HSAT3 lncRNA regulates replication re-initiation and colocalizes with TOP2A under stress conditions

Long non-coding RNAs transcribed from pericentromeric Satellite 3 repeats (HSAT3) are involved in stress-dependent splicing processes and maintenance of genome stability. The functions of the transcripts are largely unknown, which is mainly due to the predominant heterochromatic organization of satellite regions. HSAT3 expression is induced upon several cellular stressors and builds nuclear stress bodies (nSB), which recruit a large number of RNA-binding and regulatory proteins. Recently, we reported that HSAT3 transcripts induce resistance against the topoisomerase 2a (TOP2A) inhibitor etoposide in lung cancer.

We show that HSAT3 transcripts and topoisomerase IIα (TOP2A) accumulate in nuclear stress bodies. Biochemical assays indicate that HSAT3 RNA can associate with TOP2A. Using single-molecule DNA fiber analysis, we demonstrate that depletion of HSAT3 delays replication re-initiation. Consistent with this, HSAT3 knockdown alters cell cycle distribution in the presence of the TOP2A inhibitor etoposide. In vivo, reduced HSAT3 levels lead to delayed tumor growth in xenograft models. In addition, we identify epigenetic compounds that suppress HSAT3 expression and enhance cellular sensitivity to etoposide, suggesting a potential strategy for combination treatments.

Together, our findings support a functional link between stress-induced repetitive RNAs, nuclear compartmentalization, and replication-associated processes. These results provide a framework for understanding how pericentromeric lncRNAs contribute to genome stability and drug response in cancer cells.