Background △DNMT3B (a new DNMT3B subfamily) expression is initiated through a novel promoter.We identified at least 7 transcription variants of △DNMT3B as a result of alternative pre-mRNA processing.The aim of this study was to detect the expression pattern of △DNMT3B variants in non-small cell lung cancer (NSCLC) and to explore the role of △DNMT3B variants in regulating the promoter-specific DNA methylation.Methods Specific polymerase chain reaction (PCR) primer sets were designed to distinguish individual △DNMT3B variants according to their splicing pattems.The expressions of seven △DNMT3B variants were measured in 13 cell lines,109 NSCLC patients,and the corresponding normal lung tissues using reverse transcription-PCR (RT-PCR).The status of the p16 and RASSF1A promoter methylations in the tumors was detected using a methylation specific PCR (MSP).The relationships of the expression patterns of the △DNMT3B variants were analyzed by observing the status of p16 and RASSF1A promoter methylations in the tumors.The siRNA and the anti-sense oligo-dioxynucleotide specifically targeting the junction of exon 5 and 7 of △DNMT3B were designed and transfected by lipofectmane 2000 into H1299 and H358 cell lines.RASSF1A promoter methylation from cells treated by siRNA-△DNMT3B4/2 was detected using MSP and Bisulfite sequencing,and Western blotting was used to detect the protein expression of DNMT3B and △DNMT3B.Cell growth and cell cycle distribution were measured by applying real-time cell growth analysis and flowcytometry,respectively.Results △DNMT3B variants,not DNMT3B,were the predominant transcripts in both NSCLC cell lines and primary tumors.The expression of △DNMT3B4 strongly correlated to the promoter methylation status of RASSFIA in a primary NSCLC.The knockdown of △DNMT3B4/2 by RNA-interference or anti-sense approaches resulted in a complete demethylation of RASSF1A promoter with the reactJvation of a RASSFIA gene expression in less than 12 hours,but no effect resulted from the p16INK4a promoter in the NSCLC cell lines.Conclusions These results demonstrate an important role of △DNMT3B4/2 in the maintenance of promoter-specific DNA methylation in a cell type specific manner and provide a novel cell model for the study of the regulation of replication-independent DNA methylation.