The integrative study identified DNA methylation markers that could lead to the downregulation of some genes involved in important cellular functions in ATRX-low tumors: MGMT, TYMS, CLN8, PANK2 and BNIP3. We also identified that, in glioma cell line, the knockdown of ATRX expression induced apoptotic cells increasing, reduced tumor cell proliferation and repressed the cell migration. The gene discussed is BNIP3; the disease is central nervous system cancer.