DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis.
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.
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Nataliya E
NE
Yelina
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Christophe
C
Lambing
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Thomas J
TJ
Hardcastle
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Xiaohui
X
Zhao
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Bruno
B
Santos
Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
Ian R
IR
Henderson
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D002503:Centromere / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D003434:Crossing Over, Genetic / Q000235:genetics*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D053903:DNA Breaks, Double-Stranded; D019175:DNA Methylation; D057890:Epigenomics; D059765:Homologous Recombination / Q000235:genetics*; D008540:Meiosis / Q000235:genetics*; D009154:Mutation; D009707:Nucleosomes
D029681:Arabidopsis Proteins; D009707:Nucleosomes; C499608:MET1 protein, Arabidopsis; D004248:DNA (Cytosine-5-)-Methyltransferases
DNA methylation; centromeres; crossover; epigenetics; hot spots; meiosis