Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis Root Methylation and Root Nucleosome Positioning

ABSTRACT: DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE52762 | GEO | 2014/02/11

SECONDARY ACCESSION(S): PRJNA237956

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Arabidopsis Root Methylation and Root Nucleosome Positioning

Project description:DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots. No replicates, two libraries for root methylation.

2014-02-11 | E-GEOD-52762 | biostudies-arrayexpress

Quinoa gene expression under shoot or root heating

Project description:Quinoa is a highly nutritious seudocereal crop that is not well adapted to heat. Improving understanding of quinoa responses to heat would help expand its cultivation to regions with warmer climates. This study profiled gene expression of quinoa plants from accession QQ74 (PI 614886) treated with high tempreatures during anthesis of the main panicle, which lasted 11 days. Heat was applied in four different treatments to profile gene expression changes from root or shoot heating. Treatments were: 1. control with both roots and shoots at 22°C, 2. heated roots with roots at 30°C and shoots at 22°C, 3. heated shoots with roots at 22 °C and shoots at 35°C, and 4. heated roots and shoots with roots at 30°C and shoots at 35°C. Healthy leaves from 3 plants per treatment were sampled from the mid section of the plants, during the first (day 1) and last day (11) of heat treatment, at Zeitgeber time 2. Gene expression of each of the three heat treatments was compared to control using the Kallisto-Sleuth pipeline. These gene expression profiles of quinoa under heat are made available as a community resource to improve understanding of quinoa responses to heat.

2019-07-31 | GSE128155 | GEO

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (Mnase-Seq)

Project description:Methylation of cytosines (5meC) is a widespread heritable DNA modification. During mammalian development, two global demethylation events are followed by waves of de novo DNA methylation. In vivo mechanisms of DNA methylation establishment are largely uncharacterized. Here we use Saccharomyces cerevisiae as a system lacking DNA methylation to define the chromatin features influencing the activity of the murine DNMT3B. Our data demonstrate that DNMT3B and H3K4 methylation are mutually exclusive and that DNMT3B is co-localized with H3K36 methylated regions. In support of this observation, DNA methylation analysis in yeast strains without Set1 and Set2 show an increase of relative 5meC levels at the TSS and a decrease in the gene-body, respectively. We extend our observation to the murine male germline, where H3K4me3 is strongly anti-correlated while H3K36me3 correlates with accelerated DNA methylation. These results show the importance of H3K36 methylation for gene-body DNA methylation in vivo. Nucleosome mapping in yeast

2015-04-02 | E-GEOD-66907 | biostudies-arrayexpress

Arabidopsis Shoot versus Root transcriptome

Project description:Bulk RNA-Seq datasets were generated for the shoots and roots of Arabidopsis in order to compare expression of nutrient transporters between tissues

2023-03-05 | GSE226144 | GEO

DNA methylation and gene expression analyses in adipose tissue to identify new loci associated with T2D development in obesity

Project description:We investigated DNA methylation and gene expression in VAT biopsies from 19 women with obesity, without (n=9) or with T2D (n=10). We performed microarray analyses to assess global methylation patterns and to search for differences between groups. We searched for differentially methylated cytosines and differentially methylated regions

2023-01-01 | E-MTAB-11037 | biostudies-arrayexpress

Methylation profiling by array of human carcinoma cells

Project description:Genomic DNA from cell lines was extracted and treated with sodium bisulfite. Fragments were PCR-amplified from the treated template DNA, labelled and hybridized to the microarray. The array contained probe sequences complementary to formerly methylated (M) and unmethylated (U) cytosines respectively. Hence the signal intensity ratio from M/(M+U) represents each cytosines methylation level in percent.

2010-05-11 | E-MEXP-2698 | biostudies-arrayexpress

Early proteomic responses in shoot and root of FL478 under salinity stress

Project description:Climate change is affecting crop production due to soil salinization and water scarcity, and is predicted to worsen in the coming years. Rice is a major staple food and the most salt-sensitive cereal. High salinity in the soil triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian rice landrace varieties such as Pokkali and Nona Bokra. In this study, we characterized the physiological and early proteomic responses to salinity in FL478, an inbred rice line harboring the Saltol region. For this, plantlets were cultured in hydroponic cultures with 100 mM NaCl and evaluated at 6, 24 and 48h. At the physiological level, salinity significantly reduced shoot length after 48 h, whereas root length significantly increased. Moreover, the Na+/K+ ratio was maintained at lower levels in the shoots compared to the roots FL478 plantlets. On the other hand, roots showed a faster and more coordinated proteomic response than shoots, which was evident from only 6h of treatment. These responses were markedly related with transcription- and translation-related proteins. Moreover, roots exhibited a higher accumulation of stress-related proteins in response to salinity treatment, like peroxidase and SalT, which are both present in the Saltol QTL. Both, physiological and proteomic response, showed that roots respond in a highly adaptive manner to salinity stress compared to shoots, which suggests that this tissue is critical to the tolerance observed in varieties harbouring the Saltol region.

2020-12-21 | PXD014669 | Pride

Conservation and Divergence of Transcriptomic and Epigenomic Variations in Maize Hybrids

Project description:The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. We observed that whereas histone modifications vary both between tissues and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between tissues. Histone modifications were associated with transcriptomic divergence between tissues and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements (TEs), and for different TEs in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species. Together, our results suggest that despite of the variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different tissues of maize hybrids. Genome-wide integrated maps of mRNA and small RNA (sRNA) transcriptomes, DNA methylomes and genome-wide distribution of three representative histone modifications (H3K4me3, H3K9ac and H3K36me3) in the shoots and roots of 14 day old seedlings of two maize inbred lines (B73 and Mo17) and their reciprocal hybrids (B73 x Mo17 and Mo17 x B73).

2013-03-19 | E-GEOD-43142 | biostudies-arrayexpress

Cytosine methylation at CpCpG sites triggers accumulation of non-CpG methylation in gene bodies

Project description:Methylation of cytosine is an epigenetic mark involved in the regulation of transcription, usually associated with transcriptional repression. In mammals, methylated cytosines are found predominantly in CpGs but in plants non-CpG methylation (in the CpHpG or CpHpH contexts, where H is A, C or T) is also present and is associated with the transcriptional silencing of transposable elements. In addition, CpG methylation is found in coding regions of active genes. In the absence of the demethylase of lysine 9 of histone 3 (IBM1), a subset of body-methylated genes acquires non-CpG methylation. This was shown to alter their expression and affects plant development. It is not clear why only certain body-methylated genes gain non-CpG methylation in the absence of IBM1 and others do not. We described a link between CpG methylation and the establishment of methylation in the CpHpG context that explains the two classes of body-methylated genes. We provided evidence that external cytosines of CpCpG sites can only be methylated when internal cytosines are methylated and that CpCpG sites methylated in both cytosines promote spreading of methylation in the CpHpG context in genes protected by IBM1.

2017-01-04 | GSE89913 | GEO

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs (MethylC-seq)

Project description:Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. Since root hairs are single cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single cell root hairs as compared to multi-cellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated as compared to stripped roots. However, in response to heat stress, both root hairs and stripped roots showed more hypomethylation in each context, especially in the mCHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes of dynamic DNA methylation directly or indirectly is associated with expression of genes and transposons either within the context of specific tissues/cells or stress (heat).

2017-08-01 | GSE90142 | GEO

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