Biology subjects

Potolitsyna, E.

Publications and source records attributed to Potolitsyna, E..

4 recordsLinked to original sources

bioRxiv2026

Adaptive energetic tuning of nucleolar phase separation regulates rRNA transport

Eukaryotic cells adjust biochemical pathways in response to environmental stressors, stalling energetically costly processes such as protein synthesis and ribosome biogenesis. Ribosome biogenesis occurs within the multiphase nucleolus that contains three layers roughly corresponding to ribosomal RNA (rRNA) transcription, processing, and assembly. While nucleolar perturbations induced by drug treatments and optogenetic nucleolar gelation alter nucleolar stability and hinder ribosome biogenesis, it remains unclear whether nucleolar properties are actively tuned in response to metabolic and growth cues. Here, we show that nucleolar phase separation is adjusted to physiological needs. Live-cell imaging of endogenously tagged NPM1 reveals a tight relationship between NPM1 partitioning and nutrient availability. In nutrient-deprived conditions, NPM1 levels in the nucleolus increase, indicative of stabilized phase separation and a more gel-like state. Indeed, we show that rRNA diffusion decreases and the nucleolar meshwork contracts. Furthermore, this change corresponds to decreased rRNA processing, suggesting that reduced transport properties prevent the release of immature ribosome subunits from the nucleolus. Mechanistically, we show that these changes are driven by ATP levels, which broadly affect the energetically expensive process of ribosome biogenesis. Upon restoration of ATP levels by nutrient reintroduction, nucleolar composition returns to normal within minutes, suggesting active regulation. Taken together, our findings reveal that the biophysical properties of the nucleolus are not fixed, but are actively remodeled by cellular energy levels, linking phase separation dynamics to metabolic control of ribosome biogenesis.

biophysics↗

bioRxiv2025

Nuclear Phase Separation Drives NPM1-mutant Acute Myeloid Leukemia

During cancer development, mutations promote gene expression changes that cause transformation. Leukemia is frequently associated with aberrant HOXA expression driven by translocations in nucleoporin genes or KMT2A, and mutations in NPM1. How disparate mutations converge on this regulatory pathway is not understood. Here we demonstrate that mutant NPM1 (NPM1c) forms nuclear condensates in multiple human cell lines, mouse models, and primary patient samples. We show NPM1c phase separation is necessary and sufficient to coordinate the recruitment of NUP98 and KMT2A to condensates. Through extensive mutagenesis and pharmacological destabilization of phase separation, we find that NPM1c condensates are necessary for regulating gene expression, promoting in vivo expansion, and maintaining the undifferentiated leukemic state. Finally, we show that nucleoporin and KMT2A fusion proteins form condensates that are biophysically indistinguishable from NPM1c condensates. Together, these data define a new condensate underlying leukemias that we term coordinating bodies (C-bodies), and propose C-bodies as a therapeutic vulnerability.

biophysics↗

bioRxiv2025

Nanometer condensate organization in live cells derived from partitioning measurements

Biomolecules self-organize into membrane-less organelles known as condensates that compartmentalize essential biochemical processes, such as ribosome biogenesis in the nucleolus1-3. Molecular dynamics within condensates are governed by chemical preferences and interaction networks that can imbue nanoscale structure4-7. Such organization is typically inferred from ensemble-averaged measurements, such as scattering and electron microscopy, which reveal molecular arrangements8-14. However, the complexity of cells obscures the interpretability of these techniques, limiting insight into condensate internal structure and roles in macromolecular assembly and transport. Here, we develop an approach to quantify the average microenvironment surrounding specific proteins within condensates in live cells, using thermodynamic principles to interpret the partitioning of designed protein probes. Using this approach, we find that condensates in cells, including the nucleolus, stress granule, and nuclear pore, exhibit spatial inhomogeneity, aligning with emerging views of condensates as networked fluids5,6,15-18. Within the nucleolus, we link spatial inhomogeneity to ribosome biogenesis, which progressively loosens the average local meshwork, facilitating transport of assembled ribosomal subunits. Within the nuclear pore, we find that transporters experience a weaker local meshwork than nucleoporins, consistent with the selective phase model19,20. Together, our approach uncovers a distinct mode of biomolecular control arising from nanoscale structure, which we term microenvironment coupling, whereby internal interaction landscapes shape transport to enable regulation and proofreading.

biophysics↗

bioRxiv2022

De novo annotation of lncRNA HOTAIR transcripts by long-read RNA capture-seq reveals a differentiation-driven isoform switch

BackgroundLncRNAs are tissue-specific and emerge as important regulators of various biological processes and as disease biomarkers. HOTAIR is a well-established pro-oncogenic lncRNA which has been attributed a variety of functions in cancer and native contexts. However, a lack of an exhaustive, cell type-specific annotation questions whether HOTAIR functions are supported by the expression of multiple isoforms. ResultsUsing a capture long-read sequencing approach, we characterize HOTAIR isoforms expressed in human primary adipose stem cells. We identify a highly cell type-specific HOTAIR isoform and uncover a shift in the HOTAIR isoform balance at differentiation onset. Composition of the HOTAIR isoform pool is regulated by distinct promoter usage and is under control of hormonal and nutrient-sensing pathways. ConclusionOur results highlight the complexity and cell type-specificity of HOTAIR isoforms and open perspectives on functional implications of these variants and their balance to key cellular processes.

genomics↗