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Results for “cell biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,369 records · Page 76Linked to original sources

bioRxiv2022

Kidins220 promotes thymic iNKT cell development by reducing TCR signals, but enhances TCR signals in splenic iNKT cells

The stepwise development of thymic invariant natural killer T (iNKT) cells is controlled by the TCR signal strength. The scaffold protein Kinase D interacting substrate of 220 kDa (Kidins220) binds to the TCR regulating TCR signaling. T cell-specific Kidins220 knock-out (T-KO) mice contain severely decreased iNKT numbers. Very early in iNKT development TCR signals are reduced in the T-KO. In later steps, TCR signaling is increased in the T-KO leading to enhanced apoptosis of iNKT cells. Kidins220s absence affects the iNKT1 subset most as it requires the weakest TCR signals for development. We also show that in iNKT1 development, weak TCR signals promote the progressive loss of CD4. In the periphery, Kidins220 switches its role back to promoting TCR signaling as splenic T-KO iNKT cells produce less cytokines and show reduced TCR signaling after in vivo stimulation with -galactosylceramide. In conclusion, Kidins220 promotes or inhibits TCR signaling depending on the developmental context. summary statementWe demonstrate that the transmembrane scaffold protein Kidins220 switches its role twice in iNKT cell biology: from a positive to a negative regulator of TCR signal strength during thymic development and back to a positive regulator in the periphery.

immunology↗

bioRxiv2022

Metabolic-imaging of human glioblastoma explants: a new precision-medicine model to predict tumor treatment response early

BackgroundGlioblastoma (GB) is the most severe form of brain cancer, with a 12-15 month median survival. Surgical resection, temozolomide (TMZ) treatment, and radiotherapy (RT) remain the primary therapeutic options for GB, and no new therapies have been introduced in recent years. This therapeutic standstill is primarily due to preclinical approaches that do not fully respect the complexity of GB cell biology and fail to test efficiently anti-cancer treatments. Therefore, better treatment screening approaches are needed. In this study, we have developed a novel functional precision medicine approach to test the response to anticancer treatments in organoids derived from the resected tumors of glioblastoma patients. MethodsGB organoids were grown for a short period of time to prevent any genetic and morphological evolution and divergence from the tumor of origin. We chose metabolic imaging by NAD(P)H fluorescence lifetime imaging microscopy (FLIM) to predict early and non-invasively ex-vivo anti-cancer treatment responses of GB organoids. TMZ was used as the benchmark drug to validate the approach. Whole-transcriptome and whole-exome analyses were then performed to characterize tumor cases stratification. ResultsOur functional precision medicine approach was completed within one week after surgery and two groups of TMZ Responder and Non Responder tumors were identified. FLIM-based metabolic tumor stratification was well-reflected at the molecular level, confirming the validity of our approach, highlighting also new target genes associated with TMZ treatment and identifying a new 17 gene molecular signature associated with survival. The number of promoter methylated tumors for the MGMT gene was higher in the responsive group, as expected, however, some non-methylated tumor cases turned out to be nevertheless responsive to TMZ, suggesting that our procedure could be synergistic with the classical MGMT methylation biomarker. ConclusionsFor the first time, FLIM-based metabolic imaging was used on ex-vivo live glioblastoma organoids. Unlike other approaches, ex-vivo patient-tailored drug response is performed at an early stage of tumor culturing with no animal involvement and with minimal tampering with the original tumor cytoarchitecture. This functional precision medicine approach can be exploited in a range of clinical and laboratory settings to improve the clinical management of GB patients and implemented on other cancers as well.

molecular biology↗

bioRxiv2022

The transcription factor RUNX2 drives the generation of human NK cells and promotes tissue residency

NK cells are innate lymphocytes that eliminate virus-infected and cancer cells by cytotoxicity and cytokine secretion. In addition to circulating NK cells, distinct tissue-resident NK subsets have been identified in various organs. Although transcription factors regulating NK cell development and function have been extensively studied in mice, the role of RUNX2 in these processes has not been investigated, neither in mice nor in human. Here, by manipulating RUNX2 expression with either knockdown or overexpression in human hematopoietic stem cell-based NK cell differentiation cultures, combined with transcriptomic and ChIP-sequencing analyses, we established that RUNX2 drives the generation of NK cells, possibly through induction of IL-2R{beta} expression in NK progenitor cells. Importantly, RUNX2 promotes tissue residency in human NK cells. Our findings have the potential to improve existing NK cell-based cancer therapies and can impact research fields beyond NK cell biology, since tissue-resident subsets have also been described in other lymphocyte subpopulations.

