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Epigenomic features and potential functions of PEG and PDS favorable DNA G-quadruplexes in rice

ABSTRACT: Epigenomic features and potential functions of PEG and PDS favorable DNA G-quadruplexes in rice

PROVIDER: PRJNA994537 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25265400_1.fastq.gz	Fastqsanger.gz
	SRR25265400_2.fastq.gz	Fastqsanger.gz
	SRR25265401_1.fastq.gz	Fastqsanger.gz
	SRR25265401_2.fastq.gz	Fastqsanger.gz
	SRR25265402_1.fastq.gz	Fastqsanger.gz

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Epigenomic features and potential functions of PEG and PDS favorable DNA G-quadruplexes in rice

Project description:We provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology

2024-01-17 | GSE237294 | GEO

Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice

Project description:Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice

| PRJNA863283 | ENA

The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice.

Project description:A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.

| S-EPMC10779103 | biostudies-literature

RNA-seq of rat nucleus pulposus cells after stabilizing G-Quadruplexes

Project description:We report the RNA-seq data for rat nucleus pulposus cells after stabilizing G-Quadruplexes (G4). We sequenced rat nucleus pulposus cells treated with PDS, Braco-19 and Phen-DC3 separately and untreated with these G4 stabilizers, which could stabilize G4 structure in cells.

2022-11-02 | GSE194015 | GEO

Epigenomic Features and Potential Functions of K+ and Na+ Favorable DNA G-Quadruplexes in Rice

Project description:We explores the effects of K+ and Na+ on global G4 formation in vitro, thereby providing valuable resources for functional G4 studies in rice. It will provide certain G4 loci for the biotechnological engineering of rice in the future.

2022-08-01 | GSE209990 | GEO

Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190613_174740_sham_cont]

Project description:In order to better understand the context of root water stress and its relationship to other stresses, I undertook an evaluation of osmotic water stress by transcriptome analyses. Whole transcriptome MARSeq (Diego Adhemar Jaitin, 2017) analysis can enable us to study the changes in gene expression (changes in transcript prevalence) in depth under different treatments. It is a cost effective method to develop transcriptional activity. It uses relatively small amounts of RNA and reads sequences from the 3’-polyA containing end. This method can reveal underlying trends that can help us understand the less obvious processes happening in our system. To carry this out I processed whole transcriptome data separately from WT seedling roots exposure to PEG, and from roots under 30% PEG + 5mM HIS, 30% PEG + 1mM SHAM for 0, 1, 2, 3 h.

2021-05-26 | GSE152457 | GEO

Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190311_172119_Peg_SHAMf1_res]

2021-05-26 | GSE152456 | GEO

Expression data from PEG treated roots

Project description:We study differences in gene expression between 5% PEG treated and control plants’ roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by water limitation mimicked by PEG treatment.treated

2018-07-12 | GSE116922 | GEO

Identification of Poly Ethylene Glycol (PEG) and PEG-based Detergents Using Peptide Search Engines

Project description:Polyethylene glycol (PEG) is one of the most common polymer contaminations in MS samples. At present, the detection of PEG and other polymers relies largely on manual inspection of raw data which is laborious and frequently difficult due to sample complexity and retention characteristics of polymer species in reversed phase chromatography. We developed a new strategy for the automated identification of PEG molecules from MSMS data using protein identification algorithms in combination with a database containing “PEG-proteins”. Through definition of variable modifications, we extend the approach for the identification of commonly used PEG-based detergents. We exemplify the identification of different types of polymers by static nanoESI-MSMS analysis of pure detergent solutions and data analysis using Mascot. Analysis of LC-MSMS runs of a PEG contaminated sample by Mascot identified 806 PEG-spectra originating from four PEG species using a defined set of modifications covering PEG and common PEG-based detergents. Further characterization of the sample for unidentified PEG species using error tolerant and mass tolerant searches resulted in identification of 3409 and 3187 PEG related MSMS spectra, respectively. We further demonstrate the applicability of the strategy for Protein Pilot and MaxQuant.

2018-05-28 | PXD009376 | Pride

Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190311_172119_Peg_SHAMf1_res]

Project description:Transcriptome analysis of Arabidopsis thaliana shoots and roots, exposed to PEG-induced osmotic shock, PEG+Histidine, PEG+SHAM [20190311_172119_Peg_SHAMf1_res]

| PRJNA639497 | ENA

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