Gene expression analysis of the inflorescence of knu-1 and crc-1 knu-1
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE88969 | GEO | 2017/09/30
SECONDARY ACCESSION(S): PRJNA349257
REPOSITORIES: GEO
Similar Datasets
Project description:CRABS CLAW (CRC) encodes a transcription factor of the plant-specific YABBY class in the model plant Arabidopsis thaliana. This gene is highly expressed in the abaxial (external) domain of the gynoecium wall and contributes to the establishment of abaxial-adaxial (external-internal) polarity in that tissue. Here we derive a list of putative target genes of CRC, which include AUXIN RESPONSE FACTOR4 (ARF4) and ASSYMETRIC LEAVES1 (AS1), both of which are known to be involved in the establishment of abaxial-adaxial polarity in lateral organs. ETTIN (ETT), which is partially redundant with ARF4, was not identified as a direct target of CRC, and this observation led us to predict that crc/ett double mutants might resemble ett/arf4 double mutants, which show a very strong breakdown of abaxial-adaxial polarity in the gynoecium wall. We have confirmed this prediction by constructing double mutants using several available mutant alleles of crc, ett and arf4. Interestingly, AS1 plays a role in the establishment of adaxial tissue identity in lateral organs, though its expression is not restricted to the adaxial domain. The observed positive regulation of AS1 by CRC may thus occur very early in gynoecium development, before CRC expression becomes polarised, or at later stages of development, specifically in the abaxial domain.
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Project description:Floral organs, whose identity is determined by specific combinations of homeotic genes, originate from a group of undifferentiated cells called the floral meristem. In Arabidopsis, the homeotic gene AGAMOUS (AG) terminates meristem activity and promotes development of stamens and carpels. To understand the program of gene expression activated by AG, we followed genome-wide expression during early stamen and carpel development. Keywords: Developmental time course
2007-11-15 | GSE9605 | GEO
Project description:The MADS genes encode transcription factors (TF) that act as master regulators of plant reproduction and flower development. The SEPALLATA (SEP) MADS subfamily is not only absolutely required for the development of floral organs, but also plays roles in inflorescence architecture and determinacy of the floral meristem. The SEPs act as organizers of MADS complexes and are able to form both heterodimers and heterotetramers in vitro. To date, the MADS TF complexes characterized in angiosperm floral organ development contain at least one SEP TF. Whether DNA-binding by SEP-containing dimeric MADS complexes are sufficient for launching floral organ identity programs, however, is not clear as only defects in floral meristem determinacy were observed in tetramerization impaired SEP mutants. Here we used a combination of genome-wide binding studies, high resolution structural studies of the SEP3-AGAMOUS tetramerisation domain, structure-based mutagenesis and complementation experiments in sep1 sep2 sep3 and sep1 sep2 sep3 ag-4 plants transformed with versions of SEP3 encoding tetramerization mutants. We demonstrate that while SEP3 heterodimers are able to bind DNA both in vitro and in vivo and recognize the majority of SEP3 wild type binding sites genome-wide, tetramerisation is not only required for floral meristem determinacy, but also absolutely required for floral organ identity in the second, third and fourth whorls.
2024-04-30 | GSE227012 | GEO
Project description:In this study, we compare the DNA binding specifify and affinity of SEPALLATA3 and AGAMOUS complexes The MADS transcription factors, SEPALLATA3 (SEP3) and AGAMOUS (AG), are required for floral organ identity and determinacy of the floral meristem in Arabidopsis. Dimerization is obligatory for their DNA binding, however SEP3 and SEP3-AG also form tetrameric complexes. The goal of this study is to understand how homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding patterns. Using a modified sequential DNA affinity purification sequencing protocol (seq-DAP-seq), we selectively purified SEP3 homomeric and SEP3-AG heteromeric complexes, including the dimeric SEP3 tet-AG complex and the tetrameric SEP3-AG complex, and determined their genome-wide binding.
2020-09-07 | GSE150528 | GEO
Project description:Floral organs, whose identity is determined by specific combinations of homeotic genes, originate from a group of undifferentiated cells called the floral meristem. In Arabidopsis, the homeotic gene AGAMOUS (AG) terminates meristem activity and promotes development of stamens and carpels. To understand the program of gene expression activated by AG, we followed genome-wide expression during early stamen and carpel development. Experiment Overall Design: Described in Gomez-Mena et al, 2005, Development 132: 429-438. Briefly, synchronous development of stamens and carpels was initiated by steroid treatment of plants homozygous for the ap1-1 and cal-1 mutations and expressing a fusion between AGAMOUS and the rat glucocorticoid receptor (35S:AGGR). RNA was extracted one, three and seven days after steroid treatment; two independent steroid-treated samples and two independent untreated controls were used for each time point.
2008-06-16 | E-GEOD-9605 | biostudies-arrayexpress
Project description:Regulation of homeotic gene expression is critical for proper developmental patterns in plants. The Arabidopsis thaliana floral homeotic gene AGAMOUS is regulated by LEUNIG (LUG). Mutations in LUG result in homeotic transformations of floral organ identity. LUG mutants also exhibit other defects that are independent of AG, including abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in development. LUG is structurally similar to the transcription co-repressors Tup1 (S. cerevisiae) and Groucho (Drosophila), suggesting developmental pathways regulated by LUG may be controlled by a conserved eukaryotic repression mechanism. We aim to determine novel target genes regulated by LUG using transcriptome analysis. A mutant lug-3 line has been obtained from Dr. Zhongchi Liu. This line was used in the initial studies of LUG in the Meyerowitz lab. Lug-3 is a strong allele in the Lansberg erecta background, caused by a nonsense mutation that results in early termination of the protein and is likely null. The Lug-3 mutant exhibits narrow floral organs with staminoid petals and carpelloid sepals, abnormal carpel and ovule development, reduced plant height, increased lateral branching and narrow and smaller leaves. We proposed to use the lug-3 line in elucidating the role of LUG as a potential general regulator of transcription in Arabidopsis. mRNA populations will be isolated from wild type (Ler) and lug-3 plants that have produced inflorescence. This stage of development has been selected for several reasons. Firstly, mRNA populations from the widest range of tissue types from a single plant can be collected. Secondly, as AGAMOUS, which is involved in the regulation of floral development, is present in the Affymetrix gene chip, it will provided an excellent internal control to monitor between chips. Results will demonstrate whether LUG is likely to have a more global role in regulating transcription, and will identify pathways under the regulation of this co-repressor-like protein. 12 samples were used in this experiment.