immunology↗

bioRxiv2022

Interplay between Polycomb PCGF protein interactomes revealed by screening under endogenous conditions

The six PCGF proteins (PCGF1-6) define the biochemical identity of Polycomb Repressor Complex 1 (PRC1) subcomplexes. While structural and functional studies of PRC1 subcomplexes have revealed specialized roles in distinct aspects of epigenetic regulation, our understanding of variation in protein interaction networks between the PCGF subunits is incomplete. We carried out an affinity purification mass spectrometry (AP-MS) screen of subunits PCGF1 (NSPC1), PCGF2 (MEL18), and PCGF4 (BMI1), using an immunoprecipitation approach that replicated endogenous cellular conditions in a cell line capable of differentiation programs. Over 200 interactions were found, including 83 that had not been described previously. Bioinformatic analysis found that these interacting proteins covered a range of functional pathways, often focused on cell biology and chromatin regulation. We found evidence of mutual regulation (at mRNA and protein level) between distinct PCGF subunits. Furthermore, we confirmed that disruption of each subunit using shRNA results in reduced proliferation ability. Overall, our work adds to understanding of the role of PCGF proteins within the wider cellular network.

cancer biology↗

bioRxiv2022

Modeling clonal evolution and oncogenic dependency in vivo in the context of hematopoietic transformation

Cancer evolution is a multifaceted process involving the acquisition of somatic mutations and progressive epigenetic dysregulation of cellular fate. Both cell-intrinsic mechanisms and environmental interactions provide selective pressures capable of promoting clonal evolution and expansion, with single-cell and bulk DNA sequencing offering increased resolution into this process1-4. Advances in genome editing, single-cell biology and expressed lentiviral barcoding have enabled new insights into how transcriptional/epigenetic states change with clonal evolution5,6. Despite the extensive catalog of genomic alterations revealed by resequencing studies7,8, there remain limited means to functionally model and perturb this evolutionary process in experimental systems9. Here we integrated multi-recombinase (Cre, Flp, and Dre) tools for modeling reversible, sequential mutagenesis from premalignant clonal hematopoiesis to acute myeloid leukemia. We demonstrate that somatic acquisition of Flt3 activating mutations elicits distinct phases of acute and chronic activation resulting in differential cooperativity with Npm1 and Dnmt3a disease alleles. We next developed a generalizable allelic framework allowing for the reversible expression of oncogenic mutations at their endogenous loci. We found that reversal of mutant Flt3 resulted in rapid leukemic regression with distinct alterations in cellular compartments depending upon co-occurring mutations. These studies provide a path to model sequential mutagenesis and deterministically investigate mechanisms of transformation and oncogenic dependency in the context of clonal evolution.

cancer biology↗

bioRxiv2022

Structural characterization of a breast cancer-associated mutation in caveolin-1

Caveolin-1 (CAV1) is a membrane sculpting protein that oligomerizes to generate flask-shaped invaginations of the plasma membrane known as caveolae. Mutations in CAV1 have been linked to multiple diseases in humans. Such mutations often interfere with oligomerization and the intracellular trafficking processes required for successful caveolae assembly, but the molecular mechanisms underlying these defects have not been structurally explained. Here, we investigate how a breast cancer-associated mutation in one of the most highly conserved residues in CAV1, P132L, affects CAV1 structure and oligomerization. We show that P132 is positioned at a major site of protomer-protomer interactions within the CAV1 complex, providing a structural explanation for why the mutant protein fails to homo-oligomerize correctly. Using a combination of computational, structural, biochemical, and cell biological approaches, we find that despite its homo-oligomerization defects P132L is capable of forming mixed hetero-oligomeric complexes with wild type CAV1 and that these complexes can be incorporated into caveolae. These findings provide insights into the fundamental mechanisms that control the formation of homo- and hetero-oligomers of caveolins that are essential for caveolae biogenesis, as well as how these processes are disrupted in human disease.

