Transcriptomics approaches in the early Arabidopsis embryo

Palovaara, Joakim; Saiga, Shunsuke; Weijers, Dolf

doi:10.1016/j.tplants.2013.04.011

Cited by 45 publications

(36 citation statements)

References 90 publications

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“…Remarkably, 78% of Arabidopsis genes are expressed during the course of embryogenesis, and 55% in the mature embryo (Xiang et al, 2011). In the near future, marker genes identified for each embryonic tissue can be used to create high-resolution transcriptome maps of embryogenesis to study the mechanisms governing the earliest cell-fate decisions in plant life (Palovaara et al, 2013).…”

Section: Embryogenesismentioning

confidence: 99%

Vascular Cambium Development

Nieminen

Blomster

Helariutta

et al. 2015

The Arabidopsis Book

116

110

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Secondary phloem and xylem tissues are produced through the activity of vascular cambium, the cylindrical secondary meristem which arises among the primary plant tissues. Most dicotyledonous species undergo secondary development, among them Arabidopsis. Despite its small size and herbaceous nature, Arabidopsis displays prominent secondary growth in several organs, including the root, hypocotyl and shoot. Together with the vast genetic resources and molecular research methods available for it, this has made Arabidopsis a versatile and accessible model organism for studying cambial development and wood formation. In this review, we discuss and compare the development and function of the vascular cambium in the Arabidopsis root, hypocotyl, and shoot. We describe the current understanding of the molecular regulation of vascular cambium and compare it to the function of primary meristems. We conclude with a look at the future prospects of cambium research, including opportunities provided by phenotyping and modelling approaches, complemented by studies of natural variation and comparative genetic studies in perennial and woody plant species.

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Section: Embryogenesismentioning

confidence: 99%

Vascular Cambium Development

Nieminen

Blomster

Helariutta

et al. 2015

The Arabidopsis Book

116

110

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“…In general, several existing methods have been employed to overcome such difficulties for different tissues and organisms, such as laser capture microdissection (LCM), fluorescence-activated cell sorting (FACS), translating ribosome affinity purification (TRAP) and isolation of nuclei tagged in specific cell types (INTACT) (Bonner et al, 1972;Emmert-Buck et al, 1996;Heiman et al, 2008;Deal and Henikoff, 2010). At present, TRAP and INTACT are still under optimization in order to be widely used for special tissues such as those in plant embryos (Palovaara et al, 2013). LCM has been used in different studies to isolate tissues from sectioned material without the need to generate transgenic plants (Kerk et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo

et al. 2014

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In multicellular organisms, cellular differences in gene activity are a prerequisite for differentiation and establishment of cell types. In order to study transcriptome profiles, specific cell types have to be isolated from a given tissue or even the whole organism. However, wholetranscriptome analysis of early embryos in flowering plants has been hampered by their size and inaccessibility. Here, we describe the purification of nuclear RNA from early stage Arabidopsis thaliana embryos using fluorescence-activated nuclear sorting (FANS) to generate expression profiles of early stages of the whole embryo, the proembryo and the suspensor. We validated our datasets of differentially expressed candidate genes by promoter-reporter gene fusions and in situ hybridization. Our study revealed that different classes of genes with respect to biological processes and molecular functions are preferentially expressed either in the proembryo or in the suspensor. This method can be used especially for tissues with a limited cell population and inaccessible tissue types. Furthermore, we provide a valuable resource for research on Arabidopsis early embryogenesis.

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“…In the last years, many studies based on the analysis of large datasets have been carried on in order to acquire a deeper understanding of the cellular processes taking place during seed and embryo development (Belmonte et al, 2013;Wickramasuriya and Dunwell, 2015;Palovaara et al, 2013). Although these studies provide resources to support research in seed biology, much remains to be learned through classical genetic and physiology approaches, especially when 17% of Arabidopsis genes are still classified as having unknown function (The Arabidopsis Information Resource [http://www.arabidopsis.…”

mentioning

confidence: 99%

TWS1, a Novel Small Protein, Regulates Various Aspects of Seed and Plant Development

et al. 2016

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Small proteins have long been overlooked due to their poor annotation and the experimental challenges they pose. However, in recent years, their role in various processes has started to emerge, opening new research avenues. Here, we present the isolation and characterization of two allelic mutants, twisted seed1-1 (tws1-1) and tws1-2, which exhibit an array of developmental and biochemical phenotypes in Arabidopsis (Arabidopsis thaliana) seeds. We have identified AT5G01075 as the subtending gene encoding a small protein of 81 amino acids localized in the endoplasmic reticulum. TWS1 is strongly expressed in seeds, where it regulates both embryo development and accumulation of storage compounds. TWS1 loss-of-function seeds exhibit increased starch, sucrose, and protein accumulation at the detriment of fatty acids. TWS1 is also expressed in vegetative and reproductive tissues, where it is responsible for proper epidermal cell morphology and overall plant growth. At the cellular level, TWS1 is responsible for cuticle deposition on epidermal cells and organization of the endomembrane system. Finally, we show that TWS1 is a single-copy gene in Arabidopsis, and it is specifically conserved among angiosperms.Developing seeds are a complex system that integrates processes implicated in the coordinated development of different tissues and the intensive activation of many metabolic pathways aimed at massive accumulation of storage compounds and secondary metabolites. As a result, young seedlings are provided with the energy and the building materials required to restarting the plant life cycle.In oleaginous species, such as Arabidopsis (Arabidopsis thaliana), seeds typically contain 30% to 40% storage lipids and 30% to 40% proteins by weight (Baud et al., 2008).

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Transcriptomics approaches in the early Arabidopsis embryo

Cited by 45 publications

References 90 publications

Vascular Cambium Development

Vascular Cambium Development

Cell type-specific transcriptome analysis in the early Arabidopsis thaliana embryo

TWS1, a Novel Small Protein, Regulates Various Aspects of Seed and Plant Development

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