Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3.
DNA methylation has been implicated in a variety of epigenetic processes, and abnormal methylation patterns have been seen in tumors. Analysis of methylation patterns has traditionally been conducted either by using Southern analysis after cleavage with methyl-sensitive restriction endonucleases or by bisulfite sequencing. However, neither method is practical for analyzing more than a few genes. Here, we describe a simple technique for genome-wide mapping of DNA methylation patterns. Fragmentation by a methyl-sensitive restriction endonuclease is followed by size fractionation and hybridization to microarrays. We demonstrate the utility of this method by characterizing methylation patterns in Arabidopsis methylation mutants. This analysis reveals that CHROMOMETHYLASE3 (CMT3), which was previously shown to maintain CpXpG methylation, preferentially methylates transposons, even when they are present as single copies within the genome. Methylation profiling has potential applications in disease research and diagnostic screening.
Tompa
Rachel
R
Howard Hughes Medical Institute and Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
McCallum
Claire M
CM
Delrow
Jeffrey
J
Henikoff
Jorja G
JG
van Steensel
Bas
B
Henikoff
Steven
S
D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics*; D029681:Arabidopsis Proteins; D002874:Chromosome Mapping / Q000379:methods*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation; D004251:DNA Transposable Elements; D018744:DNA, Plant / Q000378:metabolism*; D015257:DNA-Cytosine Methylases / Q000235:genetics / Q000378:metabolism*; D018745:Genome, Plant; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods
D029681:Arabidopsis Proteins; D004251:DNA Transposable Elements; D018744:DNA, Plant; D015257:DNA-Cytosine Methylases; C499608:MET1 protein, Arabidopsis; C429766:CMT3 protein, Arabidopsis; D004248:DNA (Cytosine-5-)-Methyltransferases