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The most widely used method for detecting RNA foci, fluorescence in situ hybridization (FISH), is powerful but can suffer from issues related to signal above background. Here we developed a repeat-specific form of hybridization chain reaction (R-HCR) as an alternative method for detection of repeat RNA foci in two neurodegenerative disorders:\n                    <jats:italic>C9orf72<\/jats:italic>\n                    associated ALS and frontotemporal dementia (C9 ALS\/FTD) and Fragile X-associated tremor\/ataxia syndrome. R-HCR to both G\n                    <jats:sub>4<\/jats:sub>\n                    C\n                    <jats:sub>2<\/jats:sub>\n                    and CGG repeats exhibited comparable specificity but\u2009&gt;\u200940\u2009\u00d7\u2009sensitivity compared to FISH, with better detection of both nuclear and cytoplasmic foci in human C9 ALS\/FTD fibroblasts, patient iPSC derived neurons, and patient brain samples. Using R-HCR, we observed that integrated stress response (ISR) activation significantly increased the number of endogenous G\n                    <jats:sub>4<\/jats:sub>\n                    C\n                    <jats:sub>2<\/jats:sub>\n                    repeat RNA foci and triggered their selective nuclear accumulation without evidence of stress granule co-localization in patient fibroblasts and patient derived neurons. These data suggest that R-HCR can be a useful tool for tracking the behavior of repeat expansion mRNA in C9 ALS\/FTD and other repeat expansion disorders.\n                  <\/jats:p>","DOI":"10.1186\/s40478-021-01169-8","type":"journal-article","created":{"date-parts":[[2021,4,23]],"date-time":"2021-04-23T06:06:58Z","timestamp":1619158018000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Enhanced detection of expanded repeat mRNA foci with hybridization chain reaction"],"prefix":"10.1186","volume":"9","author":[{"given":"M. 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