Ontology highlight
ABSTRACT:
PROVIDER: PRJNA474698 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7264160_1.fastq.gz | Fastqsanger.gz | |||
| SRR7264160_2.fastq.gz | Fastqsanger.gz | |||
| SRR7264170_1.fastq.gz | Fastqsanger.gz | |||
| SRR7264170_2.fastq.gz | Fastqsanger.gz | |||
| SRR7264180.fastq.gz | Fastqsanger.gz |
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Project description:Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment. Wild type Arabidopisis and sdg8-5 plants were grown in hydroponics system for three weeks, then starved for carbonhydrate and light for 24 h. They were then treated with carbon and/or light or remained untreated as controls.Three biological replicates were collected, resulting in 24 samples (2 genotypes X 2 carbonhydrate treatmens X 2 light treatments X3 biological replicates).
2015-03-01 | E-GEOD-62435 | biostudies-arrayexpress
Project description:Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment.
2015-03-01 | GSE62435 | GEO
Project description:Regulation of carotenoid composition and shoot branching in Arabidopsis by a chromatin modifying histone methyltransferase, SDG8<br>Comparison of transcript profiles between wild type Columbia and ccr1 (carotenoid and chloroplast regulatory) mutant, which contains a mutation in At1g77300 (SDG8)
2009-10-01 | E-MEXP-1787 | biostudies-arrayexpress
Project description:The seed maturation program occurs only during late phase of embryo development and repression of the maturation genes is pivotal for seedling development. However, mechanisms that repress the expression of this program in vegetative tissues are not well understood. A genetic screen was performed for mutants that express maturation genes in leaves. Here, it is shown that mutations affecting SDG8 (SET DOMAIN GROUP 8), a putative histone methyltransferase, cause ectopic expression of a subset of maturation genes in leaves. Further, to investigate the relationship between SDG8 and the Polycomb Group (PcG) proteins, which are known to repress many developmentally important genes including seed maturation genes, double mutants was made and formation of somatic embryos was observed on mutant seedlings with mutations in both SDG8 and EMF2 (EMBRYONIC FLOWER 2). Interestingly, double mutant of sdg8 and mutations in VRN2 (VERNALIZATION 2), a paralog of EMF2, grow and develop normally to maturity. Analysis of histone methylation status at chromatins of a number of maturation loci revealed synergistic effect of emf2 and sdg8 on the deposition of the active histone mark, trimethylation of lysine 4 on histone 3 (H3K4me3), which is consistent with high expression of these genes (formation of somatic embryos) in emf2 sdg8 double mutants. These observations demonstrate a functional cooperative interplay between SDG8 and an EMF2-containing PcG complex in maintaining vegetative cell identity by repressing seed genes to promote seedling development. The work also indicates the functional specificities of PcG complexes in Arabidopsis. Total RNA was isolated from three independent biological replicates of Wild type (ProM-NM-2CG:GUS) and two independent biological replicates of sdg8-2 and essp4/sdg8-5, respectively. Four ATH1 chips were used for the two mutants and three for the wild type. Matrices comprising the signal intensity value of each gene per replicate hybridization and the averaged data of each gene generated from three replicate hybridizations of the wild type and two replicate hybridizations of mutant samples, respectively, are linked below as supplementary files.
2011-12-31 | E-GEOD-29771 | biostudies-arrayexpress
Project description:Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism
| PRJNA264092 | ENA
Project description:The seed maturation program occurs only during late phase of embryo development and repression of the maturation genes is pivotal for seedling development. However, mechanisms that repress the expression of this program in vegetative tissues are not well understood. A genetic screen was performed for mutants that express maturation genes in leaves. Here, it is shown that mutations affecting SDG8 (SET DOMAIN GROUP 8), a putative histone methyltransferase, cause ectopic expression of a subset of maturation genes in leaves. Further, to investigate the relationship between SDG8 and the Polycomb Group (PcG) proteins, which are known to repress many developmentally important genes including seed maturation genes, double mutants was made and formation of somatic embryos was observed on mutant seedlings with mutations in both SDG8 and EMF2 (EMBRYONIC FLOWER 2). Interestingly, double mutant of sdg8 and mutations in VRN2 (VERNALIZATION 2), a paralog of EMF2, grow and develop normally to maturity. Analysis of histone methylation status at chromatins of a number of maturation loci revealed synergistic effect of emf2 and sdg8 on the deposition of the active histone mark, trimethylation of lysine 4 on histone 3 (H3K4me3), which is consistent with high expression of these genes (formation of somatic embryos) in emf2 sdg8 double mutants. These observations demonstrate a functional cooperative interplay between SDG8 and an EMF2-containing PcG complex in maintaining vegetative cell identity by repressing seed genes to promote seedling development. The work also indicates the functional specificities of PcG complexes in Arabidopsis.
2011-12-31 | GSE29771 | GEO
Project description:To evaluate the role of SDG8 and SDG26 in genome transcription, we performed transcriptome analyses using 6-day-old seedlings and identified differentially expressed genes in the sdg8, sdg26 and sdg8 sdg26 mutants as compared to wild-type(Col).
2016-10-01 | GSE71927 | GEO
Project description:In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5â?? end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription Characterization of the genome-wide distribution of H3K36ac using ChIP-seq. Analysis of the mechanistic crosstalk in the deposition of acetylation and methylation at H3K36 by ChIP-seq of H3K36ac and H3K36me3 in sdg8-2 and gcn5-1, respectively.
2016-04-05 | E-GEOD-74841 | biostudies-arrayexpress
Project description:Nitrate is an important signaling molecule that commands genome-wide gene expression changes that impact metabolism, physiology, plant growth and development. Although gene expression responses to nitrate at the mRNA level have been characterized in great detail, the impact of nitrate signaling at the proteome level has been much less explored. Most signaling pathways involve post-translational modifications of key protein factors and chiefly among these modifications is protein phosphorylation. In an effort to identify new components involved in nitrate responses in plants, we performed analyses of the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. We identified 268 phosphoproteins that show significant changes at 5 min or 20 min after nitrate treatments. The large majority of these proteins (95%) are coded by genes that are not modulated at the expression level in response to nitrate treatments in publicly available transcriptome data. Proteins identified by 5 min include potential signaling-components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with protein binding, transporter activity or hormone metabolism functions. Interestingly, the phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants in response to nitrate at 5 min was significantly different (95%) as compared to wild-type plants, confirming its key role in nitrate signaling that involves phosphoproteomic changes. Our integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We experimentally validated the role of a new phosphorylation site in PIN2 function for both primary and lateral root growth responses to nitrate. Our data provide new insights into the phosphoproteome and identifies novel protein components that are regulated post-translationally, such as PIN2, in nitrate responses in Arabidopsis thaliana roots.
| MSV000086215 | MassIVE
Project description:Our study helps to understand the transcriptome level changes in small intestines exposed to hypoxia after nitrate supplementation, to find out which genes or signaling pathways nitrate plays a role in by activating or inhibiting them.
2024-01-02 | GSE252373 | GEO