Biology subjects

Comi, T. J.

Publications and source records attributed to Comi, T. J..

6 recordsLinked to original sources

bioRxiv2026

Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer

Cell growth requires elevated protein synthesis, which depends on the production of ribosomes. Ribosome biogenesis is a complex, multi-step pathway in which newly transcribed precursor ribosomal RNA (rRNA) undergoes coordinated processing and assembly in the nucleolus to produce the small and large ribosomal subunits (SSU and LSU).1-3 Oncogene activation stimulates rRNA transcription and processing, giving rise to enlarged nucleoli that produce thousands of ribosomes every minute.4,5 However, efficient ribosome production requires tight coordination across numerous maturation steps, and it remains unclear if elevated rDNA transcription is proportionally converted into mature ribosomes, or whether imperfect coordination constrains the output yield. Here, we quantify pre-rRNA transcription (input) and compare it with newly-assembled cytoplasmic ribosomes (output), revealing that oncogene activation reduces the efficiency of ribosome production. Using a quantitative pulse-chase sequencing approach with mathematical modeling to resolve rRNA maturation kinetics, we found that oncogene activation creates late-stage processing bottlenecks, characterized by delayed precursor maturation and increased degradation. Perturbation of late-stage ribosome biogenesis factors preferentially impaired oncogene-driven cell growth, and limited tumor growth in mouse models, suggesting that these bottlenecks represent selective vulnerabilities in cancer, created by imbalanced biosynthetic flux. Together, these findings reveal that oncogene-driven ribosome production is imperfectly coordinated across maturation steps, and suggest that capacity limits in multi-step assembly pathways may be therapeutically exploitable in cancer and other diseases.

cell biology↗

bioRxiv2026

Ribosome Molecular Aging Shapes Translation Dynamics

Cellular homeostasis relies on continual renewal of cellular components, yet some complexes like ribosomes persist for long periods, raising the question of whether extended molecular age impacts functional fidelity. Here, we introduce a spatiotemporal mapping strategy to resolve biomolecular life stages, and show that intracellular ribosome aging alters translational dynamics at specific transcripts. Molecularly aged ribosomes exhibit impaired elongation at basic amino acid-rich sequences, leading to increased pausing, premature termination, and ribosome collisions. By profiling ribosomal RNA modifications, we find that molecular aging increases the collision propensity of specific ribosome subpopulations. Consistent with our findings, enrichment of aged ribosomes in cells amplifies molecular age-dependent translation defects. In vivo labeling of ribosomes in aged C. elegans demonstrates that molecularly aged ribosomes shape translational dynamics during organismal aging. These findings identify ribosome molecular age as a determinant of translational dynamics, and link molecular aging of a core gene-expression complex to organismal aging. HIGHLIGHTSO_LIA pulse-chase labeling strategy enables mapping subcellular demographics of macromolecular complexes in space and time. C_LIO_LIMolecular aging of ribosomes drives differential mRNA translation and shapes elongation dynamics. C_LIO_LIThe collision propensity of specific ribosome subpopulations increases with molecular age. C_LIO_LIOlder ribosomes shape translation dynamics during organismal aging. C_LI

cell biology↗

bioRxiv2025

Deep Learning of Functional Perturbations from Condensate Morphology

Biomolecular condensates compartmentalize the interior of living cells to spatiotemporally organize complex functions, yet linking molecular interactions within condensates to their mesoscale organization remains a major challenge. To bridge this gap, we developed a neural network-based framework - Deep-Phase - that uses microscopy images to quantitatively classify condensate morphology changes resulting from pharmacological alterations in associated biochemical processes. We use Deep-Phase to precisely quantify time- and concentration-dependent structural perturbations to the multiphase nucleolus and show that they are tightly coupled to potencies of drugs inhibiting rRNA transcription and processing. Applying Deep-Phase in a chemical screen, we identify a unique nucleolar morphology and discover a role for a DNA topoisomerase in rRNA processing. Mechanistic studies of this morphology provide insights into how interfaces between nucleolar subcompartments are maintained. We demonstrate Deep-Phases adaptability to diverse cell lines, labels, and condensates, offering a powerful platform for uncovering cellular organizing principles and therapeutic targets. HighlightsO_LIA deep learning framework, Deep-Phase, classifies and quantifies drug-induced changes in morphologies of nucleoli, nucleolar speckles, and viral cytoplasmic condensates, directly from images. C_LIO_LITime- and concentration-dependent morphological responses to perturbation predict associated disruptions in RNA transcription and processing. C_LIO_LIUsing Deep-Phase in a high-content small molecule screen reveals a unique nucleolar morphology induced by TOP1 inhibition. C_LIO_LITOP1 inhibition leads to reduced levels and processing of large ribosomal subunit precursors and provides a mechanism for maintenance of nucleolar phase boundaries. C_LI

