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Spinocerebellar ataxia type 31 ( SCA31) is an autosomal-dominant cerebellar ataxia showing a Purkinje cell ( PC)-predominant neurodegeneration in humans. The mutation is a complex penta-nucleotide repeat containing ( TGGAA)n, ( TAGAA)n, ( TAAAA)n and ( TAGAATAAAA)n inserted in an intron shared by two different genes BEAN1 and TK2 located in the long arm of the human chromosome 16. Previous studies have shown that ( TGGAA)n is the critical component of SCA31 pathogenesis while the three other repeats, also present in normal Japanese, are not essential. Importantly, it has been shown that BEAN1 and TK2 are transcribed in mutually opposite directions in the human brain. Furthermore, abnormal RNA structures called ' RNA foci' are observed by a probe against ( UAGAAUAAAA)n in SCA31 patients' PC nuclei, indicating that the BEAN1-direction mutant transcript appears instrumental for the pathogenesis. However, it is not known whether the critical repeat ( TGGAA)n contributes to the formation of RNA foci, neither do we understand how the RNA foci formation is relevant to the pathogenesis. To address these issues, we investigated two SCA31 cerebella by fluorescence in situ hybridization using a probe against ( UGGAA)n. We also asked whether the mutant BEAN1-transcript containing ( UGGAA)n exerts toxicity compared to the other three repeats in cultured cells. Histopathologically, we confirm that the PC is the main target of SCA31 pathogenesis. We find that the RNA foci containing ( UGGAA)n are indeed observed in PC nuclei of both SCA31 patients, whereas similar foci were not observed in control individuals. In both transiently and stably expressed cultured cell models, we also find that the mutation transcribed in the BEAN1-direction yields more toxicity than control transcripts and forms RNA foci detected with probes against ( UGGAA)n and ( UAGAAUAAAA)n. Taking these findings together, we conclude that the RNA foci containing BEAN1-direction transcript ( UGGAA)n are associated with PC degeneration in SCA31. [ABSTRACT FROM AUTHOR]