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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of the effect of auxin biosynthesis inhibitor L-AOPP on the gene expression profile (shoot apical meristem)

ABSTRACT: Recently, 2-aminoxy-3-phenylpropionic acid (L-AOPP) had been demonstrated to possess an inhibitory activity against IAA biosynthesis but the molecular basis of the action was unclear. To investigate the function of L-AOPP, we conducted microarray analysis using the shoot apical meristem (SAM) part of A. thaliana in addition to whole plants after the treatment of L-AOPP. We performed microarray analysis using the shoot apical meristem (SAM) part of A. thaliana (Columbia-0) to investigate function of 2-aminoxy-3-phenylpropionic acid (L-AOPP) in relation to inhibition of auxin biosynthesis. Total RNA was extracted from SAM part of 7-day-old seedlings grown on 1/2 MS medium containing L-AOPP (50 µM),L-AOPP (50 µM) + Indole-3-acetic acid (IAA 10 nM) or Dimethyl sulfoxide (DMSO 0.1%).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Eriko Sasaki

PROVIDER: E-GEOD-30092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of the effect of auxin biosynthesis inhibitor L-AOPP on the gene expression profile (shoot apical meristem)

Project description:Recently, 2-aminoxy-3-phenylpropionic acid (L-AOPP) had been demonstrated to possess an inhibitory activity against IAA biosynthesis but the molecular basis of the action was unclear. To investigate the function of L-AOPP, we conducted microarray analysis using the shoot apical meristem (SAM) part of A. thaliana in addition to whole plants after the treatment of L-AOPP.

2015-12-31 | GSE30092 | GEO

Proteome of rice shoot apical meristem

Project description:DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.

2020-08-14 | PXD020608 | Pride

Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

Project description:The shoot apical meristem (SAM) of angiosperm plants is a highly organized minute structure that gives rise to all above-ground organs. The SAM is divided into three different functional domains. The central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or to the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations ofÂ clavata3 (clv3),Â jabba-1DÂ (jba1D) andÂ erecta (er) mutants. We demonstrate that CLV3 restricts meristem expansion along the apical basal axis, while class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. OurÂ k-means analysis reveals thatÂ clv3,Â jba-1D/+ andÂ erÂ lead to meristem enlargement by affecting different aspects of meristem function, e.g., thatÂ clv3Â displays increase in stem cell population, whereasÂ jba-1D/+Â er exhibits increase in mitotic activity and in meristematic cell population. We demonstrate that thecombination of genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type specific transcriptomes in a small structure such as the SAM. Ten samples enriched in shoot apical meristem tissue were analyzed, corresponding to 5 different genotypes (Col-0, clv3-2, jba-1D/+, jba-1D/+ er-20, and jba-1D/+ er-20 clv3-2) at two different developmental stages (8-day-old seedlings and 15-day-old seedlings).

2016-04-02 | E-GEOD-79839 | biostudies-arrayexpress

Arabidopsis AGO1 and AGO10 bound sRNAs

Project description:The shoot apical meristem (SAM) comprises a group of undifferentiated cells that divide to maintain the plant meristem and also give rise to all shoot organs. SAM fate is specified by class III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors, which are targets of miR166/165. In Arabidopsis, AGO10 is a critical regulator of SAM maintenance, and here we demonstrate that AGO10 specifically interacts with miR166/165. The association is determined by a distinct structure of the miR166/165 duplex. Deficient loading of miR166 into AGO10 results in a defective SAM. Notably, the miRNA-binding ability of AGO10, but not its catalytic activity, is required for SAM development, and AGO10 has a higher binding affinity for miR166 than does AGO1, a principal contributor to miRNA-mediated silencing. We propose that AGO10 functions as a decoy for miR166/165 to maintain the SAM, preventing their incorporation into AGO1 complexes and the subsequent repression of HD-ZIP III gene expression. Homozygous T2 progeny of complemented plants expressing ago10-3;PAGO10-HF-AGO10 and ago1;PAGO1-HF-AGO1 were used for preparation of AGO complexes. Flower samples including floral buds, open flowers, and newly set siliques (1-2 day old) were collected for protein extraction and isolation of dual-tagged AGO complexes using a two-step affinity purification. The isolated AGO complexes were divided into two parts, one aliquot was used for sRNA extraction with Trizol reagent, whereas the other part was used for monitoring protein purity by Gelcode blue staining and western blot using a monoclonal anti-Flag antibody (Sigma) as previous described.

