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Hi-C data of Solanum lycopersicum plants bearing the sulfurea epiallele versus plants bearing WT epiallele

ABSTRACT: Hi-C data of Solanum lycopersicum plants bearing the sulfurea epiallele versus plants bearing WT epiallele

PROVIDER: PRJEB45775 | ENA |

REPOSITORIES: ENA

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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

Hi-C data of Solanum lycopersicum plants bearing the sulfurea epiallele versus plants bearing WT epiallele

Project description:The aim of this experiment was to detect possible chromatin organisation differences between sulfurea and WT plants.

2021-06-27 | E-MTAB-10574 | 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

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

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

| PRJEB45854 | ENA

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 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

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

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

| PRJEB45631 | ENA

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

A variably imprinted epiallele impacts seed development

Project description:A variably imprinted epiallele impacts seed development

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Epigenetic memory marks determine epiallele stability at loci targeted by de novo DNA methylation

Project description:The transgenerational stability of DNA methylation changes is important in setting up genomic DNA methylation patterns and in the formation and transmission of epialleles. It is generally assumed that DNA methylation changes at genomic regions targeted by the de novo, RNA-directed DNA methylation (RdDM) pathway are unstable. Here, we show that RdDM targets in Arabidopsis can be classified into two groups based on their transgenerational epiallele stability following restoration of NRPD1 function in nrpd1 mutant plants: remethylable loci and non-remethylable loci. Compared to the remethylable loci, non-remethylable ones contain higher levels of the euchromatic marks H3K4me3 and H3K18ac, which interferes with the recruitment of the RdDM molecular machinery and helps to recruit the DNA demethylase ROS1 to antagonize RdDM, respectively. Using targeted de-methylation by CRISPR/dCas9-TET1, we demonstrate that mCG and mCHG are memory marks required for targeting the RdDM machinery to remethylable loci. Our results show that histone and DNA methylation marks are critical in determining the capacity of RdDM target loci to form stable epialleles, and contribute to understanding the formation and transmission of epialleles.

2020-04-17 | GSE140566 | GEO

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