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

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

PROVIDER: PRJEB45704 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR6055020_1.fastq.gz	Fastqsanger.gz
	ERR6055020_2.fastq.gz	Fastqsanger.gz
	ERR6055030_1.fastq.gz	Fastqsanger.gz
	ERR6055030_2.fastq.gz	Fastqsanger.gz
	ERR6055040_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

smallRNA-seq of Solanum lycopersicum segregating for the sulfurea epiallele in cmt3 versus WT

Project description:Plants bearing a sulfurea epiallele (TAB2sulf) were crossed with cmt3 mutants in Solanum Lycopersicum. 6 plants of a F2 progeny segregating both for TAB2sulf and cmt3 mutation were sequenced. 4 plants bear the cmt3 mutation and 2 plants have CMT3 WT alleles. the aim of the experiment was to compare sRNA accumulation between cmt3 and WT plants with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background. The WT plants had methylation levels consistent with the TAB2sulf epiallele and the cmt3 plants had methylation levels consistent with TAB2+ (low DNA methylation). cmt3 and sulfurea parental controls are added in single replicates and a WT cv M82 plant is also sequenced as control. More replicates of WT and M82 are sequenced in a related experiment.

2021-06-21 | E-MTAB-10557 | biostudies-arrayexpress

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

smallRNA-seq of Solanum lycopersicum bearing the sulfurea epiallele in nrpe1 versus WT

Project description:Plants bearing a sulfurea epiallele (TAB2sulf) were crossed with nrpe1 (largest polV subunit) mutants in Solanum Lycopersicum. 7 plants of a F3 progeny expected to be 100% TAB2sulf and segregating for the nrpe1 mutation were sequenced. 4 plants bear the nrpe1 mutation and 3 plants have NRPE1 WT alleles. The aim of the experiment was to compare sRNA accumulation between nrpe1 and WT F3 plants with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background. Both WT and nrpe1 F3 plants had methylation levels consistent with the TAB2sulf epiallele. nrpe1 and sulfurea parental controls are added in single replicates and a WT cv M82 plant is also sequenced as control. More replicates of WT and M82 are sequenced in a related experiment.

2021-07-02 | E-MTAB-10565 | biostudies-arrayexpress

smallRNA-seq of Solanum lycopersicum cv M82 WT versus Solanum lycopersicum cv Lukullus bearing the sulfurea epiallele

Project description:3 sRNA-seq bioreps of WT and sulfurea samples. The aim of this experiment was to compare sRNA abundance at between the two genotypes with particular interest on SlTAB2 (Solyc02g005200) which has been previously associated with paramutation in the sulfurea background.

2021-06-21 | E-MTAB-10556 | biostudies-arrayexpress

Paramutation of natural epialleles in tomato [sRNA]

2017-08-18 | GSE97206 | GEO

smallRNA-seq of Solanum lycopersicum segregating for the sulfurea epiallele in cmt3 versus WT

Project description:smallRNA-seq of Solanum lycopersicum segregating for the sulfurea epiallele in cmt3 versus WT

| PRJEB45632 | ENA

Paramutation of natural epialleles in tomato [BiSulfite-seq]

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

| PRJNA380948 | ENA

CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintains the <i>sulfurea</i> paramutation in <i>Solanum lycopersicum</i>.

Project description:SignificanceParamutation involves the transfer of a repressive epigenetic mark between silent and active alleles. It is best known from exceptional non-Mendelian inheritance of conspicuous phenotypes in maize but also in other plants and animals. Recent genomic studies, however, indicate that paramutation may be less exceptional. It may be a consequence of wide-cross hybridization and may contribute to quantitative trait variation or unstable phenotypes in crops. Using the sulfurea (sulf) locus in tomato, we demonstrate that a self-reinforcing feedback loop involving DNA- and histone-methyl transferases CHROMOMETHYLTRANSFERASE3 (CMT3) and KRYPTONITE (KYP) is required for paramutation of sulf and that there is a change in chromatin organization. These findings advance the understanding of non-Mendelian inheritance in plants.

| S-EPMC9060480 | biostudies-literature

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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