Lesions on the DNA template can impact transcription via distinct regulatory pathways. Ionizing radiation (IR) as the mainstay modality for many malignancies elicits most of the cytotoxicity by inducing a variety of DNA damages in the genome. How the IR treatment alters transcription cycle and whether it contributes to the development of radioresistance remain poorly understood. Here, we report an increase in the paused RNA polymerase II (RNAPII), as indicated by the phosphorylation at serine 5 residue of its C-terminal domain, in recurrent nasopharyngeal carcinoma (NPC) patient samples after IR treatment and cultured NPC cells developing IR resistance. Reducing the pool of paused RNAPII by either inhibiting TFIIH-associated CDK7 or stimulating the transcription elongation factor P-TEFb, a CDK9-CycT1 heterodimer, attenuates IR resistance of NPC cells. Interestingly, the poly(ADP-ribosyl)ation of CycT1, which disrupts its phase separation, is elevated in the IR-resistant cells. Mutation of major poly(ADP-ribosyl)ation sites of CycT1 decreases RNAPII pausing and restores IR sensitivity. Genome-wide chromatin immunoprecipitation followed by sequencing analyses reveal that several genes involved in radiation response and cell cycle control are subject to the regulation imposed by the paused RNAPII. Particularly, we identify the NIMA-related kinase NEK7 under such regulation as a new radioresistance factor, whose downregulation results in the increased chromosome instability, enabling the development of IR resistance. Overall, our results highlight a novel link between the alteration in transcription cycle and the acquisition of IR resistance, opening up new opportunities to increase the efficacy of radiotherapy and thwart radioresistance in NPC.

During ribosome biogenesis, the small subunit (SSU) processome is responsible for 40S assembly. The BMS1/RCL1 complex is a core component of SSU processome that plays an important role in 18S rRNA processing and maturation. Genetic studies using zebrafish mutants indicate that both Bms1l (Bms1-like) and Rcl1 are essential for digestive organs development. In spite of the vital functions of this complex, the mutual dependence for the stability and function of these two nucleolar proteins remains elusive. In this study, we identified an RCL1-interacting domain in BMS1 conserved in zebrafish and human. Moreover, both protein stability and nucleolar entry of RCL1 depend on BMS1, otherwise leading to RCL1 degradation through the ubiquitination-proteasome pathway. Functional studies reveal that overexpression of RCL1 in BMS1 knockdown cells can partially rescue the defects of 18S rRNA processing and cell proliferation, and hepatocyte-specific overexpression of Rcl1 can resume zebrafish liver development in the bms1l substitution mutant bms1lsq163/sq163but not the knockout mutant bms1lzju1/zju1, attributed to the nucleolar entry of Rcl1 in the former. Our data demonstrate that BMS1 and RCL1 interaction is essential not only for pre-rRNA processing but also for the communication between ribosome biogenesis and cell cycle regulation.

Estrogen receptor α (ERα) is an important driver and therapeutic target in approximately 70% of breast cancers. How ERα drives breast carcinogenesis is not fully understood. In this study, we show that ERα is a negative regulator of type I interferon (IFN) response, which is critical for breast carcinogenesis. Activation of ERα by its natural ligand estradiol inhibits IFN-β-induced transcription of downstream IFN-stimulated genes (ISGs), whereas deficiency of ERα or stimulation with its antagonist fulvestrant has opposite effects. Mechanistically, ERα inhibits type I IFN response by two distinct mechanisms. ERα induces expression of the histone 2A variant H2A.Z, which restricts engagement of the IFN-stimulated gene factor 3 (ISGF3) complex at the ISG promoters. ERα also interacts with STAT2, which leads to disruption of the ISGF3 complex. These two events mutually lead to transcriptional inhibition of ISGs induced by type I IFNs. In a xenograft mouse tumor model, fulvestrant enhances the ability of IFN-β to suppress ERα+ breast tumor growth. Consistently, clinical data suggests that ERα+ breast cancer patients with higher levels of ISGs exhibit an increased survival rate. Our findings suggest that ERα inhibits type I IFN response via two distinct mechanisms to promote breast cancer.