biophysics↗

bioRxiv2022

The canonical PilT retraction ATPase promotes both extension and retraction of the MSHA type IVa pilus in Vibrio cholerae

Diverse bacterial species use type IVa pili (T4aP) to interact with their environments. The dynamic extension and retraction of T4aP is critical for their function, but the mechanisms that regulate this dynamic activity remain poorly understood. T4aP are typically extended via the activity of a dedicated extension motor ATPase and retracted via the action of an antagonistic retraction motor ATPase called PilT. These motors are generally functionally independent, and loss of PilT commonly results in T4aP hyperpiliation due to undeterred pilus extension. However, for the mannose-sensitive hemagglutinin (MSHA) T4aP of Vibrio cholerae, the loss of PilT results in a loss of surface piliation, which is unexpected based on our current understanding of T4aP dynamics. Here, we employ a combination of genetic and cell biological approaches to dissect the underlying mechanism. Our results demonstrate that PilT is necessary for MSHA pilus extension in addition to its well-established role in promoting MSHA pilus retraction. Through a suppressor screen, we also provide genetic evidence that the MshA major pilin impacts pilus extension. Together, these findings contribute to our understanding of the factors that regulate pilus extension and describe a previously uncharacterized function for the PilT motor ATPase. AUTHOR SUMMARYMany bacteria use filamentous appendages called type IVa pili to interact with their environment. These fibers dynamically extend and retract through the activity of ATPase motor proteins. In most pilus systems, deletion of the retraction motor results in uninterrupted pilus extension, leading to hyperpiliation. However, in the MSHA pilus system of V. cholerae, deletion of the retraction motor, pilT, results in a decrease in the number of surface pili. Here, we show that PilT is unexpectedly required for MSHA pilus extension in addition to its defined role in promoting pilus retraction. These results extend our understanding of the complex mechanisms underlying the dynamic activity of these broadly conserved filamentous appendages.

microbiology↗

bioRxiv2022

Membrane wetting, molding and reticulation by protein condensates

Cells compartmentalize their components in liquid-like condensates, which can be reconstituted in vitro. Although these condensates interact with membrane-bound organelles, the potential of membrane remodeling and the underlying mechanisms are not well understood. Here, we demonstrate that interactions between protein condensates (including hollow ones) and membranes can lead to remarkable morphological transformations and describe these with theory. Modulation of solution salinity or membrane composition drives the condensate-membrane system through two wetting transitions, from dewetting, through a broad regime of partial wetting, to complete wetting. A new phenomenon, namely fingering or ruffling of the condensate-membrane interface is observed when sufficient membrane area is available, producing intricately curved structures. The observed morphologies are governed by the interplay of adhesion, membrane elasticity, and interfacial tension. Our results highlight the relevance of wetting in cell biology, and pave the way for the design of synthetic membrane-droplet based biomaterials and compartments with tunable properties.

biophysics↗

bioRxiv2022

Temporal and spatial frameworks supporting plant responses to vegetation proximity

After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). The shade-induced de-repression of active phytochrome B (phyB) releases the repression imposed over the PHYTOCHROME INTERACTING FACTORs (PIFs). In Arabidopsis thaliana seedlings, this mechanism triggers rapid and massive changes in gene expression, increases auxin production in a SHADE AVOIDANCE 3-dependent manner and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response repressing it. However, it is less clear how phyA and HY5 interact with PIFs to regulate this response. Our physiological, genetic, cell biology and transcriptomic analyses showed that these components are organized in two main branches, and incorporate into the model for the regulation of shade-induced hypocotyl elongation the temporal and spatial functional importance of the various SAS regulators analyzed in here. They also indicated that PIFs and HY5, belonging to separate branches, target common genes whose expression is rapidly modulated by shade. This transcriptional relationship, however, changes after longer shade-treatments, suggesting that it is a dynamic convergence point to modulate the hypocotyl elongation.

plant biology↗

bioRxiv2022

CaMKII binding to GluN2B flips a β-adrenergic switch from synaptic depression to potentiation

