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DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis.


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Authors

Yelina, Nataliya E 
Lambing, Christophe 
Hardcastle, Thomas J 
Santos, Bruno 

Abstract

During meiosis, homologous chromosomes undergo crossover recombination, which is typically concentrated in narrow hot spots that are controlled by genetic and epigenetic information. Arabidopsis chromosomes are highly DNA methylated in the repetitive centromeres, which are also crossover-suppressed. Here we demonstrate that RNA-directed DNA methylation is sufficient to locally silence Arabidopsis euchromatic crossover hot spots and is associated with increased nucleosome density and H3K9me2. However, loss of CG DNA methylation maintenance in met1 triggers epigenetic crossover remodeling at the chromosome scale, with pericentromeric decreases and euchromatic increases in recombination. We used recombination mutants that alter interfering and noninterfering crossover repair pathways (fancm and zip4) to demonstrate that remodeling primarily involves redistribution of interfering crossovers. Using whole-genome bisulfite sequencing, we show that crossover remodeling is driven by loss of CG methylation within the centromeric regions. Using cytogenetics, we profiled meiotic DNA double-strand break (DSB) foci in met1 and found them unchanged relative to wild type. We propose that met1 chromosome structure is altered, causing centromere-proximal DSBs to be inhibited from maturation into interfering crossovers. These data demonstrate that DNA methylation is sufficient to silence crossover hot spots and plays a key role in establishing domains of meiotic recombination along chromosomes.

Description

Keywords

DNA methylation, centromeres, crossover, epigenetics, hot spots, meiosis, Arabidopsis, Arabidopsis Proteins, Centromere, Chromosomes, Plant, Crossing Over, Genetic, DNA (Cytosine-5-)-Methyltransferases, DNA Breaks, Double-Stranded, DNA Methylation, Epigenomics, Homologous Recombination, Meiosis, Mutation, Nucleosomes

Journal Title

Genes Dev

Conference Name

Journal ISSN

0890-9369
1549-5477

Volume Title

29

Publisher

Cold Spring Harbor Laboratory
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/M004937/1)
Biotechnology and Biological Sciences Research Council (BB/L006847/1)
Biotechnology and Biological Sciences Research Council (BB/K007882/1)
We thank Korbinian Schneeberger and Beth Rowan for advice implementing TIGER and Ler polymorphism data, Donna Bond for pJawohl-Act2, Quentin Gouil for the bisulfite sequencing protocol, Simon Andrews and Felix Krueger for advice using SeqMonk, Gregory Copenhaver and Avi Levy for fluorescent lines, Raphael Mercier for zip4-2 fancm-1, Chris Franklin for the ASY1 antibody, and the Gurdon Institute Imaging Facility for access to microscopes. Research was supported by a Broodbank Fellowship (to N.E.Y.), a Royal Society University Research Fellowship (to I.R.H.), grant GAT2962 from the Gatsby Charitable Foundation (to I.R.H.), and Biotechnology and Biological Sciences Research Council grant BB/L006847/1 (to I.R.H.).