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Paramutation of natural epialleles in tomato [BiSulfite-seq]

ABSTRACT: Paramutation of natural epialleles in tomato [BiSulfite-seq]

PROVIDER: PRJNA380948 | ENA |

REPOSITORIES: ENA

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Paramutation of natural epialleles in tomato

Project description:Paramutation of natural epialleles in tomato

| PRJNA381070 | ENA

Paramutation of natural epialleles in tomato [BiSulfite-seq]

Project description:By using DNA methylation of introgression lines as a marker of past paramutation, we characterise in details the paramutation of the \textit{H06} locus in crosses between Solanum lycopersicum and a range of tomato relatives and cultivars. Paramutation of H06 depends on the timing of sRNA production and conforms to the RNA-directed model of paramutation. By scanning the methylomes of tomato introgression lines for shared regions of differential methylation, thousands of candidate regions for paramutation are identified. Analysing the segregation of the methylation patterns for a subset of these regions shows variations in the penetrance of paramutation-like interactions.

2017-08-18 | GSE97192 | GEO

Paramutation of natural epialleles in tomato [sRNA]

Project description:Paramutation of natural epialleles in tomato [sRNA]

| PRJNA381072 | ENA

Paramutation of natural epialleles in tomato [sRNA]

2017-08-18 | GSE97206 | GEO

Paramutation-like features of multiple natural epialleles in tomato.

Project description: Not available

| S-EPMC5859443 | biostudies-literature

Paramutation of natural epialleles in tomato

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

2017-08-18 | GSE97247 | GEO

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

Project description:A role for sRNAs in paramuation is emerging, but their nature and mode of action remain elusive. Paramutation between genetically identical epialleles in Arabidopsis allowed the analysis of associated sRNAs (the data deposited here) and revealed differences connected with gene expression, tissue type, and ploidy.

2020-11-28 | GSE162241 | GEO

Stable Inheritance of Spontaneous Epialleles in Arabidopsis thaliana

Project description:This research uses consecutive generations of two independent mutation accumulation (MA) lines in model organism A. thaliana to understand transgenerational stability of epialleles via self-fertilization. With whole-genome bisulfite sequencing, regions of instability were identified and quantified. The vast majority of the methylated genome is stably inherited to offspring and the identified unstable regions do not change frequently between generations. Additionally, an epigenetic cross of two MA lines was created to understand inheritance patterns of epialleles via outcrossing in the absence of genetic variation. Whole-genome bisulfite sequencing was used to predict epigenotype of the offspring without single nucleotide polymorphisms. In regions of differential methylation between the parents, about half of regions show predictable inheritance.

2017-07-24 | GSE94298 | GEO

Bisulfite-seq of the Solanum lycopersicum sulfurea paramutation in the cmt3 mutant background and upon reintroduction of WT CMT3

Project description:Whole genome bisulfite sequencing was done in F3 plants resulting from a cross between Solanum lycopersicum plants bearing the sulfurea epiallele and cmt3 mutants. 6 F3 plants were sequenced: 3 WT and 3 cmt3. The F3 WT plants had methylation levels (quantified with McrBC-qPCR) consistent with the TAB2sulf epiallele and the cmt3 plants had methylation levels consistent with TAB2+ (low DNA methylation). cmt3 mutants from the F2 generation were backcrossed with WT cv M82 plants to restore CMT3 activity and followed for 2 generations (BC2). 4 BC2 plants were sequenced 2 WT and 2 cmt3. The aim of the experiment was to compare DNA methylation levels in all contexts between cmt3 and WT F3 plants with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background. The stability of DNA methylation upon CMT3 reintroduction was assessed in the BC2 plants. WT cv M82, cmt3 and sulfurea controls were added in single replicates.

2021-06-24 | E-MTAB-10568 | biostudies-arrayexpress

AGO104 is an RdDM effector of paramutation at the maize b1 locus

Project description:Paramutation is an exception among eukaryotes, in which epigenetic information is conserved through mitosis and meiosis. It has been studied for over 70 years in maize, but the mechanisms involved are largely unknown. All previously described actors of paramutation encoding components of the RNA-dependent DNA-methylation pathway (RdDM) are involved in the biogenesis of 24nt small RNAs. However, no actors of paramutation have been identified in the effector complex of RdDM. Through a combination of reverse genetics, immunolocalization and immunoprecipitation (siRNA-IP) we found that ARGONAUTE104 (AGO104), AGO105 and AGO119 are members of the RdDM effector complex in maize and bind siRNAs produced from the tandem repeats required for paramutation at the b1 locus. We also showed that AGO104 is an effector of the b1 paramutation in maize.

2021-04-22 | GSE172479 | GEO

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