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Common alleles of CMT2 and NRPE1 are major determinants of de novo DNA methylation variation in Arabidopsis thaliana

Eriko Sasaki, View ORCID ProfileTaiji Kawakatsu, View ORCID ProfileJoseph Ecker, View ORCID ProfileMagnus Nordborg
doi: https://doi.org/10.1101/819516
Eriko Sasaki
1Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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Taiji Kawakatsu
2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
5Institute of Agrobiological Sciences, National Agriculture and Food Research Organization. Tsukuba, Ibaraki 305-8634, Japan
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Joseph Ecker
2Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
4Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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Magnus Nordborg
1Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria
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  • ORCID record for Magnus Nordborg
  • For correspondence: magnus.nordborg@gmi.oeaw.ac.at
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Abstract

DNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have previously shown that CMT2 and NRPE1 are major determinants of genome-wide patterns of TE CHH-methylation. Here we instead focus on CHH-methylation of individual TEs and TE-families, allowing us to identify the pathways involved in CHH-methylation simply from natural variation and confirm the associations by comparing them with mutant phenotypes. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.

Author Summary DNA methylation is a major component of transposon silencing, and essential for genomic integrity. Recent studies revealed large-scale geographic variation as well as the existence of major trans-acting polymorphisms that partly explained this variation. In this study, we re-analyze previously published data (The 1001 Epigenomes), focusing on de novo DNA methylation patterns of individual TEs and TE families rather than on genome-wide averages (as was done in previous studies). GWAS of the patterns reveals the underlying regulatory networks, and allowed us to comprehensively characterize trans-regulation of de novo DNA methylation and its role in the striking geographic pattern for this phenotype.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 25, 2019.
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Common alleles of CMT2 and NRPE1 are major determinants of de novo DNA methylation variation in Arabidopsis thaliana
Eriko Sasaki, Taiji Kawakatsu, Joseph Ecker, Magnus Nordborg
bioRxiv 819516; doi: https://doi.org/10.1101/819516
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Common alleles of CMT2 and NRPE1 are major determinants of de novo DNA methylation variation in Arabidopsis thaliana
Eriko Sasaki, Taiji Kawakatsu, Joseph Ecker, Magnus Nordborg
bioRxiv 819516; doi: https://doi.org/10.1101/819516

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