Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis
- Gregor Mendel Institute, Austria
- Gregor Mendel Institute; LMU Biocenter, Austria
- Gregor Mendel Institute; LMU Biocenter, Germany
- Gregor Mendel Institute; Wageningen University, Austria
Abstract
DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Our results are also consistent with CMT3-induced ectopic methylation of promoters or bodies of genes undergoing transcriptional activation reducing their expression. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.
Data availability
All sequencing data generated in this study are publicly available at the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO, https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE171198.
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Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in ArabidopsisNCBI Gene Expression Omnibus, GSE171198.
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The embryonic transcriptome of Arabidopsis thalianaNCBI Gene Expression Omnibus, GSE121236.
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Active DNA demethylation in plant companion cells reinforces transposon methylation in gametesNCBI Gene Expression Omnibus, GSE38935.
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Natural epigenetic polymorphisms lead to intraspecific variation in Arabidopsis gene imprintingNCBI Gene Expression Omnibus, GSE52814.
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Genome-wide demethylation of Arabidopsis endospermNCBI Gene Expression Omnibus, GSE15922.
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DNA methylation dynamics during early plant lifeNCBI Gene Expression Omnibus, GSE85975.
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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylomeNCBI Gene Expression Omnibus, GSE39901.
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The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in ArabidopsisNCBI Gene Expression Omnibus, GSE50942.
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Non-CG methylation patterns shape the epigenetic landscape in ArabidopsisNCBI Gene Expression Omnibus, GSE51304.
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Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in ArabidopsisNCBI Gene Expression Omnibus, GSE98214.
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DNA methylation and histone H1 jointly repress transposable elements and aberrant intragenic transcriptsNCBI Gene Expression Omnibus, GSE122394.
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MNase analysis of linker histone H1 mutantNCBI Gene Expression Omnibus, GSE113556.
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DNA methylation-linked chromatin accessibility affects genomic architecture in ArabidopsisNCBI Gene Expression Omnibus, GSE155503.
Article and author information
Author details
Funding
H2020 European Research Council (637888)
- Michael D Nodine
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Richard Amasino, University of Wisconsin Madison, United States
Publication history
- Received: April 13, 2021
- Accepted: July 21, 2021
- Accepted Manuscript published: July 23, 2021 (version 1)
- Accepted Manuscript updated: July 26, 2021 (version 2)
- Version of Record published: August 9, 2021 (version 3)
Copyright
© 2021, Papareddy et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis
eLife 10:e69396.
https://doi.org/10.7554/eLife.69396
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Genetic variation at the MTIF3 (Mitochondrial Translational Initiation Factor 3) locus has been robustly associated with obesity in humans, but the functional basis behind this association is not known. Here, we applied luciferase reporter assay to map potential functional variants in the haplotype block tagged by rs1885988 and used CRISPR-Cas9 to edit the potential functional variants to confirm the regulatory effects on MTIF3 expression. We further conducted functional studies on MTIF3-deficient differentiated human white adipocyte cell line (hWAs-iCas9), generated through inducible expression of CRISPR-Cas9 combined with delivery of synthetic MTIF3-targeting guide RNA. We demonstrate that rs67785913-centered DNA fragment (in LD with rs1885988, r2 > 0.8) enhances transcription in a luciferase reporter assay, and CRISPR-Cas9-edited rs67785913 CTCT cells show significantly higher MTIF3 expression than rs67785913 CT cells. Perturbed MTIF3 expression led to reduced mitochondrial respiration and endogenous fatty acid oxidation, as well as altered expression of mitochondrial DNA-encoded genes and proteins, and disturbed mitochondrial OXPHOS complex assembly. Furthermore, after glucose restriction, the MTIF3 knockout cells retained more triglycerides than control cells. This study demonstrates an adipocyte function-specific role of MTIF3, which originates in the maintenance of mitochondrial function, providing potential explanations for why MTIF3 genetic variation at rs67785913 is associated with body corpulence and response to weight loss interventions.