Learning, memory and cognition are thought to require forms of synaptic plasticity such as hippocampal long-term potentiation and depression (LTP and LTD), and such plasticity can be modulated by {beta}-adrenergic stimulation with isoproterenol or norepinephrine. For instance, LTP versus LTD is induced by high-versus low-frequency stimulation (HFS versus LFS) but, stimulating {beta}-adrenergic receptors ({beta}ARs) enables LTP induction also by LFS. In contrast to HFS-LTP, such {beta}AR-LTP requires signaling by L-type voltage-gated Ca2+-channels, not NMDA-type glutamate receptors (NMDARs). Surprisingly, we found that {beta}AR-LTP still required a non-ionotropic NMDAR function: the stimulus-induced binding of the Ca2+/calmodulin-dependent protein kinase II (CaMKII) that mediates CaMKII movement to excitatory synapses. In hippocampal neurons, {beta}-adrenergic stimulation with isoproterenol transformed LTD-type CaMKII movement to LTP-type movement, resulting in CaMKII movement to excitatory instead of inhibitory synapses. Additionally, isoproterenol enabled induction of a major cell-biological feature of LTP in response to LTD stimuli: increased SEP-GluA1 surface expression. Like for the {beta}AR-LTP in hippocampal slices, the effects of isoproterenol on CaMKII movement and SEP-GluA1 surface expression involved L-type Ca2+-channels. Taken together, these results indicate that isoproterenol transforms LTD stimuli to LTP signals by switching CaMKII movement and GluN2B binding to LTP mode. One Sentence SummaryBuonarati et al. show that {beta}-adrenergic stimulation enables LTP induction in response to LTD stimuli by switching synaptic CaMKII movement to LTP mode.

neuroscience↗

bioRxiv2022

Gamma-interferon-inducible lysosomal thiol reductase maintains cardiac immuno-metabolic homeostasis in heart failure

BackgroundThe lysosome is a central player in maintaining immuno-metabolic homeostasis. However, mechanistic insights into the regulation of lysosome-dependent immuno-metabolism in the heart are lacking. Lysosomal reductase Gamma Interferon-Inducible Thiol Reductase (GILT) is the only identified lysosomal reductase that controls diverse sets of lysosomal enzymes and cargoes. MethodsThe role of cardiac GILT was assessed by generating a novel genetic mouse model and employing a multidisciplinary approach including surgical interventions, live in situ high resolution microscopy, whole-tissue respirometry analysis, unbiased transcriptomic and metabolomic analyses, and various cell biology and biochemical assays. ResultsWe found that expression and activity of GILT are reduced in hearts from humans and mice with heart failure (HF). Mice with cardiac specific loss of GILT develop late onset systolic HF at baseline. In the setting of nutrient-overload and experimental left ventricular pressure overload conditions, loss of GILT in cardiomyocytes accelerates the development of heart dysfunction. Transcriptomic and metabolic analyses further revealed that cardiac GILT deficiency alters adaptive immuno-metabolic signatures in the heart. Finally, at the cellular level, cardiac GILT deletion impaired mitochondrial respiration, which was in part due to NLR Family Pyrin Domain Containing 3 (NLRP3)-mediated elevation of mitochondrial oxidative stress. ConclusionsTogether, these findings identify a causal link between a lysosome-inflammation axis, mitochondrial function and heart failure. Elucidation of these mechanisms will identify novel therapeutic strategies for treating HF.

molecular biology↗

bioRxiv2022

Afadin and zyxin contribute to coupling between cell junctions and contractile actomyosin networks during apical constriction

One of the most common cell shape changes driving morphogenesis in diverse animals is the constriction of the apical cell surface. Apical constriction depends on contraction of an actomyosin network in the apical cell cortex, but such actomyosin networks have been shown to undergo continual, conveyor belt-like contractions before the shrinking of an apical surface begins. This finding suggests that apical constriction is not necessarily triggered by the contraction of actomyosin networks, but rather can be triggered by unidentified, temporally-regulated mechanical links between actomyosin and junctions. Here, we used C. elegans gastrulation as a model to seek genes that contribute to such dynamic linkage. We found that -catenin and {beta}-catenin initially failed to move centripetally with contracting cortical actomyosin networks, suggesting that linkage is regulated between intact cadherin-catenin complexes and actomyosin. We used proteomic and transcriptomic approaches to identify new players, including the candidate linkers AFD-1/afadin and ZYX-1/zyxin, as contributing to C. elegans gastrulation. We found that ZYX-1/zyxin is among a family of LIM domain proteins that have transcripts that become enriched in multiple cells just before they undergo apical constriction. We developed a semi-automated image analysis tool to describe rates of myosin and membrane movement, which we then used to discover that ZYX-1/zyxin contributes to cell-cell junctions centripetal movement in concert with contracting actomyosin networks. These results identify several new genes that contribute to C. elegans gastrulation, and they identify zyxin as a key protein important for actomyosin networks to effectively pull cell-cell junctions inward during apical constriction. The transcriptional upregulation of ZYX-1/zyxin in specific cells in C. elegans points to one way that developmental patterning spatiotemporally regulates cell biological mechanisms in vivo. Because zyxin and related proteins contribute to membrane-cytoskeleton linkage in other systems, we anticipate that its roles in regulating apical constriction in this manner may be conserved.

