA extraction. Previous transcriptome profiling, based on cell isolation, has been conducted on 10 cells (Kryvych et al 2008); 150 cells (Asano et al 2002); 2000 cells (Inada and Wildermuth 2005); and up to 10 000 cells (Nakazono et al 2003). It is important to perform a cell-type transcriptome analysis on an optimized amount of cells in such a way that results for a so-called 'average cell' are achieved without bias due to there being too few cells (Kawasaki 2004 …”

Section: Linearly Amplify Mrna From Cell-type Enriched Samplesmentioning

confidence: 99%

Microdissection to isolate vascular cambium cells in poplar

Goué¹,

Noël-Boizot²,

Vallance³

et al. 2012

Silva Fenn.

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Vascular cambium is the lateral meristem producing xylem cells inwards and phloem cells outwards in plant stem. Thus, in trees, the quality and quantity of wood is a result of highly regulated developmental process depending initially on the vascular cambium cell production. The availability of accurate transcriptomics technologies based on high coverage sequencing raises the level of expectations on tissue sampling to a very high degree. What is the benefit of top-level transcriptomics in wood formation studies if we are using these technologies on raw tissues, mixing cells at the organ level or even higher scale? The presented work describes a nine-step procedure, from standing tree to isolated ray and fusiform cells from cryolyophilized tangential sections of the poplar cambial zone. The aim of this paper is to present a step by step procedure including advices on how to select the optimal tree, how to fell the tree while securing its physiological parameters, how to cryolyophilize and microdissect under binocular, presenting the time schedule of the whole process and RNA analysis.

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Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level

Cited by 38 publications

References 42 publications

Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells

Engineering of red cells of Arabidopsis thaliana and comparative genome-wide gene expression analysis of red cells versus wild-type cells

Comprehensive Analysis of the Cork Oak (Quercus suber) Transcriptome Involved in the Regulation of Bud Sprouting

Microdissection to isolate vascular cambium cells in poplar

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