molecular biology↗

bioRxiv2025

Genome-wide mapping of mesoscale neuronal RNA organization and condensation

Subcellular RNA organization can affect critical cellular functions. However, our understanding of RNA microenvironments, particularly biomolecular condensates, remains limited, largely due to a lack of technologies to comprehensively interrogate mesoscale RNA organization. Here, we adapt Split-Pool Recognition of Interactions by Tag Extension to map micron-scale RNA-RNA spatial proximity genome-wide across cell regions (RNA-SPRITE). Deploying RNA-SPRITE, we find extensive, conserved organization of mature mRNAs, with increased colocalization between mRNAs that share RNA-binding protein (RBP) motifs or encode functionally related proteins. Both effects are especially strong in dendrites and axons, suggesting prevalent mRNA co-regulation. Moreover, mRNAs with less compact folding, lower translation efficiency, and specific RBP motifs are more likely to be in RNA-rich condensates. However, perturbations that broadly dissolve or enhance condensation reveal that RBP motif and encoded protein-mediated colocalizations largely remain intact, independent of condensation. These results demonstrate the power of RNA-SPRITE in revealing critical aspects of RNAs functional organization. In BriefUnbiased, genome-wide maps of RNA-RNA mesoscale spatial proximity uncover extensive subcellular organization and its governing principles. HighlightsO_LIRNA-SPRITE reveals micron-scale RNA colocalization genome-wide across cell regions C_LIO_LImRNA colocalization specificity is driven by shared motifs and encoded protein function C_LIO_LImRNAs with less compact folding, lower translation efficiency, and distinct protein-binding motifs are more likely to be in condensates C_LIO_LINeurites have a particularly high degree of sequence and function-dependent mRNA organization C_LI

molecular biology↗

bioRxiv2024

Mapping and engineering RNA-controlled architecture of the multiphase nucleolus

Biomolecular condensates are key features of intracellular compartmentalization. As the most prominent nuclear condensate in eukaryotes, the nucleolus is a layered multiphase liquid-like structure and the site of ribosome biogenesis. In the nucleolus, ribosomal RNAs (rRNAs) are transcribed and processed, undergoing multiple maturation steps that ultimately result in formation of the ribosomal small subunit (SSU) and large subunit (LSU). However, how rRNA processing is coupled to the layered nucleolar organization is poorly understood due to a lack of tools to precisely monitor and perturb nucleolar rRNA processing dynamics. Here, we developed two complementary approaches to spatiotemporally map rRNA processing and engineer de novo nucleoli. Using sequencing in parallel with imaging, we found that rRNA processing steps are spatially segregated, with sequential maturation of rRNA required for its outward movement through nucleolar phases. Furthermore, by generating synthetic de novo nucleoli through an engineered rDNA plasmid system in cells, we show that defects in SSU processing can alter the ordering of nucleolar phases, resulting in inside-out nucleoli and preventing rRNA outflux, while LSU precursors are necessary to build the outermost layer of the nucleolus. These findings demonstrate how rRNA is both a scaffold and substrate for the nucleolus, with rRNA acting as a programmable blueprint for the multiphase architecture that facilitates assembly of an essential molecular machine.

cell biology↗

bioRxiv2020

Individual differences in honey bee (Apis mellifera) behavior enabled by plasticity in brain gene regulatory networks

Understanding the regulatory architecture of phenotypic variation is a fundamental goal in biology, but connections between gene regulatory network (GRN) activity and individual differences in behavior are poorly understood. We characterized the molecular basis of behavioral plasticity in queenless honey bee (Apis mellifera) colonies, where individuals engage in both reproductive and non-reproductive behaviors. Using high-throughput behavioral tracking, we discovered these colonies contain a continuum of phenotypes, with some individuals specialized for either egg-laying or foraging and "generalists" that perform both. Brain gene expression and chromatin accessibility profiles were correlated with behavioral variation, with generalists intermediate in behavior and molecular profiles. Models of brain GRNs constructed for individuals revealed that transcription factor (TF) activity was highly predictive of behavior, and behavior-associated regulatory regions had more TF motifs. These results provide new insights into the important role played by brain GRN plasticity in the regulation of behavior, with implications for social evolution.

genomics↗