Biology subjects

Chenoweth, D. M.

Publications and source records attributed to Chenoweth, D. M..

17 recordsLinked to original sources

bioRxiv2026

Mechanism-Based Discovery of New TRIDs Targeting Ribosome Pockets

Approximately 10% of all human pathogenic mutations are nonsense mutations which give rise to premature termination codon (PTC) diseases, leading to an estimated 35 million people worldwide who harbor such mutations. To date, no approaches leading to medical treatments which increase PTC readthrough have received FDA approval. However, one well-tolerated translation readthrough inducing drug (TRID), ataluren, was conditionally approved for 11 years by the European Medicines Agency for treatment of nonsense mutation Duchenne Muscular Dystrophy. In recent work we have shown that ataluren increases readthrough indirectly, by exclusively inhibiting termination without directly affecting readthrough by suppressor aminoacyl-tRNAs (sup-aa-tRNAs). Based on the idea that this mode of action (MoA) might be the reason for the low toxicity of ataluren, we have discovered potential new TRIDs, which target pockets within the ribosome to which the termination factor eRF1 binds but sup-aa-tRNAs do not. These new TRIDs, dipeptide derivatives of eRF1 and some Sartans, mimic the MoA of ataluren. Three Sartans, which are angiotensin II receptor blockers and FDA-approved for treatment of hypertension, are significantly more potent than ataluren in our reconstituted in vitro readthrough assay. These compounds might be more effective than ataluren in treating some PTC diseases. We anticipate that further development of these lead compounds will lead to more general effectiveness, used both alone and in combination with other classes of readthrough inducers.

biochemistry↗

bioRxiv2026

RNA-binding proteins activate transcription through defined molecular grammars

Transcription factors (TFs) regulate gene expression through interactions with DNA, RNA, and proteins. RNA-binding proteins (RBPs) also assemble near regulatory elements and mediate RNA processing, yet their perturbation causes transcriptional defects. Here, we find select RBPs activate transcription through latent activation domains akin to TFs. RBP activators regulate distinct genes and interact with transcriptional condensates. Their activation domains are enriched in aromatic and polar residues but depleted of basic residues - essential features that are conserved and partially mimic TF activation domains. We validated additional RBP activators across the human proteome based on this molecular grammar, including the C-terminal domain (CTD) of RPB1, the catalytic subunit of RNA polymerase II. RPB1-CTD activates transcription by recruiting coactivators, demonstrating a non-enzymatic function in transcriptional regulation. These findings position RBPs and RPB1 as transcriptional regulators, explain coupling between transcription and RNA processing, and reveal RNA-RBP regulatory networks that parallel DNA-TF networks.

molecular biology↗

bioRxiv2025

Coiled-coil interactions drive ectopic condensation of overexpressed MAD1 to promote mitotic slippage in cancer cells

The mitotic checkpoint protein MAD1 is significantly overexpressed in several cancers, weakening the checkpoint and promoting mitotic slippage. Overexpressed MAD1 forms ectopic foci in mitotic cells, yet the biophysical nature of these foci and their contributions to mitotic slippage remain unclear. Here, we report that MAD1 foci are phase-separated condensates that shorten the mitotic duration by sequestering checkpoint proteins. Our biophysical quantifications reveal that MAD1 ectopic foci in mitotic cells exhibit dynamic condensate properties rather than those of a solid aggregate. Using an inducible phase separation assay in live cells, we show that MAD1 phase separation is driven by interactions between its coiled-coil and disordered domains at the N-terminus. We decouple the contributions of condensation from concentration by inducing the formation of MAD1 ectopic condensates in mitotic cells with low levels of MAD1, demonstrating that the condensation process directly drives mitotic slippage. Mechanistically, the MAD1 ectopic condensate traps the diffusive pool of MAD2, an interaction partner of MAD1, thereby weakening the MAD2 conversion cycle necessary for a robust mitotic checkpoint. Our work illustrates a loss of function caused by ectopic condensates in MAD1-overexpressed cancer cells.

