RESEARCH ARTICLE Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations Leah Bury1†, Brittania Moodie1†, Jimmy Ly1,2, Liliana S McKay1, Karen HH Miga3, Iain M Cheeseman1,2* 1Whitehead Institute for Biomedical Research, Cambridge, United States; 2Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 3UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, United States Abstract Although originally thought to be silent chromosomal regions, centromeres are instead actively transcribed. However, the behavior and contributions of centromere-derived RNAs have remained unclear. Here, we used single-molecule fluorescence in-situ hybridization (smFISH) to detect alpha-satellite RNA transcripts in intact human cells. We find that alpha-satellite RNA- smFISH foci levels vary across cell lines and over the cell cycle, but do not remain associated with centromeres, displaying localization consistent with other long non-coding RNAs. Alpha-satellite expression occurs through RNA polymerase II-dependent transcription, but does not require established centromere or cell division components. Instead, our work implicates centromere– nucleolar interactions as repressing alpha-satellite expression. The fraction of nucleolar-localized centromeres inversely correlates with alpha-satellite transcripts levels across cell lines and transcript levels increase substantially when the nucleolus is disrupted. The control of alpha-satellite transcripts by centromere-nucleolar contacts provides a mechanism to modulate centromere transcription and chromatin dynamics across diverse cell states and conditions. *For correspondence:
[email protected] †These authors contributed equally to this work Introduction Chromosome segregation requires the function of a macromolecular kinetochore structure to con- Competing interests: The nect chromosomal DNA and spindle microtubule polymers.