Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA357353 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The evolution and diversification of proteins capable of remodelling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodelling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologues have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast-evolving under positive selection, while PKL is evolving under purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein’s intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis of gene expression in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights on gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.
2023-09-06 | GSE236025 | GEO
Project description:seed specific genes-Establishing the network of seed gene expression and analysis of its biodiversity
| PRJNA115179 | ENA
Project description:merMEDEA (MEA) is a component of the Polycomb Repressive complex 2 (PRC2) of Arabidopsis thaliana, and a maternal imprinted gene that functions during central cell, embryo and endosperm development. Seeds that develop from mea mutant egg cells abort regardless of the paternal genotype. With this approach, we aim to uncover putative genes that are downstream of MEA and might cause the seed abortion phenotype. For this, we compare three developmental time point datasets between wild-type and mea mutant: ovary (before fertilization), and seed at 1-2 and 4 days after pollination (DAP).
2021-06-25 | E-MTAB-9569 | biostudies-arrayexpress
Project description:sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
2017-08-15 | GSE94458 | GEO
Project description:Desiccation tolerance (DT) allowed seed plants to conquer ecosystems with long periods of limited water availability. This adaptive features allows seeds to remain dried for very long times without losing their ability to germinate. There is little information about all the signaling components required to achieve DT and on how transcription factors (TFs) modulate global DT processes. We performed RNA-seq experiment and carbohydrates profiles of lec1, lec2, fus3 and abi3, as well as their corresponding wild types, at three stages of seed development 15, 17 and 21 DAF (day after open flower) belonging to the seed desiccation period. A complex experimental design approach and regulatory networks prediction were used to identify differentially expressed genes specifically involved in DT process.
2016-09-06 | GSE76015 | GEO
Project description:PICKLE (PKL), a Chromodomain Helicase DNA binding domain type 3-type (CHD3) chromatin remodeler, noted for an embryonic structure called pickle root in primary root tip in pkl mutant, has been studied for decades. we obtained a comprehensive genome occupancy of PKL by Chromatin immunoprecipitation-sequencing (ChIP-seq), and found PKL co-occupy with the major repressors of seed maturation program, VIVIPAROUS1/ABI3-LIKE1/2 (VAL1/2) in genome. Furthermore, PKL physically interacts with VAL1/2 in vivo and phenotype and transcriptome data indicated that PKL and VAL1/2 function in a common pathway. Moreover, ChIP-seq and ChIP-qPCR results showed that VAL1/2 are necessary for the recruitment of PKL to co-target genes
2023-05-10 | GSE186157 | GEO
Project description:RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
2017-08-15 | GSE94457 | GEO
Project description:Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation, an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs to properly differentiate, which presents a major roadblock for dissecting the precise roles of PRC2 activity during lineage commitment. While recent studies suggest that loss of H3K27me3 leads to changes in DNA methylation in ESCs, how these two pathways coordinate to regulate gene expression programs during lineage commitment is poorly understood. Here, we analyzed gene expression and DNA methylation levels in several PRC2 mutant ESC lines that maintain varying levels of H3K27me3. We found that maintenance of intermediate levels of H3K27me3 allowed for proper temporal activation of lineage genes during directed differentiation of ESCs to spinal motor neurons (SMNs). However, genes that function to specify other lineages failed to be repressed, suggesting that PRC2 activity is necessary for lineage fidelity. We also found that H3K27me3 is antagonistic to DNA methylation in cis. Furthermore, loss of H3K27me3 leads to a gain in promoter DNA methylation in developmental genes in ESCs and in lineage genes during differentiation. Thus, our data suggest a role for PRC2 in coordinating dynamic gene repression while protecting against inappropriate promoter DNA methylation during differentiation. Embryonic Stem Cell (ESC) lines mutant for PRC2 core components Suz12 (Suz12GT and Suz12delta) and Eed (Eednull) were subjected to in vitro directed differentiation down the spinal motor neuron lineage. ESCs and day 5 differentiated cells from the three mutant lines and wild-type were used for Reduced Representation Bisulfite Sequencing (RRBS).
2014-11-17 | E-GEOD-53507 | biostudies-arrayexpress
Project description:Polycomb Repressive Complex 2 (PRC2) catalyzes histone H3 lysine 27 tri-methylation, an epigenetic modification associated with gene repression. H3K27me3 is enriched at the promoters of a large cohort of developmental genes in embryonic stem cells (ESCs). Loss of H3K27me3 leads to a failure of ESCs to properly differentiate, which presents a major roadblock for dissecting the precise roles of PRC2 activity during lineage commitment. While recent studies suggest that loss of H3K27me3 leads to changes in DNA methylation in ESCs, how these two pathways coordinate to regulate gene expression programs during lineage commitment is poorly understood. Here, we analyzed gene expression and DNA methylation levels in several PRC2 mutant ESC lines that maintain varying levels of H3K27me3. We found that maintenance of intermediate levels of H3K27me3 allowed for proper temporal activation of lineage genes during directed differentiation of ESCs to spinal motor neurons (SMNs). However, genes that function to specify other lineages failed to be repressed, suggesting that PRC2 activity is necessary for lineage fidelity. We also found that H3K27me3 is antagonistic to DNA methylation in cis. Furthermore, loss of H3K27me3 leads to a gain in promoter DNA methylation in developmental genes in ESCs and in lineage genes during differentiation. Thus, our data suggest a role for PRC2 in coordinating dynamic gene repression while protecting against inappropriate promoter DNA methylation during differentiation. Embryonic Stem Cell (ESC) lines mutant for PRC2 core components Suz12 (Suz12GT and Suz12delta) and Eed (Eednull) were subjected to in vitro directed differentiation down the spinal motor neuron lineage. ESCs and day 5 differentiated cells from the three mutant lines and wild-type were used for H3K27me3 ChIP-seq.
2014-11-17 | E-GEOD-53505 | biostudies-arrayexpress