cell biology↗

bioRxiv2025

Herpes simplex virus-1 fluidizes the nucleus enabling condensate formation

Molecular processes are profoundly influenced by the biophysical properties of the cell interior. However, the mechanisms that control these physical properties, and the processes they impact remain poorly understood, especially in the nucleus. We hypothesized that some viruses might change the biophysical properties of the nucleus to favor virus survival and replication and found that herpes simplex virus 1 (HSV-1) increases the mesoscale fluidity of the nucleus. The HSV-1 protein ICP4 caused fluidization and enabled growth of synthetic nuclear condensates. Conversely, conditions that decreased nuclear fluidity inhibited the growth of viral replication compartment condensates and reduced infectious virus production. Together, our data suggest that ICP4 increases nuclear fluidity to promote the formation of condensates that drive the progression of the HSV-1 life cycle. We speculate that a key function of ICP4 is to overcome the crowding and elastic confinement within cell nuclei that are a fundamental barrier to virus replication.

cell biology↗

bioRxiv2025

Telomeric SUMO level influences the choices of APB formation pathways and ALT efficiency

Many cancers use an alternative lengthening of telomeres (ALT) pathway for telomere maintenance. ALT telomeric DNA synthesis occurs in ALT telomere-associated PML bodies (APBs). However, the mechanisms by which APBs form are not well understood. Here, we monitored the formation of APBs with time-lapse imaging employing CRISPR knock-in to track the promyelocytic leukemia (PML) protein at endogenous levels. We found APBs form via two pathways: telomeres recruit PML proteins to nucleate PML bodies de novo, or telomeres fuse with preformed PML bodies. Both nucleation and fusion of APBs require interactions between SUMO and SUMO interaction motifs (SIMs). Moreover, APB nucleation is associated with higher levels of SUMOs and SUMO-mediated recruitment of DNA helicase BLM, resulting in more robust telomeric DNA synthesis. Finally, further boosting SUMO levels at telomeres enhances APB nucleation, BLM enrichment, and telomeric DNA synthesis. Thus, high SUMO levels at telomeres promote APB formation via nucleation, resulting in stronger ALT activity.

cell biology↗

bioRxiv2024

A toolbox for ablating excitatory and inhibitory synapses

Recombinant optogenetic and chemogenetic proteins are potent tools for manipulating neuronal activity and controlling neural circuit function. However, there are few analogous tools for manipulating the structure of neural circuits. Here, we introduce three rationally designed genetically encoded tools that use E3 ligase-dependent mechanisms to trigger the degradation of synaptic scaffolding proteins, leading to functional ablation of synapses. First, we developed a constitutive excitatory synapse ablator, PFE3, analogous to the inhibitory synapse ablator GFE3. PFE3 targets the RING domain of the E3 ligase Mdm2 and the proteasome-interacting region of Protocadherin 10 to the scaffolding protein PSD-95, leading to efficient ablation of excitatory synapses. In addition, we developed a light-inducible version of GFE3, paGFE3, using a novel photoactivatable complex based on the photocleavable protein PhoCl2c. paGFE3 degrades Gephyrin and ablates inhibitory synapses in response to 400 nm light. Finally, we developed a chemically inducible version of GFE3, chGFE3, which degrades inhibitory synapses when combined with the bio-orthogonal dimerizer HaloTag ligand-trimethoprim. Each tool is specific, reversible, and capable of breaking neural circuits at precise locations.

neuroscience↗

bioRxiv2024

Conditional Localization Pharmacology Manipulates the Cell Cycle with Spatiotemporal Precision

Traditional pharmacology has limited control of drug activity and localization in space and time. Herein, we described an approach for kinase regulation using conditional localization pharmacology (CLP), where an inactive caged inhibitor is localized to a site of interest in a dormant state using intracellular protein tethering. The activity of the inhibitor can be regulated with spatial and temporal precision in a live cellular environment using light. As a proof of concept, a photocaged MPS1 kinase inhibitor (reversine) bearing a Halo-tag ligand tether was designed to manipulate the cell cycle. We demonstrate that this new caged reversine halo probe (CRH) strategy is capable of efficient localization and exceptional spatiotemporal control over spindle assembly checkpoint (SAC) silencing and mitotic exit. Table of Contents artwork O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/612697v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@cd44f8org.highwire.dtl.DTLVardef@6b14f7org.highwire.dtl.DTLVardef@2d8945org.highwire.dtl.DTLVardef@18f4985_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

