Alpha-satellite RNA transcripts are repressed by centromere–nucleolus associations

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.

Centromeric transcription maintains centromeric cohesion in human cells

“…Accordingly, the amounts of the tested centromeric transcripts were also increased (Fig. 4 D), which is consistent with a recent report showing that CENP-B knockout increased centromeric RNA Fluorescence In Situ Hybridization signals (Bury et al, 2020). We next examined if CENP-B knockdown could strengthen centromeric cohesion.…”

“…As treatment of transcriptional inhibitors for a few hours dramatically decreased the ongoing centromeric transcription but seemed not to do so for total RNAs, we believe that actively ongoing transcription rather than RNA transcripts plays a more important role in maintaining centromeric cohesion. This might explain why RPE-1 cells still exhibit strong centromeric cohesion even though they have a low amount of total centromeric RNA transcripts (Bury et al, 2020). Our findings here also suggest that increased centromeric transcription overall strengthens centromeric cohesion.…”

The Role of Human Centromeric RNA in Chromosome Stability

“…Similarly, in mice, forced accumulation of the centromeric minor satellite transcripts leads to defects in chromosome segregation ( Bouzinba-Segard et al, 2006 ), while in human cells, the inhibition of the RNA polymerase II during mitosis leads to a decrease in centromeric α satellite transcription, anaphase lagging cells and abnormal chromosome splitting ( Chan et al, 2012 ; McNulty et al, 2017 ). This suggests that, in mammals, the transcription at the centromere is tightly regulated, maybe by its interaction with the nucleolus that may induce its repression ( Bury et al, 2020 ). In human cells, one of the regulators of cenRNA transcription is ZFAT, which binds to a specific DNA sequence present on each centromere ( Ishikura et al, 2020 ).…”

An emerging role of transcription in chromosome segregation: Ongoing centromeric transcription maintains centromeric cohesion

“…More recently, a study found that human centromeric RNAs appear as multiple foci, which do not associate with centromeres. [26] The levels of these RNA foci vary over the cell cycle and across cell lines. However, the biochemical nature of these α-satellite RNA foci and their functions remain to be addressed.…”