genetics↗

bioRxiv2022

Sequence analysis and structural predictions of lipid transfer bridges in the repeating beta groove (RBG) superfamily reveals past and present domain variations affecting form, function and interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek

Lipid transfer between organelles requires proteins that shield the hydrophobic portions of lipids as they cross the cytoplasm. In the last decade a new structural form of lipid transfer protein (LTP) has been found: long hydrophobic grooves made of beta-sheet that bridge between organelles at membrane contact sites. Eukaryotes have five families of bridge-like LTPs: VPS13, ATG2, SHIP164, Hobbit and Tweek. These are unified into a single superfamily through their bridges being composed of just one domain, called the repeating beta groove (RBG) domain, which builds into rod shaped multimers with a hydrophobic-lined groove and hydrophilic exterior. Here, sequences and predicted structures of the RBG superfamily were analyzed in depth. Phylogenetics showed that the last eukaryotic common ancestor contained all five RBG proteins, with duplicate VPS13s. These appear to have arisen in even earlier ancestors from shorter forms with 4 RBG domains. The extreme ends of most RBG proteins have amphipathic helices that might be an adaptation for direct or indirect bilayer interaction, although this has yet to be tested. The one exception to this is the C-terminus of SHIP164, which instead has a coiled-coil. Finally, almost the entire length of the exterior surfaces of the RBG bridges are shown to have conserved residues, indicating sites for partner interactions almost all of which are unknown. These findings can inform future cell biological and biochemical experiments.

bioinformatics↗

bioRxiv2022

An optimised transformation protocol for Anthoceros agrestis and three more hornwort species

Land plants comprise two large monophyletic lineages, the vascular plants and the bryophytes, which diverged from their most recent common ancestor approximately 480 million years ago. Of the three lineages of bryophytes, only the mosses and the liverworts are systematically investigated, while the hornworts are understudied. Despite their importance for understanding fundamental questions of land plant evolution, they only recently became amenable to experimental investigation, with Anthoceros agrestis being developed as a hornwort model system. Availability of a high quality genome assembly and a recently developed genetic transformation technique makes A. agrestis an attractive model species for hornworts. Here we describe an updated and optimised transformation protocol for A. agrestis which can be successfully used to genetically modify one more strain of A. agrestis and three more hornwort species, Anthoceros punctatus, Leiosporoceros dussi and Phaeoceros carolinianus. The new transformation method is less laborious, faster and results in the generation of greatly increased numbers of transformants compared to the previous method. We have also developed a new selection marker for transformation. Finally, we report the development of a set of different cellular localisation signal peptides for hornworts providing new tools to better understand hornwort cell biology.

plant biology↗

bioRxiv2022

Dermal appendage-dependent patterning of zebrafish atoh1a+ Merkel cells

Touch system function requires precise interactions between specialized skin cells and somatosensory axons, as exemplified by the vertebrate mechanosensory Merkel cell-neurite complex. Development and patterning of Merkel cells and associated neurites during skin organogenesis remains poorly understood, partly due to the in utero development of mammalian embryos. Here, we discover Merkel cells in the zebrafish epidermis and identify Atonal homolog 1a (Atoh1a) as a marker of zebrafish Merkel cells. We show that zebrafish Merkel cells derive from basal keratinocytes, express neurosecretory and mechanosensory machinery, extend actin-rich microvilli, and complex with somatosensory axons, all hallmarks of mammalian Merkel cells. Merkel cells populate all major adult skin compartments, with region-specific densities and distribution patterns. In vivo photoconversion reveals that Merkel cells undergo steady loss and replenishment during skin homeostasis. Merkel cells develop concomitant with dermal appendages along the trunk, and preventing dermal appendage formation reduces Merkel cell density by affecting both cell differentiation and maintenance. By contrast, altering dermal appendage morphology changes the distribution, but not density, of Merkel cells. Overall, our studies provide insights into touch system maturation during skin organogenesis and establish zebrafish as an experimentally accessible in vivo model for the study of Merkel cell biology.

