Comprehensive high-throughput arrays for relative methylation (CHARM)

Abstract

DNA methylation (DNAm) is a term used to describe the heritable covalent addition of a methyl group to cytosines at CpG dinucleotides in mammals. While methods for examining DNAm status at specific loci have existed for several years, recent technological advances have begun to enable the examination of DNAm across the genome. In this unit, we describe comprehensive high-throughput arrays for relative methylation (CHARM), a highly sensitive and specific approach to measure DNA methylation across the genome. This method makes no assumptions about where functionally important DNAm occurs, i.e., CpG island or promoter regions, and includes lower-CpG-density regions of the genome. In addition, it uses a novel genome-weighted smoothing algorithm to correct for CpG density and fragment biases present in methyl-enrichment or methyl-depletion DNA-fractionation methods. It can be applied to studying epigenomic changes in DNAm for normal and diseased samples.

Figure 20.1.1

Overview of McrBC-based fractionation (Lippman et al., 2005; Ordway et al., 2006) coupled with CHARM analysis (Irizarry et al., 2008). Genomic DNA is sheared to 1.5 to 3.0 kb and divided into two equal parts. The first is digested with McrBC, a methyl-cytosine insensitive enzyme that recognizes Pu^mC(N_40–3000)^mCPu, and the second is untreated. Both fractions are then resolved side by side on a 1% agarose gel, and fragments between 1.65 kb and 3.0 kb are excised and purified. Next, the untreated fraction, representing total input DNA, is labeled with cyanine-3 (Cy3) and the McrBC-treated fraction, representing unmethylated DNA, is labeled with cyanine-5 (Cy5) followed by cohybridization to a CHARM microarray. Sequences that are methylated will be present in the input fraction (Cy3) and depleted in the methyl-depleted fraction (Cy5). For each probe on the array, a log ratio of the Cy3 to Cy5 intensity is calculated and represents the methylation level (M-value) at each locus, with larger M-values representing more methylation and smaller M-values representing less methylation.

Figure 20.1.2

Tab-delimited sample description file (example).

Figure 20.1.3

Table listing DMRs (example of output generated using commands in step 9).

Figure 20.1.4

The expected size distribution, from 1.5 kb to 3.0 kb, of genomic DNA after shearing with a HydroShear device. We ran 500 ng of DNA on a 1% agarose gel in 1× TAE buffer for 60 min at 110 volts. Lane 1 contains a 1 Kb Plus DNA Ladder with the upper and lower arrows denoting 3.0 kb and 1.65 kb, respectively. Lane 2 contains unsheared, high-quality, high-molecular-weight genomic DNA as a reference. Lane 3 contains genomic DNA that was sheared using a standard shearing assembly on a HydroShear device. The two straight horizontal lines denote the expected size distribution of DNA.

Figure 20.1.5

Genomic DNA is size fractionated using a high-molecular-weight agarose gel. Mock (UT) and McrBC (MD) digestions were run side by side for 3.5 hr at 30 V. Lanes 1, 4, 5, 8, 9, 12, 13, and 16 contain a 1 Kb Plus DNA Ladder. Lanes 2 and 3 contain sheared gDNA from sample 1 that was mock digested (UT) and McrBC-treated (MD), respectively. Lanes 6 and 7 contain sheared gDNA from sample 2 that was mock digested (UT) and McrBC-treated (MD), respectively. Lanes 10 and 11 contain sheared gDNA from sample 3 that was mock digested (UT) and McrBC-treated (MD), respectively. Lanes 14 and 15 contain sheared gDNA from sample 4 that was mock digested (UT) and McrBC-treated (MD), respectively. Images on the left represent the agarose gel prior to extracting DNA and the images on the right show the agarose gel image after extracting DNA ranging in size from 1.65 to 3.0 kb. Well 1, 1 Kb Plus DNA Ladder (1 μg); Well 2, Sample 1-UT; Well 3, Sample 1-MD; Well 4, 1 Kb Plus DNA Ladder (1 μg); Well 5, 1 Kb Plus DNA Ladder (1 μg); Well 6, Sample 2-UT; Well 7, Sample 2-MD; Well 8, 1 Kb Plus DNA Ladder (1 μg); Well 9, 1 Kb Plus DNA Ladder (1 μg); Well 10, Sample 3-UT; Well 11, Sample 3-MD; Well 12, 1 Kb Plus DNA Ladder (1 μg); Well 13, 1 Kb Plus DNA Ladder (1 μg); Well 14, Sample 4-UT; Well 15, Sample 4-MD; Well 16, 1 Kb Plus DNA Ladder (1 μg).

Figure 20.1.6

Suggested timeline for CHARM analysis of DNA methylation.