Differential human telomerase RNA knockdown by antisense oligonucleotides reveals the existence and potential function of a robust RNA domain.

Telomere length governs replicative capacity and cellular fate. In most cancers, telomeres are maintained by telomerase, a holoenzyme comprising an RNA component (hTR), a protein component (hTERT), and associated accessory proteins. hTR contains two major domains: a 5' domain that associates with hTERT, and a 3' domain that binds core H/ACA proteins. Beyond telomere maintenance, hTR also exerts extra-telomeric roles. Here, we identified a potent antisense oligonucleotide (ASO) against hTR, which inhibited telomerase activity, leading to telomere shortening and cell growth impairment. Surprisingly, this ASO only mediated hTR degradation up to nucleotide 209, leaving the 3' domain intact. Profiling of hTR using ASO tiling also supported this observation: whereas 3'-targeting ASOs could deplete the whole molecule, 5'-targeting ASOs could selectively deplete only the 5' domain, leaving the 3' domain intact, or even increase in abundance. Furthermore, the 3' domain persisted at a steady state following prolonged treatment and was detected in untreated cells, suggesting its natural existence.