Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana: wild type vs. scl15 mutant

ABSTRACT: Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a HISTONE DEACETYLASE19 (HDA19)-associated regulator, SCARECROW LIKE15 (SCL15), is essential for repressing the seed maturation program in vegetative tissues. SCL15 is expressed and GFP-tagged SCL15 predominantly localizes to the vascular bundles, particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds. In scl15 seedlings, many genes involved in seed maturation are markedly derepressed and 12S globulin accumulates; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci. SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies revealed that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE67395 | GEO | 2015/03/30

SECONDARY ACCESSION(S): PRJNA279808

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Arabidopsis thaliana: wild type vs. scl15 mutant

Project description:Epigenetic regulation of gene expression is critical for controlling embryonic properties during the embryo-to-seedling phase transition. Here we report that a HISTONE DEACETYLASE19 (HDA19)-associated regulator, SCARECROW LIKE15 (SCL15), is essential for repressing the seed maturation program in vegetative tissues. SCL15 is expressed and GFP-tagged SCL15 predominantly localizes to the vascular bundles, particularly in the phloem companion cells and neighbouring specialized cells. Mutation of SCL15 leads to a global shift in gene expression in seedlings to a profile resembling late embryogenesis in seeds. In scl15 seedlings, many genes involved in seed maturation are markedly derepressed and 12S globulin accumulates; this is correlated with elevated levels of histone acetylation at a subset of seed-specific loci. SCL15 physically interacts with HDA19 and direct targets of HDA19-SCL15 association are identified. These studies revealed that SCL15 acts as an HDA19-associated regulator to repress embryonic traits in seedlings. Two-condition experiment: wild type vs. scl15 mutant seedlings. Biological replicates: 3 wild type and 3 mutant, independently grown and harvested. One replicate per array. Dye-swaps were performed.

2015-03-30 | E-GEOD-67395 | biostudies-arrayexpress

Differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants

Project description:We characterized the biological and molecular functions of AtC3H17, a unique Arabidopsis gene encoding a non-tandem CCCH zinc finger protein, in plant development. To investigate the downstream regulatory mechanisms of AtC3H17, whole genome microarray expression profiling was carried out. The experiment was designed to identify differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants (AtC3H17 OXs) grown for 14 days under SD growth conditions. Interestingly, the most up-regulated genes were 12S seed storage globulin genes, CRUCIFERIN A (CRA1) and CRUCIFERIN 3 (CRU3), and seed oil-body protein genes such as OLEOSIN 1 (OLEO1) and OLEO2 in AtC3H17 OXs compared with WT. We performed quantitative RT-PCR and confirmed that transcription levels of CRU3, OLEO1, OLEO2, and 2S seed storage albumin 1 (At2S1) were higher in AtC3H17 OX seedlings than in WT seedlings.

2015-12-05 | GSE75702 | GEO

Differentially expressed genes between WT and AtC3H17-overexpressing transgenic plants

2015-12-05 | E-GEOD-75702 | biostudies-arrayexpress

SCL15 is a critical regulator for plant development, germination, seed dormancy and seed vigor in Arabidopsis thaliana

Project description:Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.

2020-11-04 | GSE160707 | GEO

Identification of target genes of ABI3 [Agilent 44k]

2012-06-01 | GSE33951 | GEO

Transcription profiling of developing wild type pea seeds and those expressing anti-ABA antibodies

Project description:ABA regulates in plants a wide range of developmental events, mediates responses to environmental stress and is necessary to proceed through seed maturation and to acquire desiccation tolerance and dormancy. Immuno-modulation is a suitable means to study ABA functions during seed maturation. Anti-ABA single chain antibody was expressed in pea seed driving LeB4-promoter (Saalbach et al., High-level expression of a single chain Fv fragment (scFv) antibody in transgenic pea seeds J. Plant Physiol. 2001 158: 529-533), which produced only a weak phenotype with slightly decreased seed weight, globulin/albumin and total nitrogen content (aABA line 16 cultivar Erbi). In another approach with a stronger, improved USP-promoter used to express the anti-ABA antibody in pea seeds a different phenotype emerged (aABA line 7, cultivar Eifel). In this line individual seed weight increased by 20 to 30% together with higher globulin and albumin content. To dissect the aABA phenotype at the molecular level, a search for genes with differential expression patterns in transgenic plant versus wild type seeds has been performed using 6k-oligo microarray analysis. cDNA probes were prepared from RNA isolated from embryo of developing seeds of wild type (12, 18, and 22 DAP) and transgenic aABA plants (12, 18, and 22 DAP), which correspond to the transition phase of seed development, and 6k-oligo microarray.

2008-07-31 | E-MEXP-1555 | biostudies-arrayexpress

Gene Expression Changes during embryo and seed maturation, quiescence and germination in soybean

Project description:To understand the molecular events underlying seed maturation, quiescence and germination, we performed transcriptome analysis of soybean (Glycine max) embryos at four seed developmental stages (cotyledon, early, mid and late maturation), mature dry seeds, and seedlings, eight days after seed sowing.

2017-07-12 | GSE99571 | GEO

Identification of target genes of ABI3 [Agilent 44k]

Project description:ABI3 is a key regulator of seed development in Arabidopsis and other plants.To identify genes regulated by ABI3 we performed array based transcriptome analysis of Dexamethasone inducible ABI3 transgenic seedlings. ABI3 mostly in concert with abscisic acid (ABA) was found to activate genes specifically expressed during the maturation phase of seed development. Two weeks old wildtype and 35S::ABI3::GR seedlings were treated with ABA, Dexamethasone (DEX) and ABA plus Dexamethasone for 4 h. Two biological independent experiments were performed. Wildtype was induced to control for DEX-induction of genes.

2012-05-31 | E-GEOD-33951 | biostudies-arrayexpress

The interactome of histone deacetylase HDA19 in dark-grown Arabidopsis seedlings

Project description:In this Data Report, we provide an immunoprecipitation (IP)-based analysis of the HDA19 interactome in etiolated Arabidopsis seedlings. We believe that the interactome presented here provides a valuable resource for follow-up research on novel interacting partners of this central protein. The material used for this experiment was derived from hypocotyls of 6-day-old etiolated Arabidopsis seedlings. The dataset contains a total of 6 files, 3 independent biological replicates of each Col-0 (control plants) and 35S::HDA19-GFP plants.

2023-09-19 | PXD045454 | Pride

Epigenetic Regulation of the Transition from Seed Maturation to Germination in Soybean

Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels. Illumina sequencing of transcripts from cotyledons of mid-maturation (B1 stage) and late maturation (AA1 stage) seeds, whole dry seeds, and cotyledons of seedlings six days after imbibition.

2011-05-10 | E-GEOD-29134 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data