DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes.

David B Lyons,Daniel Zilberman

doi:10.7554/elife.30674

Abstract

Cytosine methylation regulates essential genome functions across eukaryotes, but the fundamental question of whether nucleosomal or naked DNA is the preferred substrate of plant and animal methyltransferases remains unresolved. Here, we show that genetic inactivation of a single DDM1/Lsh family nucleosome remodeler biases methylation toward inter-nucleosomal linker DNA in Arabidopsis thaliana and mouse. We find that DDM1 enables methylation of DNA bound to the nucleosome, suggesting that nucleosome-free DNA is the preferred substrate of eukaryotic methyltransferases in vivo. Furthermore, we show that simultaneous mutation of DDM1 and linker histone H1 in Arabidopsis reproduces the strong linker-specific methylation patterns of species that diverged from flowering plants and animals over a billion years ago. Our results indicate that in the absence of remodeling, nucleosomes are strong barriers to DNA methyltransferases. Linker-specific methylation can evolve simply by breaking the connection between nucleosome remodeling and DNA methylation.

Highlights

Cytosine methylation provides a mechanism to heritably alter the genome without permanent modification of the DNA sequence (Kim and Zilberman, 2014; Du et al, 2015)
To investigate the relationship between nucleosomes and DNA methylation, we deep sequenced unamplified DNA isolated from micrococcal nuclease (MNase)-digested chromatin of Arabidopsis plants with inactivating mutations in both canonical linker histone H1 genes (h1), ddm1 mutants, compound h1ddm1 mutants, and in WT controls
We focused our initial analysis on heterochromatic sequences, where H1 is most abundant (Rutowicz et al, 2015) and DDM1 is most important for maintenance of DNA methylation (Zemach et al, 2013)

Summary

Introduction

Cytosine methylation provides a mechanism to heritably alter the genome without permanent modification of the DNA sequence (Kim and Zilberman, 2014; Du et al, 2015). Dnmt family methyltransferases, called MET1 in plants, rely on selective recognition of hemi-methylated symmetrical CG dinucleotides by an obligate cofactor (Kim and Zilberman, 2014). This mechanism semiconservatively propagates methylation patterns following cell division, and – especially in plants – across generations. The related CMT2 family can methylate cytosines outside CG and CNG contexts (Zemach et al, 2013; Stroud et al, 2014), a pattern of specificity referred to as CHH. Plants possess an RNA-directed DNA methylation (RdDM) pathway, in which 24 nucleotide RNA molecules guide DRM methyltransferases (homologs of animal Dnmt3) to initiate DNA methylation in all sequence contexts, and to maintain CHH methylation at relatively euchromatic TEs (Matzke and Mosher, 2014)

Methods

Results

Conclusion