Transcriptional Profiling of the Arabidopsis Embryo

Spencer, Matthew W.B.; Casson, Stuart A.; Lindsey, Keith

doi:10.1104/pp.106.087668

Cited by 121 publications

(103 citation statements)

References 63 publications

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“…The observed down-regulation of plastid-specific gene products in the mutant embryos is consistent with the fact that nuclear genes encoding photosynthesis-related proteins normally are up-regulated in WT torpedo A. thaliana embryos compared with the late heart and globular stages (30).…”

Section: Ise2 Is Found In Chloroplastssupporting

confidence: 64%

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Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified increased size exclusion limit (ise) 1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, whereas ISE2 encodes a DEVH-type RNA helicase. Here, we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function, we performed whole-genome expression analyses. The most significantly affected class of transcripts in both mutants encode products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus cross-talk, add PD as a critical player in the plant cell communication network, and thereby illuminate a previously undescribed signaling pathway dubbed organelle-nucleus-plasmodesmata signaling. Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function.

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Section: Ise2 Is Found In Chloroplastssupporting

confidence: 64%

“…Embryos express a large fraction of the genome. Studies using the ATH1 arrays estimate that between 51% and 77% of genes are expressed in torpedo stage embryos (30). For our analyses, we selected genes exhibiting twofold or greater changes in expression compared with WT embryos.…”

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 99%

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…5). LCM technology has been used successfully in rice (Oryza sativa), maize (Zea mays), tobacco, soybean, and Arabidopsis in which a variety of plant tissues and cell types have been isolated and studied, including those in an early Arabidopsis embryo (Asano et al, 2002;Kerk et al, 2003;Nakazono et al, 2003;Casson et al, 2005;Klink et al, 2005;Sanders et al, 2005;Spencer et al, 2007).…”

Section: Using Soybean To Identify Genes Required To Make a Seedmentioning

confidence: 99%

Using Genomics to Study Legume Seed Development

Wagmaister²,

Kawashima³

et al. 2007

Plant Physiology

150

157

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“…Only a few of these studies, however, have focused exclusively on seeds and/or embryos to identify important regulators and processes required for seed development (27)(28)(29)(30)(31). In this paper, we present results of Affymetrix GeneChip experiments that profile genes that are active before, during, and after Arabidopsis seed formation.…”

mentioning

confidence: 99%

Global analysis of gene activity duringArabidopsisseed development and identification of seed-specific transcription factors

Le¹,

Cheng²,

Bui³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

514

493

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Most of the transcription factors (TFs) responsible for controlling seed development are not yet known. To identify TF genes expressed at specific stages of seed development, including those unique to seeds, we used Affymetrix GeneChips to profile Arabidopsis genes active in seeds from fertilization through maturation and at other times of the plant life cycle. Seed gene sets were compared with those expressed in prefertilization ovules, germinating seedlings, and leaves, roots, stems, and floral buds of the mature plant. Most genes active in seeds are shared by all stages of seed development, although significant quantitative changes in gene activity occur. Each stage of seed development has a small gene set that is either specific at the level of the GeneChip or up-regulated with respect to genes active at other stages, including those that encode TFs. We identified 289 seed-specific genes, including 48 that encode TFs. Seven of the seed-specific TF genes are known regulators of seed development and include the LEAFY COTYLEDON ( LEC ) genes LEC1, LEC1-LIKE, LEC2 , and FUS3 . The rest represent different classes of TFs with unknown roles in seed development. Promoter-β -glucuronidase ( GUS ) fusion experiments and seed mRNA localization GeneChip datasets showed that the seed-specific TF genes are active in different compartments and tissues of the seed at unique times of development. Collectively, these seed-specific TF genes should facilitate the identification of regulatory networks that are important for programming seed development.

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Transcriptional Profiling of the Arabidopsis Embryo

Cited by 121 publications

References 63 publications

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Using Genomics to Study Legume Seed Development

Global analysis of gene activity duringArabidopsisseed development and identification of seed-specific transcription factors

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