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Pervasive transcription is widespread in eukaryotes, generating large families of noncoding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production. [ABSTRACT FROM AUTHOR]

Pervasive transcription is widespread in eukaryotes, generating large families of non-coding RNAs. Such pervasive transcription is a key player in the regulatory pathways controlling chromatin state and gene expression. Here, we describe long non-coding RNAs generated from the ribosomal RNA gene promoter called UPStream-initiating transcripts (UPS). In yeast, rDNA genes are organized in tandem repeats in at least two different chromatin states, either transcribed and largely depleted of nucleosomes (open) or assembled in regular arrays of nucleosomes (closed). The production of UPS transcripts by RNA Polymerase II from endogenous rDNA genes was initially documented in mutants defective for rRNA production by RNA polymerase I. We show here that UPS are produced in wild-type cells from closed rDNA genes but are hidden within the enormous production of rRNA. UPS levels are increased when rDNA chromatin states are modified at high temperatures or entering/leaving quiescence. We discuss their role in the regulation of rDNA chromatin states and rRNA production.

We provide a graphical abstract to summarize the antitumor mechanisms of CX5461 and INK128 individually and in combination in OSCC. The RNA polymerase I inhibitor CX5461 remarkably suppresses rRNA transcription and induces nucleolar disruption and oxidative stress, which leads to DNA damage. The mTORC1/2 inhibitor INK128 primarily suppresses cell proliferation and cell cycle progression. The antioxidant NAC significantly prevents CX5461-induced ROS generation, DNA damage, and apoptosis. INK128 treatment compromises the NHEJ-DNA repair pathway to reinforce CX5461-induced DNA damage. The combined administration of CX5461 and INK128 acts synergistically to trigger OSCC cell apoptosis. OSCC tumor cells, with a reduced 45S rDNA copy number, are highly sensitive to treatments with CX5461 and coadministration of CX5461 and INK128. • CX5461 and INK128 synergistically suppress oral squamous cell carcinoma. • Primary oral tumors frequently exhibit a partial loss of 45S rDNA copy number. • Fewer rDNA copies can improve sensitivity to CX5461 and the combined treatment. • CX5461 and INK128 are more cytotoxic towards oral cancer cells than normal cells. • INK128 impairs the NHEJ repair pathway to reinforce the antitumor effect of CX5461. Oral squamous cell carcinoma (OSCC) is the major cause of morbidity and mortality in head and neck cancer patients worldwide. This malignant disease is challenging to treat because of the lack of effective curative strategies and the high incidence of recurrence. This study aimed to investigate the efficacy of a single and dual approach targeting ribosome biogenesis and protein translation to treat OSCC associated with the copy number variation (CNV) of ribosomal DNA (rDNA). Here, we found that primary OSCC tumors frequently exhibited a partial loss of 45S rDNA copy number and demonstrated a high susceptibility to CX5461 (a selective inhibitor of RNA polymerase I) and the coadministration of CX5461 and INK128 (a potent inhibitor of mTORC1/2). Combined treatment displayed the promising synergistic effects that induced cell apoptosis and reactive oxygen species (ROS) generation, and inhibited cell growth and proliferation. Moreover, INK128 compromised NHEJ-DNA repair pathway to reinforce the antitumor activity of CX5461. In vivo , the cotreatment synergistically suppressed tumor growth, triggered apoptosis and strikingly extended the survival time of tumor-bearing mice. Additionally, treatment with the individual compounds and coadministration appeared to reduce the incidence of enlarged inguinal lymph nodes. Our study supports that the combination of CX5461 and INK128 is a novel and efficacious therapeutic strategy that can combat this cancer and that 45S rDNA may serve as a useful indicator to predict the efficacy of this cotreatment. [ABSTRACT FROM AUTHOR]