Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer.
OBJECTIVE
To isolate and analyze the DNA sequences which are methylated differentially between gastric cancer and normal gastric mucosa.


METHODS
The differentially methylated DNA sequences between gastric cancer and normal gastric mucosa were isolated by methylation-sensitive representational difference analysis (MS-RDA). Similarities between the separated fragments and the human genomic DNA were analyzed with Basic Local Alignment Search Tool (BLAST).


RESULTS
Three differentially methylated DNA sequences were obtained, two of which have been accepted by GenBank. The accession numbers are AY887106 and AY887107. AY887107 was highly similar to the 11th exon of LOC440683 (98%), 3' end of LOC440887 (99%), and promoter and exon regions of DRD5 (94%). AY887106 was consistent (98%) with a CpG island in ribosomal RNA isolated from colorectal cancer by Minoru Toyota in 1999.


CONCLUSIONS
The methylation degree is different between gastric cancer and normal gastric mucosa. The differentially methylated DNA sequences can be isolated effectively by MS-RDA.
Liao
Ai-Jun
AJ
Cancer Research Institute, Nanhua University, The First Affiliated Hospital, Hengyang 421001, Hunan Province, China.
Su
Qi
Q
Wang
Xun
X
Zeng
Bin
B
Shi
Wei
W
D000230:Adenocarcinoma / Q000378:metabolism*; D001483:Base Sequence; D018899:CpG Islands / Q000235:genetics; D053938:DNA Fragmentation; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D005091:Exons / Q000235:genetics; D005753:Gastric Mucosa / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D013274:Stomach Neoplasms / Q000378:metabolism*
D004273:DNA, Neoplasm