Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes

Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show th...

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Autores principales: Sasaki, Eriko, Gunis, Joanna, Reichardt-Gomez, Ilka, Nizhynska, Viktoria, Nordborg, Magnus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Research Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491579/
https://www.ncbi.nlm.nih.gov/pubmed/36084135
http://dx.doi.org/10.1371/journal.pgen.1010345
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author Sasaki, Eriko
Gunis, Joanna
Reichardt-Gomez, Ilka
Nizhynska, Viktoria
Nordborg, Magnus
author_facet Sasaki, Eriko
Gunis, Joanna
Reichardt-Gomez, Ilka
Nizhynska, Viktoria
Nordborg, Magnus
author_sort Sasaki, Eriko
collection PubMed
description Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture—once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization.
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spelling pubmed-94915792022-09-22 Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes Sasaki, Eriko Gunis, Joanna Reichardt-Gomez, Ilka Nizhynska, Viktoria Nordborg, Magnus PLoS Genet Research Article Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture—once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization. Public Library of Science 2022-09-09 /pmc/articles/PMC9491579/ /pubmed/36084135 http://dx.doi.org/10.1371/journal.pgen.1010345 Text en © 2022 Sasaki et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Sasaki, Eriko
Gunis, Joanna
Reichardt-Gomez, Ilka
Nizhynska, Viktoria
Nordborg, Magnus
Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title_full Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title_fullStr Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title_full_unstemmed Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title_short Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes
title_sort conditional gwas of non-cg transposon methylation in arabidopsis thaliana reveals major polymorphisms in five genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9491579/
https://www.ncbi.nlm.nih.gov/pubmed/36084135
http://dx.doi.org/10.1371/journal.pgen.1010345
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