BackgroundThe long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a cancer biomarker. Furthermore, fusion of theMALAT1gene with glioma-associated oncogene 1 (GLI1) is a diagnostic marker of plexiform fibromyxoma and gastroblastoma; however, the function of this fusion gene remains unexplored.MethodIn this study, we elucidate the structure and function of theMALAT1::GLI1fusion gene. To this end, we determined a transcriptional start site (TSS) and promoter region for truncated GLI1 expression using rapid amplification of the 5' cDNA end and a luciferase reporter assay in cultured cells transfected with a plasmid harboring theMALAT1::GLI1fusion gene.ResultsWe found that the TATA box, ETS1 motif, and TSS were located inMALAT1and thatMALAT1exhibited transcriptional activity and induced expression ofGLI1from theMALAT1::GLI1fusion gene. Truncated GLI1, lacking SUMOylation and SUFU binding sites and located in the nucleus, upregulated mRNA expression of GLI1 target genes in the hedgehog signaling pathway.ConclusionsWe demonstrate a distinct and alternative function ofMALAT1as a transcriptional promoter for expression of theMALAT1::GLI1fusion gene. Our findings will aid future research onMALAT1and its fusion gene partners.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12885-023-10867-6.