The central spindle drives anaphase chromosome segregation

Anaphase chromosome segregation depends on forces exerted by spindle microtubules. Current models propose two mechanisms of force generation: kinetochore microtubules (kMTs) depolymerize to pull chromosomes toward the spindle poles (anaphase A), while antiparallel microtubule sliding in the central spindle further separates the chromosomes by elongating the spindle (anaphase B). Experimental evidence in cells supports the sliding mechanism, but contributions of the depolymerization mechanism remain unclear. Here we show that kMT depolymerization limits spindle elongation rather than moving chromosomes apart. We developed a chemical optogenetic approach to recruit a microtubule depolymerase to kinetochores at anaphase onset, thereby increasing the rate of kMT depolymerization without perturbing earlier stages of mitosis. We find that increased depolymerization slows the velocity at which spindle poles move apart without changing kinetochore separation velocities. Our findings support a model in which kinetochores selectively couple to central spindle microtubules parallel to their kMTs, so that antiparallel sliding drives chromosome segregation while kMT depolymerization pulls poles inward.

cell biology↗

bioRxiv2024

Interplay of condensate material properties and chromatin heterogeneity governs nuclear condensate ripening

Nuclear condensates play many important roles in chromatin functions, but how cells regulate their nucleation and growth within the complex nuclear environment is not well understood. Here, we report how condensate properties and chromatin mechanics dictate condensate growth dynamics in the nucleus. We induced condensates with distinct properties using different proteins in human cell nuclei and monitored their growth. We revealed two key physical mechanisms that underlie droplet growth: diffusion-driven or ripening-dominated growth. To explain the experimental observations, we developed a quantitative theory that uncovers the mechanical role of chromatin and condensate material properties in regulating condensate growth in a heterogeneous environment. By fitting our theory to experimental data, we find that condensate surface tension is critical in determining whether condensates undergo elastic or Ostwald ripening. Our model also predicts that chromatin heterogeneity can influence condensate nucleation and growth, which we validated by experimentally perturbing the chromatin organization and controlling condensate nucleation. By combining quantitative experimentation with theoretical modeling, our work elucidates how condensate surface tension and chromatin heterogeneity govern nuclear condensate ripening, implying that cells can control both condensate properties and the chromatin organization to regulate condensate growth in the nucleus.

biophysics↗

bioRxiv2024

SUMO Promotes DNA Repair Protein Collaboration to Support Alterative Telomere Lengthening in the Absence of PML

Alternative lengthening of telomeres (ALT) pathway maintains telomeres in a significant fraction of cancers associated with poor clinical outcomes. A better understanding of ALT mechanisms can provide a basis for developing new treatment strategies for ALT cancers. SUMO modification of telomere proteins plays a critical role in the formation of ALT telomere-associated PML bodies (APBs), where telomeres are clustered and DNA repair proteins are enriched to promote homology-directed telomere DNA synthesis in ALT. However, whether and how SUMO contributes to ALT beyond APB formation remains elusive. Here, we report that SUMO promotes collaboration among DNA repair proteins to achieve APB-independent telomere maintenance. By using ALT cancer cells with PML protein knocked out and thus devoid of APBs, we show that sumoylation is required for manifesting ALT features, including telomere clustering and telomeric DNA synthesis, independent of PML and APBs. Further, small molecule-induced telomere targeting of SUMO produces signatures of phase separation and ALT features in PML null cells in a manner depending on both sumoylation and SUMO interaction with SUMO interaction motifs (SIMs). Mechanistically, SUMO-induced effects are linked to the enrichment of DNA repair proteins, including Rad52, Rad51AP1, and BLM, to the SUMO-containing telomere foci. Finally, we find that Rad52 can undergo phase separation, enrich SUMO on telomeres, and promote telomere DNA synthesis in collaboration with the BLM helicase in a SUMO-dependent manner. Collectively, our findings suggest that, in addition to forming APBs, SUMO also promotes collaboration among DNA repair proteins to support telomere maintenance in ALT cells. Given the promising effects of sumoylation inhibitors in cancer treatment, our findings suggest their potential use in perturbing telomere maintenance in ALT cancer cells.

cell biology↗

bioRxiv2023

'Off-pore' nucleoporins relocalize heterochromatic breaks through phase separation

