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Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, tiling array data

ABSTRACT: The number of cells in an organ is a major factor for the determination of organ size. However, genetic basis of cell number determination is not well understood. Three grandifolia-D (gra-D) mutants of Arabidopsis thaliana developed huge leaves containing two- to three-fold increased number of cells of the wild type. Tiling array and microarray analysis of gra-D mutants suggested that genes found in a lower part of chromosome 4 were upregulated, suggesting the occurrence of segmental chromosomal duplications in the gra-D mutants. These region contain positive regulators of cell proliferation such as AINTEGUMENTA (ANT) and cyclin genes such as CYCD3;1.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE15725 | GEO | 2009/06/02

SECONDARY ACCESSION(S): PRJNA122999

REPOSITORIES: GEO

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Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, expression data

Project description:The number of cells in an organ is a major factor for the determination of organ size. However, genetic basis of cell number determination is not well understood. Three grandifolia-D (gra-D) mutants of Arabidopsis thaliana developed huge leaves containing two- to three-fold increased number of cells of the wild type. Tiling array and microarray analysis of gra-D mutants suggested that genes found in a lower part of chromosome 4 were upregulated, suggesting the occurrence of segmental chromosomal duplications in the gra-D mutants. These region contain positive regulators of cell proliferation such as AINTEGUMENTA (ANT) and cyclin genes such as CYCD3;1.

2009-06-02 | GSE15722 | GEO

Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana

2009-06-02 | GSE15726 | GEO

Chromosomal duplication in the grandifolia-D mutants of Arabidopsis thaliana, expression data

2010-05-18 | E-GEOD-15722 | biostudies-arrayexpress

Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development

Project description:We are interested in examining the transcriptional hierarchies that are required for proper formation and function of the carpel margin meristem in Arabidopsis thaliana. The carpel margin meristem (CMM) gives rise to the ovule primorida (which begin to form around flower stage 8). We know that the loss of the seuss-3 (seu-3) and aintegumenta-1(ant-1) separately leads to a mild disruption of ovule formation, while the loss of both causes a complete loss of ovule formation. In this study we wanted to examine expression levels changed between each single mutant and the double mutant. We dissected out stage 8-10 carpel of each of the four genotypes (seu-3, ant-1, Col-0, seu-3 ant-1) pooling 15-25 carpels into one biological replicate. Then using 16 ATH1 arrays we hybridized, amplified and labeled cDNA to 16 arrays (4 replicates for each genotype). We then analyzed our data to reveal transcripts that went down in the double compared to either single mutant, and transcripts that went down more than additively in the double mutant compared to added level of the decrease of the single mutant levels. 16 arrays: 4 seuss-3, 4 aintegumenta-1, 4 Col-0, 4 seuss-3 aintegumenta-1. Each biological replicate was a sample of 15-25 pooled stage 8-10 carpels manually dissected by hand.

2011-07-31 | E-GEOD-30492 | biostudies-arrayexpress

Transcription profiling of pistils from Arabidopsis wild type, ant-4 mutant and ino-1mutant plants at different developmental stages

Project description:This experiment was designed to identify genes expressed preferentially in the two integuments of the Arabidopsis ovule. Pistils from wild type and two ovule mutants were compared against each aintegumenta-4 (ant-4) which lacks both integuments and inner no outer (ino-1) which lacks the outer integument. Genes that are highly expressed only in the integuments were expected to be reduced in expression in the mutants, as compared with wild type. Pistils containing ovules through all stages of ovule development prior to pollination were pooled for one experiment (FULL arrays), and for two separate experiments, a set of early differentiation stages (EARLY arrays) and a set of later differentiation stages (LATE ARRAYS) were pooled. Wild type and mutant lines are in the ecotype Landsberg erecta.

2009-06-01 | E-MEXP-1920 | biostudies-arrayexpress

Transcriptome analysis in rice smos1 mutant

Project description:In this study, we identified a new rice loss-of-function mutant, small organ size1 (smos1), that decreases the final size of various organs due to decreased cell size and abnormal microtubule orientation. SMOS1 encodes an unusual APETALA2 (AP2)-type transcription factor with an imperfect AP2 domain, and its product belongs to the basal AINTEGUMENTA (ANT) lineage, including WRINKLED1 (WRI1) and ADAP. SMOS1 expression was induced by exogenous auxin treatment, and the auxin response element (AuxRE) of the SMOS1 promoter acts as a cis-motif through interaction with auxin response factor (ARF). Furthermore, a functional fluorophore-tagged SMOS1 was localized to the nucleus, supporting the role of SMOS1 as a transcriptional regulator for organ size control. Microarray analysis showed that the smos1 mutation represses expression of several genes involved in microtubule-based movement and DNA replication. Expression profiling with the rice 44K-Agilent microarray was conducted using RNAs extracted from the leaf sheaths of WT and smos1 mutant. Each dataset was obtained from three biological replicates.

2014-03-01 | E-GEOD-54357 | biostudies-arrayexpress

Transcriptome analysis in rice smos1 mutant

2014-03-01 | GSE54357 | GEO

Translocation of dense granule effectors across the parasitophorous vacuole membrane in Toxoplasma-infected cells requires the activity of ROP17, a rhoptry protein kinase

Project description:Toxoplasma gondii tachyzoites co-opt host cell functions through introduction of a large set of rhoptry- and dense granule-derived effector proteins. These effectors reach the host cytosol through different means: direct injection for rhoptry effectors and translocation across the parasitophorous vacuolar membrane (PVM) for dense granule (GRA) effectors. The machinery that translocates these GRA effectors has recently been partially elucidated, revealing 3 components, MYR1, MYR2 and MYR3. To determine if other proteins might be involved, we returned to a library of mutants defective in GRA translocation and selected one that has a partial defect, suggesting it might be in a gene encoding a new component of the machinery. Whole-genome sequencing showed that this mutant indeed has a missense mutation in a gene encoding a known serine/threonine protein kinase, ROP17, which has not previously been reported to be involved in GRA translocation. ROP17 resides at the PVM in infected cells and has previously been known for its activity in phosphorylating and, thereby, inactivating host immunity-related GTPases. Here, we show that null or catalytically dead mutants of ROP17 are defective in GRA translocation across the PVM, and that translocation across the PVM surrounding a Δrop17 mutant can be rescued “in trans” by ROP17 delivered by other tachyzoites infecting the same host cell. This strongly argues for a role for ROP17 at the PVM, not within the parasites or parasitophorous vacuole space. Hence, ROP17 plays a crucial part in GRA translocation, adding another function to the role it plays in modulating the interaction of Toxoplasma tachyzoites and the infected host cell.

2019-07-02 | GSE133144 | GEO

Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development

Project description:We were testing the expression differences of seuss, aintegumenta, and double mutants in stage 8-10 dissected carpels from Arabidopsis thaliana.

2011-08-01 | E-MEXP-3293 | biostudies-arrayexpress

Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana

2011-08-01 | GSE30492 | GEO

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