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Background Long non-coding RNA Hox transcript antisense intergenic RNA (HOTAIR) has been characterized as a negative prognostic factor in breast and colon cancer patients.The clinical significance and function of HOTAIR in glioma remains unclear.Methods We analyzed the clinical significance of HOTAIR in 3 different glioma cohorts with gene expression data, including the correlation with tumor grade, prognosis and molecular subtype.The function of HOTAIR in glioma was explored by performing gene set enrichment analysis (GSEA) and in vitro and in vivo experiments.Results HOTAIR expression was closely associated with glioma grade and poor prognosis.Multivariate Cox regression analysis revealed that HOTAIR was an independent prognostic factor in GBM (glioblastoma) patients.HOTAIR expression correlated with glioma molecular subtype, including the TCGA subtype.HOTAIR was preferentially expressed in the Classical and Mesenchymal subtypes compared with the Neural and Proneural subtypes.A GSEA designed to showing gene set differences between patients with high and low HOTAIR expression indicated that HOTAIR expression is associated with gene sets involved in cell cycle progression.A reduction in HOTAIR expression induced colony formation suppression and cell cycle G0/G1 arrest and orthotopic tumor growth inhibition.Conclusion Our data establish that HOTAIR is an important long non-coding RNA that primarily serves as a prognostic factor for glioma patient survival, and a biomarker for identifying glioma molecular subtypes, a critical regulator of cell cycle progression.