Mobile small RNAs and their role in regulating cytosine methylation of DNA

Hardcastle, Thomas J.; Lewsey, Mathew G.

doi:10.1080/15476286.2016.1218591

Cited by 10 publications

(8 citation statements)

References 64 publications

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“…The transmission of epigenetic marks from one generation to another through the gametes has been clearly reported so far in model organisms. However in humans, we can find clear genetic aberrations that involve repeats (CGG) and transposable elements [52,56,57] and those seem to rely on DNA methylation and RNAs [58]. An involvement of these players in human diseases and cancer has been recently proposed [52,53,57].…”

Section: Resultsmentioning

confidence: 99%

A new paramutation-like example at the Delta gene of Drosophila

Capovilla¹,

Robichon²,

Rassoulzadegan³

2017

PLoS ONE

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The hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate paramutation in Drosophila, we used the P{ry+t7.2 = PZ}Dl05151 P-element insertion in the Drosophila melanogaster genome that causes a dominant visible phenotype: the presence of characteristic extra-veins in the fly wings. This extra-vein phenotype presents variable expressivity and incomplete penetrance. The insert is a PZ element located 680 bp upstream from the ATG of the Delta (Dl) gene, encoding the Notch ligand involved in wing vein development, and acts as a null allele. In the G2 offspring from a cross between the heterozygous transgenic stock and wild-type flies, we observed the transmission of the extra-vein phenotype to wild-type flies without the transgene, independently of gender and across many generations. This is a “paramutation-like” example in the fly: the heritable transmission of a phenotypic change not linked to a classical genetic mutation. A “paramutagenic” allele in heterozygotes transmits the phenotype of the heterozygotes to the wild-type allele (“paramutant”) in a stable manner through generations. Distinct from paramutation events so far described in Drosophila, here we deal with a dominant effect on a single gene involving variable hereditary signals.

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Section: Resultsmentioning

confidence: 99%

A new paramutation-like example at the Delta gene of Drosophila

Capovilla¹,

Robichon²,

Rassoulzadegan³

2017

PLoS ONE

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“…Genomic loci corresponding to six classes of interaction were identified. The classes of interaction were defined by specific combinations of sRNA and DNA abundance at the individual genomic loci across the graft combinations (Hardcastle & Lewsey, ; Lewsey et al ., ). We discuss the six classes in the following paragraphs.…”

Section: Classes Of Interactions Between Shoot–root Mobile Sirnas Andmentioning

confidence: 99%

“…In the case of indirect loci, no shoot‐derived siRNAs were detected at the sites of DNA methylation, but if the supply of shoot‐derived siRNAs was removed, DNA methylation was lost in root cells. It is possible that this observation is attributable to the change in DNA methylation being dependent on some intermediate signal, to the siRNAs targeting these loci being of low abundance and consequently undetectable, or to nonperfect matching of the siRNAs with the genomic sequence of the loci which confounded bioinformatics analyses (Hardcastle & Lewsey, ). The third class was rare, but has potential biological and biotechnological importance, which we discuss in Section VIII.…”

Section: Classes Of Interactions Between Shoot–root Mobile Sirnas Andmentioning

confidence: 99%

“…Interactions between mobile siRNAs and DNA methylation were either limited, or absent, at loci of the remaining classes (Hardcastle & Lewsey, ; Lewsey et al ., ). In the fourth class, mobile sRNA was detected at genomic loci but was not associated with DNA methylation.…”

Section: Classes Of Interactions Between Shoot–root Mobile Sirnas Andmentioning

confidence: 99%

“…Moreover, the methylation at direct and indirect loci is predominantly in the non‐CG (CHG and CHH) contexts and is dependent upon the DRM1/2 RdDM pathway (Lewsey et al ., ). However, the two classes of loci are associated with different histone modifications (Hardcastle & Lewsey, ). This was discovered by comparing their locations to genome‐wide histone modification maps generated previously (Luo et al ., ).…”

Section: Loci Targeted Directly and Indirectly By Shoot–root Mobile Smentioning

confidence: 99%

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Regulation of genome‐wide DNA methylation by mobile small RNAs

2017

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Contents Summary540I.Introduction540II.There are different types of sRNA mobility541III.Mechanisms of sRNA movement541IV.Long‐distance, shoot–root, mobile siRNAs influence DNA methylation in recipient tissues541V.Classes of interactions between shoot–root mobile siRNAs and DNA methylation542VI.Loci targeted directly and indirectly by shoot–root mobile siRNAs are associated with different histone modifications543VII.Is mobile siRNA‐regulated DNA methylation important in specific tissues or under specific conditions?543VIII.Mobile sRNAs can be used to modify plant traits544IX.Conclusions544Acknowledgements544References544 Summary RNA‐directed DNA methylation (RdDM) at cytosine residues regulates gene expression, silences transposable elements and influences genome stability. The mechanisms responsible for RdDM are guided to target loci by small RNAs (sRNAs) that can move within plants cell to cell and long distance. Here we discuss recent advances in the understanding of interactions between mobile sRNAs and DNA methylation. We describe the mechanisms of sRNA movement, the differences between known classes of mobile sRNA–DNA methylation interactions and the limits of current knowledge. Finally, we discuss potential applications of mobile sRNAs in modifying plant traits.

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Geminiviruses Versus Host’s Gene Silencing Mechanism

Eini

2019

Geminiviruses

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Mobile small RNAs and their role in regulating cytosine methylation of DNA

Cited by 10 publications

References 64 publications

A new paramutation-like example at the Delta gene of Drosophila

A new paramutation-like example at the Delta gene of Drosophila

Regulation of genome‐wide DNA methylation by mobile small RNAs

Geminiviruses Versus Host’s Gene Silencing Mechanism

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