Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn1,6,
- James P.B. Lloyd1,2,6,
- Ino D. Karemaker3,
- Pascal W.T.C. Jansen3,
- Jahnvi Pflueger1,4,
- Owen Duncan1,
- Jakob Petereit1,
- Ozren Bogdanovic1,
- A. Harvey Millar1,2,
- Michiel Vermeulen3,5 and
- Ryan Lister1,2,4
- 1ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
- 2ARC Centre of Excellence in Plants for Space, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia;
- 3Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525 GA, The Netherlands;
- 4Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia;
- 5Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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↵6 These authors contributed equally to this work.
Abstract
In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (gbM). gbM is correlated with ubiquitously expressed genes; however, its function, or absence thereof, is highly debated. The different outputs that mC can have raise questions as to how it is interpreted—or read—differently in these sequence and genomic contexts. To screen for potential mC-binding proteins, we performed an unbiased DNA affinity pull-down assay combined with quantitative mass spectrometry using methylated DNA probes for each DNA sequence context. All mC readers known to date preferentially bind to the methylated probes, along with a range of new mC-binding protein candidates. Functional characterization of these mC readers, focused on the MBD and SUVH families, was undertaken by ChIP-seq mapping of genome-wide binding sites, their protein interactors, and the impact of high-order mutations on transcriptomic and epigenomic profiles. Together, these results highlight specific context preferences for these proteins, and in particular the ability of MBD2 to bind predominantly to gbM. This comprehensive analysis of Arabidopsis mC readers emphasizes the complexity and interconnectivity between DNA methylation and chromatin remodeling processes in plants.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279379.124.
- Received March 19, 2024.
- Accepted October 17, 2024.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
