Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide research of epigenetic regulation in arabidopsis

ABSTRACT: In Arabidopsis, there are still many areas of epigenetic modification functions that remain to be explored. In this study, we used multiple high-throughput sequencing technologies to investigate the regulation of histone modifications in the model organism Arabidopsis.

ORGANISM(S): Arabidopsis thaliana Oryza sativa

PROVIDER: GSE253972 | GEO | 2025/02/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide research of epigenetic regulation in arabidopsis

Project description:Genome-wide research of epigenetic regulation in arabidopsis

| PRJNA1068029 | ENA

Analysis and comprehensive comparison of Pacbio and Nanopore-based RNA-sequencing in Arabidopsis transcriptome

Project description:Rapidly increased studies by third-generation sequencing [Pacific Biosciences (Pacbio) and Oxford Nanopore Technologies (ONT)] have been used in all kinds of research areas. Among them, the plant full-length single-molecule transcriptome studies were most used by Pacbio while ONT was rarely used. Therefore, in this study, we developed ONT RNA-sequencing methods in plants. We performed a detailed evaluation of reads from Pacbio and Nanopore PCR cDNA (ONT Pc) sequencing in plants (Arabidopsis), including the characteristics of raw data and identification of transcripts. We aimed to provide a valuable reference for applications of ONT in plant transcriptome analysis.

2019-12-15 | GSE141641 | GEO

Pseudouridine guides germline small RNA transport and epigenetic inheritance

Project description:Epigenetic modifications that arise during plant and animal development, such as DNA and histone modification, are mostly reset during gamete formation, but some are inherited from the germline including those marking imprinted genes. Small RNAs guide these epigenetic modifications, and some are also inherited by the next generation. In C. elegans, inherited small RNA precursors have poly (UG) tails, but how inherited small RNAs are distinguished in other animals and plants is unknown. Pseudouridine (Ψ) is the most abundant RNA modification but has not been explored in small RNAs. Here, we develop novel assays to detect Ψ in short RNA sequences, demonstrating its presence in mouse and Arabidopsis microRNAs and their precursors. We also detect substantial enrichment in germline small RNAs, namely epigenetically activated siRNAs (easiRNAs) in Arabidopsis pollen, and piwi-interacting piRNAs in mouse testis. In pollen, pseudouridylated easiRNAs are localized to sperm cells, and we found that PAUSED/HEN5 (PSD), the plant homolog of Exportin-t, interacts genetically with Ψ and is required for transport of easiRNAs into sperm cells from the vegetative nucleus. We further show that Exportin-t is required for the triploid block: chromosome dosage-dependent seed lethality that is epigenetically inherited from pollen. Thus, Ψ has a conserved role in marking inherited small RNAs in the germline. These studies were funded by a grant from the Polish National Science Centre (2020/39/D/NZ1/01918).

2024-04-29 | PXD042662 | Pride

PRC2-mediated epigenetic signatures associate with pathogn-induced programmed cell death in Arabidopsis

Project description:The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated H3K27me3 histone modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.

2021-02-10 | GSE140410 | GEO

CATseq a comparative Arabidopsis Transcriptome - RNA-Seq part

Project description:A comparative assessment between both technologies, RNASeq and microarrays to detect differential expression in Arabidopsis transcriptome. The sequencing approach use High-throughput sequencing on different Solexa technologies (GAII,HiSeq2000 multiplex or not) Wild type samples were analyzed from 2 tissus (flower buds and leaves) which have a very contrasted transcriptomic profile (i.e very high number of genes differentially expressed).

2014-06-01 | GSE53673 | GEO

Tolerance of Arabidopsis to thrip feeding

Project description:We analyzed the interaction between Arabidopsis and western flower thrips (Frankliniella occidentalis), which are one of the most serious insect pests of cultivated plants. A total of 1.2K potential biotic and abiotic stress-related genes were selected from the genes covered by the Arabidopsis 7K array (RIKEN, Japan) and Arabidopsis oligo microarray (Agilent Technologies, USA) for this study. The 21- day-old plants were feeded by western flower thrips in an acryl cylinder chamber with air ventilation windows covered with a fine mesh. Leaves were harvested several time after the feeding. Our results indicate that JA plays an important role in Arabidopsis in terms of response to, and tolerance against, thrip feeding.

2008-10-25 | GSE13304 | GEO

Single cell level analysis of the Arabidopsis root transcriptome and chromatin accessibility

Project description:The nuclei of Arabidopsis root seedlings were isolated then use to establish a single cell level resolution transcriptome (sNucRNA-seq) and profile of chromatin accessibility (sNucATAC-seq) applying 10X Genomics technologies.

2021-01-11 | GSE155304 | GEO

Arabidopsis thaliana

Project description:Temperature-responsive N4-acetylcytidine mRNA modification modulates thermosensory flowering in Arabidopsis

| PRJNA1126445 | ENA

Multiplex genome-editing in Arabidopsis thaliana using Mb3Cas12a

Project description:The use of CRISPR/Cas proteins for the creation of multiplex genome-engineering represents an important avenue for crop improvement, and further improvements for creation of knock-in plant lines via CRISPR-based technologies may enable the high-throughput creation of designer alleles. To circumvent limitations of the commonly used CRISPR/Cas9 system for multiplex genome-engineering, we explored the use of Moraxella bovoculi 3 Cas12a (Mb3Cas12a) for multiplex genome-editing in Arabidopsis thaliana. We identified optimized promoter sequences for driving expression of single transcript multiplex crRNA arrays in A. thaliana, resulting in stable germline transmission of Mb3Cas12a-edited alleles at multiple target sites. By utilizing this system, we demonstrate single-transcript multiplexed genome-engineering using of up to 13 crRNA targets. We further show high target specificity of Mb3Cas12a-based genome-editing via whole-genome sequencing. Taken together, our method provides a simplified platform for efficient multiplex-genome-engineering in plant-based systems.

2021-09-15 | GSE162875 | GEO

Chromatin immunoprecipitation of GCN5 target sites in Arabidopsis gcn5 mutant and wild type seedlings

Project description:GCN5 plays an essential role in chromatin modification and transcriptional regulation, its mode of action is not understood. It is therefore crucial to determine what are the sites targeted by GCN5 in the Arabidopsis genome to decipher the regulatory mechanisms in which it is involved. Array technologies have been used in recent years to determine, at the scale of whole genomes, the sites bound in vivo by chromatin-associated proteins (Hanlon and Lieb 2004) or targeted by chromatin-modifying enzymes (Millar and Grunstein 2006; Zhang et al. 2006). In this study we took advantage of the chromatin immunoprecipitation (ChIP) technique coupled with hybridization to a novel Arabidopsis promoter array to show that GCN5 is recruited to a large number of transcriptionally active promoters.

2007-10-01 | E-MEXP-1233 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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