By using direct immunocytochemistry of BrU incorporated to RNA in the nuclei, we evaluated the effect of mutant huntingtin and ataxin-1 on general transcription in primary cortical and cerebellar neurons. Our quantitative analyses clearly showed that these mutant polyglutamine disease proteins repress general transcription. In addition, we found that general transcription level was almost similar in inclusion body-positive and -negative neurons. The result suggests that presence of inclusion body is not essential for repressing general transcription in contrast to its reported role for suppressing specific gene transcription in the polyglutamine disease pathology. (C) 2003 Elsevier Inc. All rights reserved.