【Abstract】 Objective To study the effect on the DNA methylation level of MS1 cell by inhibiting the expression of Clock gene, and explore the mechanism underlying Clock gene regulation of cell proliferation. Methods We knockeddown the expression of Clock gene by RNA interference, detected the DNA methylation level by Methylated DNA Quantification Kit, and the expression of Mecp2 and βCatenin by Realtime PCR and Western blot. Results Knockdown the expression of Clock gene causes reduced DNA methylation level of MS1 cell, and the expression of Mecp2 and βCatenin. The DNA methylation levels of Clock gene Konckeddown group and Neagtive Control group(NC) were 1067±0034% and 1983±0154%，p<005, respectively. The Realtime PCR results display the expression of Mecp2 and βCatenin in CK group were 098824±012243 and 100000±009547，compare with the NC group 180979±018520 and 162584±017167，respectively. The relative protein levels of MECP2/βTUBLLIN and βCATENIN/βTUBLLIN were 0289546±0104738 and 1093368±0214433 in CK group, compare with 0649544±0140909 and 3305374±0260016 in the NC group, respectively. Conclusion The DNA methylation level of MS1 cell could be affected by Clock gene. Clock gene may regulate cell proliferation by inhibiting the expression of Mecp2 and βCatenin.