2012-08-03 | E-GEOD-39885 | biostudies-arrayexpress

Molecular Dissection of Pea Shoot Apical Meristem

Project description:Knowledge about an organism’s cell and tissue-specific transcriptional repertoire is essential for understanding the gene regulatory circuits that control key developmental events. The shoot apical meristem (SAM) is responsible for development of all the above ground parts of plants. Our understanding of SAM at the molecular level is far from complete. The present work investigates the global gene expression repertoire of SAMs in the garden pea (Pisum sativum). To this end, 10,346 EST sequences representing 7611 unique genes were generated from pea SAM cDNA libraries. These sequences, together with previously reported ESTs, were used to construct a 12K oligonucleotide array used to identify genes exhibiting differential SAM expression, as compared to the axillary meristem, root apical meristem, and non-meristematic tissues. We identified a number of genes that are predominantly expressed in specific cell layers or domains of the SAM, and thus are likely components of the gene networks involved in stem cell maintenance and initiation of lateral organ primordial cells. In situ hybridization confirmed the spatial localisation of some of these key genes within the SAM. Our data also indicate the diversification of some gene expression patterns and functions in legume crop plants.

2009-10-26 | GSE13451 | GEO

Transcriptomic analysis of REVOLUTA and mir165a cell-types of Arabidopsis shoot apical meristem

Project description:Dorso-ventral (DV) patterning at the Shoot Apical meristem (SAM) is essential for organogenesis in Arabidopsis. Dorsal and ventral gene expressed domains are separated by boundaries from where the new organ initiation starts. Here by using cell-types specific transcriptomics approach, we have identified dorsal, ventral and boundary specific genes in SAM.

2023-12-20 | GSE221138 | GEO

Transcriptomic analysis of dorso-ventral cell-types of Arabidopsis shoot apical meristem

2020-04-16 | GSE90169 | GEO

Differential regulation of meristem size, morphology and organization by the ERECTA, CLAVATA and class III HD-ZIP pathways

Project description:The shoot apical meristem (SAM) of angiosperm plants is a highly organized minute structure that gives rise to all above-ground organs. The SAM is divided into three different functional domains. The central zone (CZ) at the SAM tip harbors the self-renewing pluripotent stem cells and the organizing center, providing daughter cells that are continuously displaced into the interior rib zone (RZ) or to the surrounding peripheral zone (PZ), from which organ primordia are initiated. Despite the constant flow of cells from the CZ into the RZ or PZ, and cell recruitment for primordium formation, a stable balance is maintained between the distinct cell populations in the SAM. Here we combined an in depth phenotypic analysis with a comparative RNA-Seq approach to characterize meristems from selected combinations of clavata3 (clv3), jabba-1D (jba1D) and erecta (er) mutants. We demonstrate that CLV3 restricts meristem expansion along the apical basal axis, while class III HD-ZIP and ER pathways restrict meristem expansion laterally, but in distinct and possibly perpendicular orientations. Our k-means analysis reveals that clv3, jba-1D/+ and er lead to meristem enlargement by affecting different aspects of meristem function, e.g., that clv3 displays increase in stem cell population, whereas jba-1D/+ er exhibits increase in mitotic activity and in meristematic cell population. We demonstrate that thecombination of genetic and mRNA-Seq comparative approach provides a precise and sensitive method to identify cell type specific transcriptomes in a small structure such as the SAM.

2016-04-02 | GSE79839 | GEO

Expression data for reproductive development in rice

Project description:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Keywords: Development time course

2007-05-17 | GSE6893 | GEO

Zea mays Transcriptome or Gene expression

Project description:To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).

2013-04-02 | E-MTAB-4205 | biostudies-arrayexpress

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