DDX18 coordinates nucleolus phase separation and nuclear organization to control the pluripotency of human embryonic stem cells. Nature communications Pluripotent stem cells possess a unique nuclear architecture characterized by a larger nucleus and more open chromatin, which underpins their ability to self-renew and differentiate. Here, we show that the nucleolus-specific RNA helicase DDX18 is essential for maintaining the pluripotency of human embryonic stem cells. Using techniques such as Hi-C, DNA/RNA-FISH, and biomolecular condensate analysis, we demonstrate that DDX18 regulates nucleolus phase separation and nuclear organization by interacting with NPM1 in the granular nucleolar component, driven by specific nucleolar RNAs. Loss of DDX18 disrupts nucleolar substructures, impairing centromere clustering and perinucleolar heterochromatin (PNH) formation. To probe this further, we develop NoCasDrop, a tool enabling precise nucleolar targeting and controlled liquid condensation, which restores centromere clustering and PNH integrity while modulating developmental gene expression. This study reveals how nucleolar phase separation dynamics govern chromatin organization and cell fate, offering fresh insights into the molecular regulation of stem cell pluripotency. 10.1038/s41467-024-55054-8

Mapping the cleavage sites on mammalian pre-rRNAs: where do we stand? Mullineux Sahra-Taylor,Lafontaine Denis L J Biochimie Ribosomal RNAs are produced as lengthy polycistronic precursors containing coding and non-coding sequences, implying that extensive pre-rRNA processing is necessary for the removal of non-coding spacers. Remarkably, this feature is conserved in all three kingdoms of life and pre-rRNA processing has even become more complex during the course of evolution. While the need for such extensive processing remains unclear, it likely offers increased opportunities to finely regulate ribosome synthesis and to temporally and spatially integrate the various components of ribosome synthesis. In this review we discuss our current understanding of pre-rRNA processing pathways in mammals (human and mouse), with a particular focus on the known and putative cleavage sites, and we compare it to budding yeast, the best eukaryotic model, thus far, regarding ribosome synthesis. Based on the emerging research, we suggest that there are likely more pre-rRNA processing sites and alternative processing pathways still to be identified in humans and that a certain level of functional redundancy can be found in the trans-acting factors involved. These features might have been selected because they increase the robustness of pre-rRNA processing by acting as "back-up" mechanisms to ensure the proper maturation of rRNA. 10.1016/j.biochi.2012.02.001

An overview of pre-ribosomal RNA processing in eukaryotes. Henras Anthony K,Plisson-Chastang Célia,O'Donohue Marie-Françoise,Chakraborty Anirban,Gleizes Pierre-Emmanuel Wiley interdisciplinary reviews. RNA Ribosomal RNAs are the most abundant and universal noncoding RNAs in living organisms. In eukaryotes, three of the four ribosomal RNAs forming the 40S and 60S subunits are borne by a long polycistronic pre-ribosomal RNA. A complex sequence of processing steps is required to gradually release the mature RNAs from this precursor, concomitant with the assembly of the 79 ribosomal proteins. A large set of trans-acting factors chaperone this process, including small nucleolar ribonucleoparticles. While yeast has been the gold standard for studying the molecular basis of this process, recent technical advances have allowed to further define the mechanisms of ribosome biogenesis in animals and plants. This renewed interest for a long-lasting question has been fueled by the association of several genetic diseases with mutations in genes encoding both ribosomal proteins and ribosome biogenesis factors, and by the perspective of new anticancer treatments targeting the mechanisms of ribosome synthesis. A consensus scheme of pre-ribosomal RNA maturation is emerging from studies in various kinds of eukaryotic organisms. However, major differences between mammalian and yeast pre-ribosomal RNA processing have recently come to light. 10.1002/wrna.1269