developmental biology↗

bioRxiv2022

SEC-seq: Association of molecular signatures with antibody secretion in thousands of single human plasma cells

Protein secretion drives many functions in vivo; however, methods to link secretions with surface markers and transcriptomes have been lacking. By accumulating secretions close to secreting cells held within cavity-containing hydrogel nanovials, we demonstrate workflows to analyze the amount of IgG secreted from single human antibody-secreting cells and link this information to surface marker expression and transcriptional profiles from the same cells. Measurements using flow cytometry and imaging flow cytometry corroborated an association between levels of IgG secretion and CD138 expression. Using oligonucleotide-labeled antibodies and droplet-based sequencing, we show that pathways encoding protein localization to the endoplasmic reticulum, NADH complex assembly, and mitochondrial respiration were most associated with high IgG secretion. Altogether, this method links secretion information to cell surface and single-cell sequencing information (SEC-seq) and enables exploration of links between genome and secretory function, laying the foundation for numerous discoveries in immunology, stem cell biology, and beyond.

bioengineering↗

bioRxiv2022

Structural studies reveal that endosomal cations promote formation of infectious CVA9 A particles, facilitating RNA and VP4 release.

Coxsackievirus A9, an enterovirus, is a common cause of paediatric aseptic meningitis and neonatal sepsis. During cell entry, enterovirus capsids undergo conformational changes leading to expansion, formation of large pores, externalization of VP1 N-termini and loss of the lipid factor from VP1. Factors such as receptor binding, heat, and acidic pH can trigger capsid expansion in some enteroviruses. Here we show that fatty-acid free bovine serum albumin or neutral endosomal ionic conditions can independently prime CVA9 for expansion and genome release. Our results show that CVA9 treatment with albumin or endosomal ions generates a heterogeneous population of virions, which could be physically separated by asymmetric flow field flow fractionation and computationally by cryo-EM and image processing. We report cryo-EM structures of CVA9 A-particles obtained by albumin or endosomal ion treatment and a control non-expanded virion to 3.5, 3.3 and 2.9 [A] resolutions, respectively. Where albumin promotes stabile expanded virions, the endosomal ionic concentrations induce unstable CVA9 virions which easily disintegrate losing their genome. Loss of most of the VP4 molecules and exposure of negatively-charged amino acid residues in the capsids interior after expansion, create a repulsive viral RNA-capsid interface, aiding genome release. ImportanceCoxsackievirus A9 (CVA9) is a common cause of meningitis and neonatal sepsis. The triggers and mode of action of RNA release into the cell unusually do not require receptor interaction. Rather, a slow process in the endosome, independent of low pH is required. Here, we show by biophysical separation, cryogenic electron microscopy and image reconstruction that albumin and buffers mimicking the endosomal ion composition can separately and together expand and prime CVA9 for uncoating. Furthermore, we show in these expanded particles that VP4 is present at only ~10% of the occupancy found in the virion, VP1 is externalised and the genome is repelled by the negatively-charged, repulsive inner surface of the capsid that occurs due to the expansion. Thus, we can now link observations from cell biology of infection with the physical processes that occur in the capsid to promote genome uncoating.

microbiology↗

bioRxiv2022

Organization and regulation of nuclear condensates by gene activity

Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties characteristic of nuclear condensates are shaped by genome organization and activity is poorly understood. Here, we develop a physics-based model to interrogate this interplay between condensation, active transcription, and genome organization. We show that spatial clustering of active genes enables precise localization and de novo nucleation of condensates. We find that strong clustering and activity drives aspherical condensate morphologies. Condensates flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, genome structure, and multicomponent condensates in cell biology.

biophysics↗