Transcriptome analyses of ragged seedling2 shoot apical meristem (SAM) vs non-mutant SAM
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
SUBMITTER: Michael Scanlon
PROVIDER: E-GEOD-11325 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The recessive mutation ragged seedling2-R (rgd2-R) conditions defective lateral development of maize leaves. Although dorsiventral patterning is established in rgd2-R mutant leaves, some swapping of adaxial/abaxial epidermal identity may occur. Molecular analyses indicate that RGD2 is required for the coordination of dorsiventral and lateral patterning during maize leaf development, yet the RGD2 gene product and the mechanisms of RGD2 function are unknown. In order to investigate the genetic mechanisms downstream of RGD2 gene function, SAM-specific transcriptional profiling of rgd2-R is compared to that of nonmutant using laser microdissection microarray. Whole SAMs were laser-microdissected from rgd2-R mutant and non-mutant seedlings grown under the same controlled conditions. Microarray profiles were generated for 28,671 maize cDNAs contained on gene chips SAM 1.1and SAM 3.0 (http://www.plantgenomics.iastate.edu/maizechip/). Keywords: Genetic modification
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Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures termed shoot apical meristems (SAMs). The SAM exhibits distinctive structural organization, marked by cell layering. Maize SAMs are comprised of two cell layers, L1 (single cell layered tunica) and L2 (corpus). To identify genes required for layer-specific functions intact maize SAMs were fixed, embedded in paraffin and sectioned. L1 and L2 cells were isolated from these sections via laser capture microdissection (LCM). RNA was isolated from six biological replications of L1 and L2, amplified and hybridized to microarrays spotted with ~37,000 maize cDNA clones. This experiment identified ~700 ESTs that are preferentially expressed in the L1 or the L2 (P <0.001). The L1-up-regulated ESTs included ZmOCL1 and ZmOCL4, which are known to exhibit L1-specific expression in the maize SAM. The L2-up-regulated ESTs included KNOTTED1, whose transcripts are known to accumulate in the L2 but not in the L1 of the maize SAM. Differentially expressed ESTs included genes involved in transcription, signal transduction, transport and metabolism, many of which are novel candidates that are required for layer-specific functions in the maize SAM. Several L1-up-regulated ESTs were annotated as yabby family genes or basic helix-loop-helix transcription factor-like genes, which have not previously been reported as having layer-specific expression in the SAM. Novel WW domain-containing genes (WW genes) were identified in this study. The WW domain mediates protein-protein interactions, often with signal transduction components. These WW genes were substantially up-regulated in the L1 relative to the L2. Keywords: Cell Type Comparison An experimental aim is to identify genes that are differentially expressed in distinct histological cell layers of maize SAM by comparing the transcript accumulation between L1 (single cell layered tunica) and L2 (corpus) using cDNA microarrays that have over 37,000 informative spots from maize.
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Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both whole SAMs (SAMs, P0 and P1) and whole seedlings (above ground part of seedlings) collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have about 30,000 maize cDNA clones. Statistical analyses showed that approximately 7% and 8% of the tested genes were significantly up-regulated and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were significantly up-regulated. Many histone genes and cell cycle related genes were also significantly up-regulated. Those observations validated our microarray results. The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kind of enzymes, suggesting those genes play important roles in meristem maintenance and the early stage of leaf development in maize. Surprisingly, several retrotransposon-related genes were greatly up-regulated with the statistical significance. This finding raised the possibility that retrotransposons are involved in regulatory mechanism of maize SAM. An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between whole SAMs and whole seedlings using cDNA microarrays that have about 30,000 maize cDNA clones.
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Project description:Scaffold proteins such as CNK1 are hubs for coordinating signalling pathways. Here, we demonstrate that CNK1 is a crucial transducer of growth factor-stimulated and oncogenic signalling. Activation of CNK1 depends on its dimerization executed by the N-terminal sterile motif alpha (SAM) domain. Accordingly, a CNK1 mutant lacking the SAM domain prevents CNK1-driven cell proliferation and matrix metalloproteinase 14 promoter activation. We identified phosphorylation of Ser22 by AKT as trigger for CNK1 dimerisation. Consistently, the mutant CNK1S22D mimicking constitutive phosphorylation stimulates CNK1 signalling, whereas the phosphoylation-dead mutant CNK1S22A does not. Searching the COSMIC database revealed Ser22 as target for oncogenic activation of CNK1. The mutant CNK1S22D and the oncogenic mutant CNK1S22F form clusters in serum-starved cells comparable to clusters of CNK1 in growth factor stimulated cells. Light-activatable CNK1, optoCNK1, based on the light-induced oligomerisation of cryptochrome 2 confirms that dimerization is the trigger for CNK1 activation. CNK1 dimers induced by activating Ser22 mutants or by light enhance cell invasion and ADP ribosylation factors 1 signalling associated with tumour formation. Positive and negative feedback mechanisms regulates CNK1 dimerisation and in this way its activity. Oncogenic mutants of CNK1 support the positive feedback while escape from negative feedback regulation.
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2010-10-15 | E-GEOD-24703 | biostudies-arrayexpress
Project description:All above ground organs of higher plants are ultimately derived from specialized organogenic structures called shoot apical meristems (SAMs). It is comprised of pluripotent stem cells, which divide to regenerate themselves as well as to provide cells to form other organs such as leaves and stems. To study global gene expression in maize SAM and very young primordia (P0 and P1), RNA was extracted from both SAMs (SAMs per se plus P0 and P1) and above-ground portions of seedlings collected from 14-day old B73 seedlings. These RNA samples were labeled and hybridized with cDNA microarrays that have 14,400 informative spots from maize. Statistical analyses showed that approximately 6.3% and 6.5% of the tested genes were significantly (p <0.0001) up- and down-regulated, respectively. Several control genes, whose expressions were confirmed in the maize SAM in the previous studies, were also up-regulated (p <0.01). The significantly up-regulated genes involved many novel transcription factor genes and regulatory genes as well as some kinds of enzymes, suggesting these genes play important roles in meristem maintenance and the early stage of leaf development in maize. Interestingly, several retrotransposon-related genes were greatly up-regulated in the SAM. This finding raised the possibility that retrotransposons are involved in regulatory mechanisms of maize SAM. An experimental aim is to identify genes preferentially expressed in maize SAM by comparing the transcript abundant between SAMs and seedlings using cDNA microarrays that have 14,400 informative spots from maize.
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