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Paramutation of natural epialleles in tomato

ABSTRACT: Paramutation of natural epialleles in tomato

PROVIDER: PRJNA381070 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5388830_1.fastq.gz	Fastqsanger.gz
	SRR5388830_2.fastq.gz	Fastqsanger.gz
	SRR5388831_1.fastq.gz	Fastqsanger.gz
	SRR5388831_2.fastq.gz	Fastqsanger.gz
	SRR5388832_1.fastq.gz	Fastqsanger.gz

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Paramutation of natural epialleles in tomato [sRNA]

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

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Paramutation of natural epialleles in tomato [sRNA]

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 | GSE97206 | GEO

Paramutation of natural epialleles in tomato [BiSulfite-seq]

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

| PRJNA380948 | ENA

Paramutation of natural epialleles in tomato [BiSulfite-seq]

2017-08-18 | GSE97192 | GEO

Paramutation of natural epialleles in tomato

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

2017-08-18 | GSE97247 | GEO

Paramutation-like features of multiple natural epialleles in tomato.

Project description:BACKGROUNDFreakish and rare or the tip of the iceberg? Both phrases have been used to refer to paramutation, an epigenetic drive that contravenes Mendel's first law of segregation. Although its underlying mechanisms are beginning to unravel, its understanding relies only on a few examples that may involve transgenes or artificially generated epialleles.RESULTSBy using DNA methylation of introgression lines as an indication of past paramutation, we reveal that the paramutation-like properties of the H06 locus in hybrids of Solanum lycopersicum and a range of tomato relatives and cultivars depend on the timing of sRNA production and conform to an RNA-directed mechanism. In addition, by scanning the methylomes of tomato introgression lines for shared regions of differential methylation that are absent in the S. lycopersicum parent, we identify thousands of candidate regions for paramutation-like behaviour. The methylation patterns for a subset of these regions segregate with non Mendelian ratios, consistent with secondary paramutation-like interactions to variable extents depending on the locus.CONCLUSIONTogether these results demonstrate that paramutation-like epigenetic interactions are common for natural epialleles in tomato, but vary in timing and penetrance.

| S-EPMC5859443 | biostudies-literature

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

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

A pioneer protein encoded by required to maintain repression2 facilitates locus-specific paramutation in Zea mays

Project description:This research identifies a novel protein required for paramutation at the maize purple plant1 locus. This 'required to maintain repression2' (RMR2) protein represents the founding member of a plant-specific clade of hypothetical proteins. We show that RMR2 is required for transcriptional repression at the Pl1-Rhoades haplotype, for accumulation of 24 nt RNA species, and for maintenance of a 5-methylcytosine pattern distinct from that maintained by RNA polymerase IV. Genetic tests indicate that RMR2 is not required for paramutation occurring at the red1 locus. These results distinguish the paramutation-type mechanisms operating at specific haplotypes. The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants.

2012-04-16 | GSE37204 | GEO

Locus-specific paramutation in Zea mays is maintained by a chromodomain helicase DNA-binding 3 protein controlling development and male gametophyte function

Project description:Paramutations represent directed and meiotically-heritable changes in gene regulation leading to apparent violations of Mendelian inheritance. Although the mechanism and evolutionary importance of paramutation behaviors remain largely unknown, genetic screens in maize (Zea mays) identify five components affecting 24 nucleotide RNA biogenesis as required to maintain repression of a paramutant purple plant1 (pl1) allele. Currently, the RNA polymerase IV largest subunit represents the only component also specifying proper development. Here we identify a chromodomain helicase DNA-binding 3 (CHD3) protein orthologous to Arabidopsis (Arabidopsis thaliana) PICKLE as a second component maintaining both pl1 paramutation, and normal somatic development. In addition, genetic tests show this protein contributes to proper male gametophyte function. The similar mutant phenotypes documented in Arabidopsis and maize implicate some evolutionarily-conserved gene regulation while developmental defects associated with the two paramutation mutants are largely distinct. Our results show that a CHD3 protein responsible for normal plant ontogeny and sperm transmission also maintains meiotically-heritable epigenetic regulatory variation for specific alleles. This finding implicates an intersection of RNA polymerase IV function and nucleosome positioning in the paramutation process.

2020-11-24 | GSE158990 | GEO

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