Publication Date:
2013-03-08
Description:
Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798000/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798000/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmitz, Robert J -- Schultz, Matthew D -- Urich, Mark A -- Nery, Joseph R -- Pelizzola, Mattia -- Libiger, Ondrej -- Alix, Andrew -- McCosh, Richard B -- Chen, Huaming -- Schork, Nicholas J -- Ecker, Joseph R -- F32 HG004830/HG/NHGRI NIH HHS/ -- F32HG004830/HG/NHGRI NIH HHS/ -- K99 GM100000/GM/NIGMS NIH HHS/ -- K99GM100000/GM/NIGMS NIH HHS/ -- UL1 RR025774/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23467092" target="_blank"〉PubMed〈/a〉
Keywords:
Arabidopsis/*genetics
;
DNA Methylation/genetics
;
DNA Transposable Elements/genetics
;
Epigenesis, Genetic/*genetics
;
Epigenomics
;
Genetic Variation/*genetics
;
Genome, Plant/*genetics
;
Linkage Disequilibrium/genetics
;
Pollen/genetics
;
Polymorphism, Genetic/genetics
;
Quantitative Trait Loci
;
RNA, Messenger/analysis/genetics
;
RNA, Plant/genetics
;
Seeds/genetics
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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