title: Identification of potential genes regulated by DNA methyltransferase 3B in a hepatocellular carcinoma cell line by RNA interference and microarray analysis.
abstract: Whether DNA methyltransferase 3B (DNMT3B) is deregulated in hepatocellular carcinoma cell lines is still unclear. The expression levels of DNMT3B protein in normal liver cell line, pericacinoma cell line and hepatocellular carcinoma cell lines were compared by both Western blotting and immunocytochemistry. Long-term downregulated DNMT3B in a hepatocellular carcinoma cell line SMMC-7721 was achieved using a RNAi recombinant plasmid. The suppression of DNMT3B induced by RNA interference was confirmed using semi-quantitative RT-PCR and Western blotting. High throughput cDNA microarray was used to analyze the expression profiling of downstream genes of DNMT3B displayed in the treated cell lines and control. In the result,DNMT3B in hepatocellular carcinoma cell lines was expressed at a significantly higher level compared to those in pericacinoma cell line and normal liver cell line. A specific DNMT3B siRNA stably expressed from a plasmid vector effectively suppressed the expression of DNMT3B in SMMC-7721 cell line. By microarray analysis,26 downregulated genes and 115 upregulated genes have been identified in the DNMT3B knockdown cell line,including some important developmental genes and tumor-related genes such as SNCG, NOTCH1, MBD3, WNT11, MAOA and FACL4. The discovery showed DNMT3B was over-expressed in most hepatocellular carcinoma cell lines examined and may be linked to the carcinogenesis of hepatocytes. An array of candidate genes that are involved in the action of DNMT3B have been identified,including those related to development.
authors.affiliation: State Education Ministry Laboratory of Developmental Genes and Human Diseases, Jiangsu Provincial Key Laboratory of Gene Diagnosis and Therapy, Genetics Research Center, Southeast University Medical School, Nanjing 210009, China. bioxu01@yahoo.com.cn
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.forename: Hong
authors.initials: H
authors.lastname: Fan
authors.forename: Zhu-Jiang
authors.initials: ZJ
authors.lastname: Zhao
authors.forename: Jian-Qiong
authors.initials: JQ
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Xie
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000473:pathology; D045744:Cell Line, Tumor; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects* / Q000502:physiology; D006801:Humans; D046228:Microarray Analysis / Q000379:methods; D034622:RNA Interference / Q000502:physiology*; D034741:RNA, Small Interfering / Q000494:pharmacology*; D000097584:DNA Methyltransferase 3B
chemical_list: D004248:DNA (Cytosine-5-)-Methyltransferases; D034741:RNA, Small Interfering; D000097584:DNA Methyltransferase 3B