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The studies aimed to determine the changes of histone methylation in synovial tissues of patients with osteoarthritis (OA) and rheumatoid arthritis (RA). Synovial tissues were obtained from 30 patients including 12 OA, 16 RA, and 2 trauma that were used as control. A histone methyltransferase DOT1L of the tissues was examined for transcript level with quantitative RT-PCR and protein expression with western blot. Methylation status of DOT1L substrate, H3K79, was examined with immunohistochemistry and western blot. Two-tailed non-pair T test and chi-square test were applied for age/disease duration and gender distribution, respectively. Kruskal-Wallis test and Post hoc Dunn's test were used for examine the difference between control, OA and RA. Both transcript and protein levels of DOT1L appeared the highest in synovial tissues of RA patients and increased in that of OA patients compared to the controls with ratios of 13.8/4.7/1 and 15.5/11.2/1.0 for RA/OA/control, respectively. The changes between RA and control, and RA and OA patients were statistically significant. Both immunohistochemistry study and western blot showed an increased methylation of H3K79 in synovial tissues of OA and RA patients. Gene and protein expression of DOT1L was increased in synovial tissues of both OA and RA patients. A high level of di-methylated H3K79 was also observed in the patients. Considering the important functions of DOT1L and H3K79 contributing to the initiation and maintenance of active transcription in the genome, these unprecedented findings, although still unclear how to impact diseases, may provide novel insights to further explore pathological mechanism of OA and RA.