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A phase-separating microprotein partitions DDX21 to coordinate nucleolar transcription and rRNA processing

ABSTRACT: Ribosome biogenesis is fundamental to cell growth and is frequently dysregulated in cancer, yet how nucleolar transcription is coordinated with rRNA processing remains incompletely understood. Here, we identify TaYü, a 148–amino-acid microprotein encoded by the annotated lncRNA SLC12A5-AS1, as a key regulator of nucleolar compartmentalization. TaYü promotes ribosome biogenesis by partitioning the RNA helicase DDX21 to rDNA, thereby enhancing RNA polymerase I–dependent transcription while restricting its over participation in RNA polymerase II–associated programs. In parallel, TaYü promotes the assembly of DDX21 with fibrillarin and U3 snoRNA to couple rRNA processing. Mechanistically, TaYü undergoes phase separation and co-condenses with DDX21 and rDNA to organize nucleolar transcriptional hubs. Functionally, TaYü is upregulated in cancer and supports tumor growth. Together, these findings identify microprotein-mediated phase separation as a mechanism for partitioning multifunctional factors, thereby coordinating gene expression programs within the nucleolus.

ORGANISM(S): Homo sapiens

PROVIDER: GSE327150 | GEO | 2026/09/10

REPOSITORIES: GEO

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Project description:Myriad of craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as ribosome biogenesis. While it is understood that many of these highly tissue-specific malformations are a consequence of defects in cranial neural crest cells (cNCCs), an embryonic cell group that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell type-selectivity of these effects remains largely unknown. Here we show that DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I and Pol II dependent transcriptional arms of ribosome biogenesis, is a key mediator of the nucleolar stress response. Using an in vitro model of Treacher Collins Syndrome (TCS), a craniofacial disorder caused by heterozygous mutations in components of the Pol I transcriptional machinery, we demonstrate that perturbations in ribosomal RNA (rRNA) transcription induce DDX21-mediated surveillance mechanism in cNCCs, leading to DDX21 relocalization from the nucleolus to the nucleoplasm, its eviction from Pol I and Pol II chromatin targets and inhibition of rRNA processing. Importantly, these effects are cell type-selective, cell-autonomous and involve activation of the p53 pathway. We further show that cNCCs are characterized by the inherently high reservoir of p53 mRNA and sensitivity to p53-mediated apoptosis. Remarkably, preventing the loss of DDX21 from nucleolus and chromatin can rescue both the sensitivity to apoptosis and TCS-associated craniofacial phenotypes in vivo. This mechanism is not restricted to TCS, as gene function perturbations linked to other ribosomopathies with craniofacial manifestations also lead to the activation of DDX21 surveillance. Lastly, we provide evidence that inhibition of rRNA synthesis leads to rDNA damage, and furthermore, that rDNA damage is sufficient to activate DDX21 surveillance and elicits tissue-selective and dosage-dependent effects on craniofacial development in vivo.

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A phase-separating microprotein partitions DDX21 to coordinate nucleolar transcription and rRNA processing

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