Table 1. PCR and pyrosequencing primers and assays for DNMT genes.

GeneA	Assay CpG sitesB	Primers	SequenceC
DNMT3b	6: 10203733	Forward	5′-GAGGGTTTTTTGGTTGGTTAAGT-3′
	10203737	Reverse	5′-GGGACACCGCTGATCGTTTA CCTCCAACAACAAAACAACAATAT-3′
	10203747	Sequencing	5′-GTTATGAAAAAGGAGAAGAG-3′
	10203775	Assay sequence	5′-TTAYGGTYGG GATGAGGYGG ATTGTAGGGT AGAGTTGATTTTTTT YGAYG
	10203778		GGGATTGTAT YGATTTTATT-3′
	10203790
DNMT3a	8: 107432308	Forward	5′-GGTTYGTCGTYGGTTGATTTG-3′
	107432311	Reverse	5′-GGGACACCGCTGATCGTTTAAACCCCCCTACCTCACAACAAC-3′
	107432314	Sequencing	5′-TTGATTTGGATGTGTTTT-3′
	107432317	Assay sequence	5′-GTYGAYGGYGTYGGTTATTATAGGTTTAGGYGTGGTGGTTAYGTTGGGYGA
	107432336		GGTAGGGT YGGTGGGTTG -3′
	107432347
	107432354
	107432365
DNMT1	4: 49757939	Forward	5′-TGGGAAGAGGAAGGGGATAT-3′
	49757957	Reverse	5′-GGGACACCGCTGATCGTTTA TCCCCAATAAAATCTCCTACCA-3′
	49757946	Sequencing	5′-GGAAGAGGAAGGGGATA-3′
	49757980	Assay sequence	5′-TYGATTTTTTGGAAAATAYGTTTAGGATGGTGGGTTGTYG GTYGGAGTTG-3′
		Universal	5′-/Biotin labeled/GGGACACCGCTGATCGTTTA-3′

^A: Gene name. ^B: DNMT3b, based on the UCSC DNA sequence (May 2006, Chr20) that BLAT from DNMT3b cDNA sequence (NCBI: NM_001024828), it is in the exon1 region of DNMT3b. DNMT3a, based on the UCSC DNA sequence (May 2006, Chr3) that BLAT from DNMT3a cDNA sequence (NCBI: NM_001024832), it is in the exon1 region of DNMT3a. DNMT1, based on the UCSC DNA sequence (May 2006, Chr-Un-random) that BLAT from predicted DNMT1 DNA sequence (NCBI: NM_001475597). ^C: Y and R stand for C/T and G/A, respectively. Bold Y is the CpG sites assayed in each gene.