TY - JOUR
T1 - Genome-wide profiling of DNA methylation in human cancer cells
AU - Ogoshi, Katsumi
AU - Hashimoto, Shin ichi
AU - Nakatani, Yoichiro
AU - Qu, Wei
AU - Oshima, Kenshiro
AU - Tokunaga, Katsushi
AU - Sugano, Sumio
AU - Hattori, Masahira
AU - Morishita, Shinichi
AU - Matsushima, Kouji
PY - 2011/10
Y1 - 2011/10
N2 - Global changes in DNA methylation correlate with altered gene expression and genomic instability in cancer. We have developed a methylation-specific digital sequencing (MSDS) method that can assess DNA methylation on a genomic scale. MSDS is a simple, low-cost method that combines the use of methylation-sensitive restriction enzymes with second generation sequencing technology. DNA methylation in two colon cancer cell lines, HT29 and HCT116, was measured using MSDS. When methylation levels were compared between the two cell lines, many differentially methylated regions (DMRs) were identified in CpG island shore regions (located within 2 kb of a CpG island), gene body regions and intergenic regions. The number of DMRs in the vicinity of gene transcription start sites correlated with the level of expression of TACC1, CLDN1, and PLEKHC1 (FERMT2) genes, which have been linked to carcinogenesis. The MSDS method has the potential to provide novel insight into the functional complexity of the human genome.
AB - Global changes in DNA methylation correlate with altered gene expression and genomic instability in cancer. We have developed a methylation-specific digital sequencing (MSDS) method that can assess DNA methylation on a genomic scale. MSDS is a simple, low-cost method that combines the use of methylation-sensitive restriction enzymes with second generation sequencing technology. DNA methylation in two colon cancer cell lines, HT29 and HCT116, was measured using MSDS. When methylation levels were compared between the two cell lines, many differentially methylated regions (DMRs) were identified in CpG island shore regions (located within 2 kb of a CpG island), gene body regions and intergenic regions. The number of DMRs in the vicinity of gene transcription start sites correlated with the level of expression of TACC1, CLDN1, and PLEKHC1 (FERMT2) genes, which have been linked to carcinogenesis. The MSDS method has the potential to provide novel insight into the functional complexity of the human genome.
KW - Colon cancer
KW - Differentially methylated regions
KW - DNA methylation
KW - Second generation sequencing technology
UR - http://www.scopus.com/inward/record.url?scp=84860389965&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84860389965&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2011.07.003
DO - 10.1016/j.ygeno.2011.07.003
M3 - Article
C2 - 21821115
AN - SCOPUS:84860389965
SN - 0888-7543
VL - 98
SP - 280
EP - 287
JO - Genomics
JF - Genomics
IS - 4
ER -
