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Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

ABSTRACT: Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

PROVIDER: PRJNA744574 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15067126.fastq.gz	Fastqsanger.gz
	SRR15067127.fastq.gz	Fastqsanger.gz
	SRR15067128.fastq.gz	Fastqsanger.gz
	SRR15067129.fastq.gz	Fastqsanger.gz
	SRR15067130.fastq.gz	Fastqsanger.gz

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Similar Datasets

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

Project description:Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

| PRJNA744571 | ENA

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

Project description:Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

| PRJNA744559 | ENA

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [BiSulfite-seq]

Project description:The "triploid block" prevents interploidy hybridizations in flowering plants, and is characterized by failure in endosperm development and function, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed imprinted genes (PEGs) that are up-regulated in the tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed abortion is bypassed in plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early plant growth. We have identified strong suppressor lines showing transgenerational inheritance of hypomethylation in CG context, as well as normalized expression of PEGs. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow the identification of epialleles involved in the triploid block response in future studies. Finally, we demonstrate that chemically-induced epimutagenesis allows bypassing interploidy hybridizations in Arabidopsis and interspecific hybridization barriers in crosses between Capsella species, thus potentially emerging as a novel strategy for seed-based breeding of triploids and interspecific hybrids with agronomical interest.

2021-11-23 | GSE179702 | GEO

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds [RNA-seq]

2021-11-23 | GSE179697 | GEO

Chemically-induced epimutagenesis allows bypassing reproductive barriers in hybrid seeds

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-11-23 | GSE179704 | GEO

Bypassing reproductive barriers in hybrid seeds using chemically induced epimutagenesis.

Project description:The triploid block, which prevents interploidy hybridizations in flowering plants, is characterized by a failure in endosperm development, arrest in embryogenesis, and seed collapse. Many genetic components of triploid seed lethality have been successfully identified in the model plant Arabidopsis thaliana, most notably the paternally expressed genes (PEGs), which are upregulated in tetraploid endosperm with paternal excess. Previous studies have shown that the paternal epigenome is a key determinant of the triploid block response, as the loss of DNA methylation in diploid pollen suppresses the triploid block almost completely. Here, we demonstrate that triploid seed collapse is bypassed in Arabidopsis plants treated with the DNA methyltransferase inhibitor 5-Azacytidine during seed germination and early growth. We identified strong suppressor lines showing stable transgenerational inheritance of hypomethylation in the CG context, as well as normalized expression of PEGs in triploid seeds. Importantly, differentially methylated loci segregate in the progeny of "epimutagenized" plants, which may allow epialleles involved in the triploid block response to be identified in future studies. Finally, we demonstrate that chemically induced epimutagenesis facilitates hybridization between different Capsella species, thus potentially emerging as a strategy for producing triploids and interspecific hybrids with high agronomic interest.

| S-EPMC8894923 | biostudies-literature

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Project description:Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

| PRJNA1132984 | ENA

TET-mediated epimutagenesis of the Arabidopsis thaliana methylome

Project description:DNA methylation in the promoters of plant genes sometimes leads to transcriptional repression, and the wholesale removal of DNA methylation as seen in methyltransferase mutants results in drastic changes in gene expression and severe developmental defects. However, many cases of naturally-occurring DNA methylation variations have been reported, whereby the altered expression of differentially methylated genes is responsible for agronomically important traits. The ability to manipulate plant methylomes to generate populations of epigenetically distinct individuals could provide invaluable resources for breeding and research purposes. Here we describe “epimutagenesis”, a novel method to rapidly generate variation of DNA methylation through random demethylation of the Arabidopsis thaliana genome. This method involves the expression of a human Ten-eleven translocation (TET) enzyme, and results in widespread hypomethylation that can be inherited to subsequent generations, mimicking mutants in the maintenance DNA methyltransferase met1. Application of TET-mediated epimutagenesis to agriculturally significant plants may result in differential expression of alleles normally silenced by DNA methylation, uncovering previously hidden phenotypic variations.

2018-03-02 | GSE93024 | GEO

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Project description:G-quadruplex (G4) structures can form in guanine-rich stretches of DNA or RNA and have been found to modulate a variety of cellular processes including replication, transcription, and translation. Most studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing G4s in bacteria. We utilized a chemical-genetic approach to identify genes in Escherichia coli that are important for growth in conditions that stabilize G4s. Our screens reveal translation elongation to be a key process that is impacted by G4 stabilization. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, downregulating the levels of certain essential translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation generally are less abundantly expressed under G4-stabilizing conditions. Taken together, the results suggest that RNA G4s present barriers to E. coli growth in G4-stabilizing conditions and reducing the rate of translation can help compensate for G4-related stress.

2024-08-19 | GSE271718 | GEO

Nucleosomes are context-specific, H2A.Z modulated barriers to RNA polymerase

Project description:Nucleosomes are barriers to transcription in vitro, however, their effects on RNA polymerase in vivo are unknown. Here we describe a simple and general strategy to comprehensively map the positions of elongating and arrested RNA Polymerase II (RNAPII) at nucleotide resolution. Our results suggest that nucleosomes present significant, context-specific barriers to RNAPII in vivo that can be tuned by the incorporation of H2A.Z. 8 sets of two replicates each of paired-end and 3 sets of two replicates each of single-end samples were sequenced and analyzed.

2014-03-06 | E-GEOD-49106 | biostudies-arrayexpress

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