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Paramutation of natural epialleles in tomato [sRNA]

ABSTRACT: Paramutation of natural epialleles in tomato [sRNA]

PROVIDER: PRJNA381072 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5398270.fastq.gz	Fastqsanger.gz
	SRR5398280.fastq.gz	Fastqsanger.gz
	SRR5398290.fastq.gz	Fastqsanger.gz
	SRR5398300.fastq.gz	Fastqsanger.gz
	SRR5398310.fastq.gz	Fastqsanger.gz

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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

Project description:Paramutation of natural epialleles in tomato

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Paramutation of natural epialleles in tomato [BiSulfite-seq]

2017-08-18 | GSE97192 | GEO

Paramutation of natural epialleles in tomato [BiSulfite-seq]

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

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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

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

Large scale sequencing of PSTVd-RG1 sRNA in tomato plants

Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid- RG1 strain (PSTVd-RG1) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-RG1. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

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Large scale sequencing of PSTVd-I sRNA in tomato plants

Project description:In order to analyze the production of small RNA (sRNA) by Potato spindle tuber viroid-intermediate strain (PSTVd-I) upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the PSTVd-I. After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina MiSeq platform. The primers were trimmed and the 21- to 24-nt long small RNA species were filtered after quality check of the raw data.

2017-09-20 | GSE70096 | 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.

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