Phase separation forms membraneless compartments in the nuclei, including by establishing heterochromatin "domains" and repair foci. Pericentromeric heterochromatin mostly comprises repeated sequences prone to aberrant recombination, and "safe" homologous recombination (HR) repair of these sequences requires the movement of repair sites to the nuclear periphery before Rad51 recruitment and strand invasion. How this mobilization initiates is unknown, and the contribution of phase separation to these dynamics is unclear. Here, we show that Nup98 nucleoporin is recruited to heterochromatic repair sites before relocalization through Sec13 or Nup88 nucleoporins, and downstream from the Smc5/6 complex and SUMOylation. Remarkably, the phase separation properties of Nup98 are required and sufficient to mobilize repair sites and exclude Rad51, thus preventing aberrant recombination while promoting HR repair. Disrupting this pathway results in heterochromatin repair defects and widespread chromosome rearrangements, revealing a novel "off-pore" role for nucleoporins and phase separation in nuclear dynamics and genome integrity in a multicellular eukaryote. HighlightsO_LINup88 and Sec13 recruit Nup98 to heterochromatic DSBs downstream from Smc5/6 C_LIO_LINup88, Sec13 and Nup98 promote repair focus mobilization in heterochromatin off-pore C_LIO_LINup98 excludes Rad51 from repair sites inside the heterochromatin domain C_LIO_LIPhase separation by Nup98 is required and sufficient for relocalization and Rad51 exclusion C_LI

cell biology↗

bioRxiv2023

Pan-tissue scaling of stiffness versus fibrillar collagen reflects contractility-driven strain that inhibits fibril degradation

Polymer network properties such as stiffness often exhibit characteristic power laws in polymer density and other parameters. However, it remains unclear whether diverse animal tissues, composed of many distinct polymers, exhibit such scaling. Here, we examined many diverse tissues from adult mouse and embryonic chick to determine if stiffness (Etissue) follows a power law in relation to the most abundant animal protein, Collagen-I, even with molecular perturbations. We quantified fibrillar collagen in intact tissue by second harmonic generation (SHG) imaging and from tissue extracts by mass spectrometry (MS), and collagenase-mediated decreases were also tracked. Pan-tissue power laws for tissue stiffness versus Collagen-I levels measured by SHG or MS exhibit sub-linear scaling that aligns with results from cellularized gels of Collagen-I but not acellular gels. Inhibition of cellular myosin-II based contraction fits the scaling, and combination with inhibitors of matrix metalloproteinases (MMPs) show collagenase activity is strain - not stress- suppressed in tissues, consistent with past studies of gels and fibrils. Beating embryonic hearts and tendons, which differ in both collagen levels and stiffness by >1000-fold, similarly suppressed collagenases at physiological strains of [~]5%, with fiber-orientation regulating degradation. Scaling of Etissue based on use-it-or-lose-it kinetics provides insight into scaling of organ size, microgravity effects, and regeneration processes while suggesting contractility-driven therapeutics.

molecular biology↗

bioRxiv2021

CRISPR Cas13-based tools to track and manipulate endogenous telomeric repeat-containing RNAs in living cells

TERRA, TElomeric Repeat-containing RNA, is a long non-coding RNA transcribed from telomeres. Emerging evidence indicates that TERRA regulates telomere maintenance and chromosome end protection in normal and cancerous cells. However, the mechanism of how TERRA contributes to telomere functions is still unclear, partially owing to the shortage of approaches to track and manipulate endogenous TERRA molecules in live cells. Here, we developed a method to visualize TERRA in live cells via a combination of CRISPR Cas13 RNA labeling and Suntag technology. Single-particle tracking reveals that TERRA foci undergo anomalous diffusion in a manner that depends on the timescale and telomeric localization. Furthermore, we used a chemically-induced protein dimerization system to manipulate TERRA subcellular localization in live cells. Overall, our approaches to monitor and control TERRA locations in live cells provide powerful tools to better understand its roles in telomere maintenance and genomic integrity.

cell biology↗

bioRxiv2021

Heterogeneous strains in tissue collagen show that high strains locally suppress degradation by collagenase

