Methylation of lysine K4 (K4) within histone H3 has been linked to active transcription and is removed by LSD1 and the JmjC-domain-containing proteins by amino-oxidation or hydroxylation, respectively. Here we describe the deamination catalyzed by Lysyl oxidase-like 2 protein (LOXL2) as an unconventional chemical mechanism for H3K4 modification. Infrared spectroscopy and mass spectrometry analyses demonstrated that recombinant LOXL2 specifically deaminates tri-methylated H3K4. Moreover, LOXL2 activity is linked with the transcriptional control of CDH1 gene by regulating H3K4me3 deamination. These results reveal another H3 modification and provide a different mechanism for H3K4 modification.