DNA methyltransferase 3-like affects promoter methylation of thymine DNA glycosylase independently of DNMT1 and DNMT3B in cancer cells.
DNA methyltransferase (DNMT) 1 and 3 are primarily responsible for abnormal methylation in cancer. Unlike these DNMTs, DNA methyltransferase 3-like (DNMT3L) harbors no conserved catalytic domain, and has been shown to function as a regulatory cofactor for DNA methylation. However, it is unclear whether DNMT3L directly regulates DNA methylation in cancer cells. To address this, we investigated the methylation targets of DNMT3L by conducting methylation microarray trials after the siRNA-induced knockdown. We determined that methylation of 242 out of 1,505 CpG sites was significantly altered by DNMT3L knockdown. Among these 242 CpG sites, 204, 12, and 11 CpG sites were identified as common targets of DNMT 1/3B/3L, 1/3L, and 3B/3L, respectively; this indicates that DNMT3L participates in DNA methylation via cooperation with other DNMTs. However, we also determined that the methylation of 15 CpG sites was significantly altered by DNMT3L knockdown only. As a validation, we confirmed that thymine DNA glycosylase (TDG), an enzyme involved in the base excision repair of mismatched-DNA, was up-regulated in DNMT3L knockdown cells, but neither in DNMT1 nor 3B knockdown cells. Methylation-specific PCR (MSP) also showed that promoter methylation of TDG was decreased in DNMT3L knockdown cells. Interestingly, 5-aza-2'-deoxycitidine (5-aza-dC) re-expressed DNMT3L, leading to down-regulation of TDG. This study is the first to show that DNMT3L exerts a major effect on the transcriptional regulation of a specific target gene, such as TDG, despite the absence of enzymatic activity.
Kim
Heesun
H
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
Park
Jinah
J
Jung
Yeonjoo
Y
Song
Sang-Hyun
SH
Han
Sae-Won
SW
Oh
Do-Youn
DY
Im
Seock-Ah
SA
Bang
Yung-Jue
YJ
Kim
Tae-You
TY
D045744:Cell Line, Tumor; D018899:CpG Islands / Q000235:genetics; D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D055785:Gene Knockdown Techniques; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000032:analysis; D034741:RNA, Small Interfering; D020133:Reverse Transcriptase Polymerase Chain Reaction; D044502:Thymine DNA Glycosylase / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D000097584:DNA Methyltransferase 3B
D000076123:DNA (Cytosine-5-)-Methyltransferase 1; D004248:DNA (Cytosine-5-)-Methyltransferases; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D044502:Thymine DNA Glycosylase; D000097584:DNA Methyltransferase 3B; C412484:DNMT3L protein, human; C000619380:DNMT1 protein, human