Abstract
DNA methylation in plants targets cytosines in three sequence contexts, CG, CHG and CHH (H representing A, C or T). Each of these patterns has traditionally been associated with distinct DNA methylation pathways with CHH methylation being controlled by the RNA dependent DNA methylation (RdDM) pathway employing small RNAs as a guide for the de novo DOMAINS REARRANGED METHYLTRANSFERASE (DRM2), and maintenance DNA METHYLTRANSFERASE1 (MET1) being responsible for faithful propagation of CG methylation. Here we report an unusual 'dense methylation' pattern under the control of MET1, with methylation in all three sequence contexts. We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242) in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1. This suggests that, in addition to its classical CG maintenance function, at certain loci MET1 plays a role in creating transcriptional diversity based on the generation of independent epi-alleles. Database inspection identified several other loci with MET1-dependent dense methylation patterns. Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region. In Arabidopsis, dense methylation appears to be an exception as it is only found at a small number of loci. Its presence does, however, highlight the potential for MET1 as a contributor to epigenetic diversity, and it will be interesting to investigate the representation of dense methylation in other plant species.
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Claims 7
Claim · model-written summary
Under MET1 control, Arabidopsis thaliana shows an unusual dense methylation pattern with methylation in all three sequence contexts.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianat0 - Gene
- MET1e0
- Outcome
- methylation in all three sequence contextse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Transmission of Epi-Alleles with MET1-Dependent Dense Methylation in Arabidopsis thaliana”
e0“Here we report an unusual 'dense methylation' pattern under the control of MET1, with methylation in all three sequence contexts”
Claim · model-written summary
Epi-alleles of dense methylation at non-coding RNA locus At4g15242 differ in dense methylation and expression characteristics among Arabidopsis ecotypes.
- Taxon
- ArabidopsisArabidopsise1
- Material
- Arabidopsis ecotypese1
- Gene
- At4g15242e1
- Outcome
- distinct dense methylation and expression characteristicse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242) in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1”
Claim · model-written summary
The At4g15242 epi-alleles are stably maintained and transmitted in genetic crosses.
- Taxon
- ArabidopsisArabidopsise1
- Gene
- At4g15242e1
- Outcome
- stably maintained and transmitted in genetic crossese1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242) in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1”
Claim · model-written summary
Depletion of MET1 can heritably alter the dense methylation of the At4g15242 epi-alleles in Arabidopsis.
- Taxon
- ArabidopsisArabidopsise1
- Treatment
- depletion of MET1e1
- Gene
- MET1e1
- Outcome
- epi-alleles of dense methylatione1
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e1“We identified epi-alleles of dense methylation at a non coding RNA locus (At4g15242) in Arabidopsis ecotypes, with distinct dense methylation and expression characteristics, which are stably maintained and transmitted in genetic crosses and which can be heritably altered by depletion of MET1”
Claim · model-written summary
In Arabidopsis ecotypes, expression of epi-alleles at these loci decreases as methylation density increases, mainly within the transcribed region.
- Taxon
- ArabidopsisArabidopsise3
- Material
- Arabidopsis ecotypese3
- Outcome
- expression patternse3
- Direction
- decreaseinferrede3
- Qualifier
- with methylation densitye3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e3“Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region”
Claim · model-written summary
Database inspection identified several other loci with MET1-dependent dense methylation patterns in Arabidopsis.
- Taxon
- ArabidopsisArabidopsise3
- Gene
- MET1e2
- Outcome
- loci with MET1-dependent dense methylation patternse2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e2“Database inspection identified several other loci with MET1-dependent dense methylation patterns”
e3“Arabidopsis ecotypes contain distinct epi-alleles of these loci with expression patterns that inversely correlate with methylation density, predominantly within the transcribed region”
Claim · model-written summary
Dense methylation appears to be an exception in Arabidopsis, being found only at a small number of loci.
- Taxon
- ArabidopsisArabidopsise4
- Outcome
- only found at a small number of locie4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e4“In Arabidopsis, dense methylation appears to be an exception as it is only found at a small number of loci”