2010-07-09 | E-GEOD-20227 | biostudies-arrayexpress
Project description:Successful floral meristem (FM) determinacy is critical for the subsequent reproductive development and life cycle. Although phytohormones cytokinin and auxin interact to coordinately regulate many aspects of plant development, whether, if so how, cytokinin and auxin function in FM determinacy remain unclear. Here we show that the homeostasis of cytokinin is critical for the FM determinacy. Auxin promotes the expression of AUXIN RESPONSE FACTOR3 (ARF3) to repress cytokinin activity in FM determinacy. We found that ARF3 represses the expression of the ISOPENTENYLTRANSFERASE (IPT) family genes directly and the LONELY GUY (LOG) family genes indirectly, whose products are enzymes required for cytokinin biosynthesis. Furthermore, ARF3 directly inhibits the expression of ARABIDOPSIS HISTIDINE KINASE4 (AHK4), one of cytokinin receptor genes, to depress cytokinin activity. Genome-Wide Transcriptional Profiling reveals multiple functions of ARF3 in flower development. Consequently, ARF3 controls cell division by regulating cell cycle genes expression through cytokinin. Eventually, we show that AGAMOUS (AG) dynamically regulates the expression of ARF3 and IPTs resulting in coordinated regulation of FM maintenance and termination through cell division. Therefore, our findings reveal the molecular linkage between phytohormones auxin/cytokinin and AG in FM determinacy and shed light on the mechanisms of FM maintenance and termination.
2018-08-24 | GSE103054 | GEO
Project description:Most developmental processes associated with fruit patterning take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) integrate to control flowering time, but it is unclear how GA and miR156 interplay during fruit patterning. Here, we used genetic, molecular, and imaging tools to demonstrate that GA and age synergistically control tomato reproductive development. We found that low levels of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL/SBP) transcripts or high GA responses/levels led to enlarged FMs, defects in FM determinacy, and fruits with increased locule number. Conversely, low GA responses reduced locule number and indeterminacy, and the expression of a miR156-resistant form of SlSBP15 (rSBP15) reduces FM size by decreasing cell size and cell number. Importantly, we discovered that GA levels/responses may be partially responsible for the fruit defects observed in 156OE and rSBP15 plants. GA and miR156-targeted SlSBPs regulate classical genes associated with floral determinacy, such as CRABS CLAWa (SlCRCa), and GA and SlSBPs act synergistically with tomato CLAVATA3 (SlCLV3) to control early flower and fruit development. Our findings indicate that gibberellins and age-dependent miR156-targeted SlSBPs co-operate to regulate FM activity and locule formation, thereby offering a novel mechanism of controlling fruit patterning.
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Project description:Regulation of homeotic gene expression is critical for proper developmental patterns in plants. The Arabidopsis thaliana floral homeotic gene AGAMOUS is regulated by LEUNIG (LUG). Mutations in LUG result in homeotic transformations of floral organ identity. LUG mutants also exhibit other defects that are independent of AG, including abnormal carpel and ovule development, reduced female and male fertility, and narrower leaves and floral organs, suggesting that LUG has a wider role in development. LUG is structurally similar to the transcription co-repressors Tup1 (S. cerevisiae) and Groucho (Drosophila), suggesting developmental pathways regulated by LUG may be controlled by a conserved eukaryotic repression mechanism. We aim to determine novel target genes regulated by LUG using transcriptome analysis. A mutant lug-3 line has been obtained from Dr. Zhongchi Liu. This line was used in the initial studies of LUG in the Meyerowitz lab. Lug-3 is a strong allele in the Lansberg erecta background, caused by a nonsense mutation that results in early termination of the protein and is likely null. The Lug-3 mutant exhibits narrow floral organs with staminoid petals and carpelloid sepals, abnormal carpel and ovule development, reduced plant height, increased lateral branching and narrow and smaller leaves. We proposed to use the lug-3 line in elucidating the role of LUG as a potential general regulator of transcription in Arabidopsis. mRNA populations will be isolated from wild type (Ler) and lug-3 plants that have produced inflorescence. This stage of development has been selected for several reasons. Firstly, mRNA populations from the widest range of tissue types from a single plant can be collected. Secondly, as AGAMOUS, which is involved in the regulation of floral development, is present in the Affymetrix gene chip, it will provided an excellent internal control to monitor between chips. Results will demonstrate whether LUG is likely to have a more global role in regulating transcription, and will identify pathways under the regulation of this co-repressor-like protein.
2010-07-09 | GSE20227 | GEO
Project description:S. reilianum triggered loss of organ and meristem identity, and loss of meristem determinacy in male and female inflorescences and flowers. Microarray analysis showed that these developmental changes were accompanied with transcriptional regulation of genes proposed to regulate floral organ and meristem identity, and meristem determinacy in maize.
2011-09-01 | GSE29747 | GEO