A fragment of the promoter region of the gene encoding human catecholamine O-methyltransferase (COMT) was amplified as follows. 10× PCR Buffer, 2 mM MgCl2, 2.5 mM dNTP, 1 M Betaine, 0.4 mM primers and 1 U of Taq polymerase (New England Biolabs), primers: comtF1 5′-agaccacaggtgcagtcagcacag-3′ and comtR1 5′-caccctatcccagtgttccacccta-3′ at 95°C for 5 min, 30 cycles (94°C for 1 min, 61°C for 1.5 min and 72°C for 1 min), and 72°C for 5 min. CCGG and GCGC sites of the amplicon were subsequently methylated using M-HpaII and M-HhaI, respectively, in two separate fractions. The third fraction of the amplicon was left unmethylated. Both methylated and unmethylated DNA samples were then subjected to bisulfite modification (21 (link)). Briefly, DNA was boiled for 5 min, cooled on ice and denatured for 15 min at 50°C after adding 4 μl of fresh 2 M NaOH in a total reaction volume of 25 μl. Two volumes of 2% LMP agarose in distilled water was added and 10 μl aliquots of this solution was pipetted into cold mineral oil and placed immediately back into dry ice to create beads. The mineral oil was removed and a solution of 1.9 g sodium metabisulfite in 2.5 ml H2O, 720 μl of 2 M NaOH and 500 μl of 1 mM hydroquinone was added. Samples were incubated on ice for 30 min followed by incubation at 50°C for 3.5 h. The agarose beads were washed four times for 15 min with 1 ml TE, two times for 15 min with 0.2 M NaOH, three times for 10 min with 1 ml TE and two times for 15 min with H2O. This was followed by semi-nested PCR using identical reaction and cycling conditions as above with semi-nested primers: BisF1, 5′-gaagggggttatttgtggttagaa-3′, BisF2 5′-gatttttgagtaagattagattaag-3′ and BisR1 5′-aacaaccctaactaccccaa-3′. C (metC in the amplicon) containing templates were mixed with the T (unmethylated C in the amplicon) containing fraction to create a standard curve from 100 to 0% of C signal in increments of 5%: (100% C: 0% T), (95% C: 5% T), (90% C: 10% T), …, (0% C: 100% T). This was done for those templates containing C at M-HpaII sites and M-HhaI sites separately. The M-HpaII sites were interrogated with three forward primers, while three primers for the M-HhaI sites were added as negative controls. In a similar way, M-HhaI sites were interrogated with all six forward primers (three of which were for the M-HpaII sites as negative controls) in one run and the three reverse primers in a second run ( 5′-agtaagattagattaagaggt-3′, 5′-[gact]1gatatttttatgaggatattt-3′ and 5′-[gact]6ttatggtttgtgtttgttat-3′ for the HpaII sites; 5′-[gact]4ggatattttggttattgttg-3′, 5′-[gact]6ttttgattttattttatttgttg-3′ and 5′-[gact]7agtgtttttttaatttttgtag-3′ for the HhaI sites (direct primers); 5′-ccacaataaatatccac-3′, 5′-[gact]2tataacaaacaaaatacaaaac-3′ and 5′-[gact]3acactacaaaaattaaaaaaac-3′ for the remaining three HhaI sites (reverse primers).
In order to investigate the effects of quantitative G/A and C/T polymorphisms in the SNaPshot primer binding region, sets of oligonucleotides containing variable C/T and G/A were synthesized. Five polymorphic positions were investigated: −2, −5, −10, −15 and −18 (A−2/G−2, A−5/G−5, T−10/C−10, A−15/G−15 and T−18/C−18) upstream of the nucleotide that was interrogated (‘target’ nucleotide, Ntarget) (
To verify that degenerative SNaPshot primers are able to interrogate numerous polymorphic C/T and A/G containing DNA sequence targets, two types of DNA templates were used: Six oligonucleotide templates were synthesized with quantitative G/A polymorphisms in different positions of the SNaPshot primer annealing region ( Two human genomic DNA samples from brain and placenta were bisulfite modified and subjected to both SNaPshot interrogation and to cloning plus sequencing-based measurement of metC density. The two selected CpG island regions were identified as exhibiting DNA methylation differences according to our microarray-based DNA methylation profiling (A. Schumacher, A. Petronis, et al., unpublished data). These regions are located between 28 and 276 bp upstream of known genes coding for LGALS1 (lectin, galactoside-binding, soluble, 1), otherwise referred to as galectin 1 and humanin, respectively. Three CpG positions were selected for each CpG island and will be referred to as gal1, gal2 and gal3 for galectin 1 and hum1, hum2 and hum3 for humanin (