Epigenetic natural variation in Arabidopsis thaliana.
Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA using tiling microarrays of Arabidopsis Chromosome 4 in two distinct ecotypes, Columbia and Landsberg erecta. We also used comparative genome hybridization to profile copy number polymorphisms. Repeated sequences and transposable elements (TEs), especially long terminal repeat retrotransposons, are densely methylated, but one third of genes also have low but detectable methylation in their transcribed regions. While TEs are almost always methylated, genic methylation is highly polymorphic, with half of all methylated genes being methylated in only one of the two ecotypes. A survey of loci in 96 Arabidopsis accessions revealed a similar degree of methylation polymorphism. Within-gene methylation is heritable, but is lost at a high frequency in segregating F(2) families. Promoter methylation is rare, and gene expression is not generally affected by differences in DNA methylation. Small interfering RNA are preferentially associated with methylated TEs, but not with methylated genes, indicating that most genic methylation is not guided by small interfering RNA. This may account for the instability of gene methylation, if occasional failure of maintenance methylation cannot be restored by other means.
Vaughn
Matthew W
MW
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.
Tanurdzić
Milos
M
Lippman
Zachary
Z
Jiang
Hongmei
H
Carrasquillo
Robert
R
Rabinowicz
Pablo D
PD
Dedhia
Neilay
N
McCombie
W Richard
WR
Agier
Nicolas
N
Bulski
Agnès
A
Colot
Vincent
V
Doerge
R W
RW
Martienssen
Robert A
RA
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D032461:Chromosomes, Plant / Q000235:genetics; D055028:Comparative Genomic Hybridization; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic; D017343:Genes, Plant; D014644:Genetic Variation; D020411:Oligonucleotide Array Sequence Analysis; D011110:Polymorphism, Genetic; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics
D004251:DNA Transposable Elements; D018744:DNA, Plant; D018749:RNA, Plant; D034741:RNA, Small Interfering