Collagen, the most abundant protein in mammals, contributes to the physical properties of different tissues during development, homeostasis, and disease. The adaptation of physical properties of tissues to mechanical stimuli is thus dependent on the control of tissue collagen levels by well-regulated synthesis and degradation of collagen. Importantly, how various molecular-level events within a tissue sustaining a range of mechanical strains contribute towards maintaining its collagen levels, remains unclear to date. Such molecular level processes in tissues are studied here in the case of isolated tendons consisting of collagen fibrils oriented along tissue loading-axis and beating embryonic hearts to gain understanding of mechanical load dependent tissue sculpting. Using a novel bioreactor design, starved mice tail tendon fascicles were used as a "cell-free" model and were subjected to heterogeneous and uniaxial deformation modes. Patterned photobleaching of fluorescent probes, a novel Aza-peptide or dye, on fascicles used to quantify tissue strains. Tissue microstructure was simultaneously imaged using second harmonic generation (SHG) signal to assess tissue collagen content while deformed fascicle samples were exposed to purified matrix metalloproteinase-1 (MMP-1) or bacterial collagenase (BC). A decrease in the degradation rate (relative to strain-free) was observed for physiological strain limits of tendon tissue (i.e. [~]5-8%) while at higher strains (i.e. pathological) the degradation rate was independent of strain magnitude changes. Interestingly, the strain dependence of degradation rate was independent of cleavage-site specificity of the collagenase molecules and the mode of tendon tissue deformation. Although spatially different within a tissue sample, the values of strain, degradation rate and collagen fiber organization with time during degradation of each tendon fascicle region were highly correlated. Tendon regions dominated by collagen fibers inclined to fascicle-axis were observed to follow non-affine deformation. The dependence of the degradation rate on mechanical strain is due to sequestration of collagen cleavage sites within fibrils. Permeation, tissue mass density and mobility of fluorescent collagenase and dextran are strain-independent for fascicle strains up to [~]5-8% while the degradation rate is positively correlated to unfolded triple-helical collagen content. Normal beating chick hearts subjected to [~]5% peak strain in a spatiotemporal coordinate contractile wave were observed to maintain their collagen mass until the beating strain is suppressed by inhibition of myosin-II. Based on the presence of exogeneous MMP inhibitors, endogenous MMPs within the non-beating hearts degrade the collagens immediately (in [~]30-60 mins). Both tissue systems under mechanical strains suggest degradative sculpting where mechanical strain-dependent collagen fibril architecture changes appear to play a key role in determining collagen lifetime within tissues. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=139 HEIGHT=200 SRC="FIGDIR/small/430141v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@17da11borg.highwire.dtl.DTLVardef@dbfb8forg.highwire.dtl.DTLVardef@6069b9org.highwire.dtl.DTLVardef@1bd273e_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Tension promotes kinetochore-microtubule release in response to Aurora B activity

Aurora B kinase regulates kinetochore-microtubule interactions to ensure accurate chromosome segregation in cell division. Tension provides a signal to discriminate attachment errors from bi-oriented kinetochores with sisters correctly attached to opposite spindle poles. Current models focus on tension as an input to locally regulate Aurora B activity. Here we show that the outcome of Aurora B activity depends on tension. Using an optogenetic approach to manipulate Aurora B at individual kinetochores, we find that kinase activity promotes microtubule release when tension is high. Conversely, when tension is low, Aurora B activity promotes depolymerization of kinetochore-microtubule bundles while maintaining attachment. We propose that tension is a signal inducing distinct error-correction mechanisms, with release or depolymerization advantageous for typical errors characterized by high or low tension, respectively.

cell biology↗

bioRxiv2019

Liquid condensation drives telomere clustering during ALT

Telomerase-free cancer cells employ a recombination-based alternative lengthening of telomeres (ALT) pathway that depends on ALT-associated promyelocytic leukemia (PML) nuclear bodies (APBs), whose function is unclear. We find that APBs behave as liquid condensates, suggesting two potential mechanisms to promote telomere elongation: condensation to enrich DNA repair factors for telomere synthesis and coalescence to cluster telomeres to provide repair templates. Using chemically-induced dimerization, we show that telomere sumoylation nucleates APB condensation via SUMO-SIM (SUMO interaction motif) interactions and clusters telomeres. The induced APBs lack DNA repair factors, indicating that these factors are clients recruited to the APB scaffold rather than components that drive condensation. Telomere clustering, however, relies only on liquid properties of the condensate, as an alternative condensation chemistry also induces clustering. Our results demonstrate how the material properties and chemical composition of APBs independently contribute to ALT, suggesting a general framework for how liquid condensates promote cellular functions.

cancer biology↗

bioRxiv2017

Spindle asymmetry drives non-Mendelian chromosome segregation

Genetic elements compete for transmission through meiosis, when haploid gametes are created from a diploid parent. Selfish elements can enhance their transmission through meiotic drive, in violation of Mendels Law of Segregation. In female meiosis, selfish elements drive by preferentially attaching to the egg side of the spindle, which implies some asymmetry between the two sides of the spindle, but molecular mechanisms underlying spindle asymmetry are unknown. Here we show that CDC42 signaling from the cell cortex regulates microtubule tyrosination to induce spindle asymmetry, and non-Mendelian segregation depends on this asymmetry. These signals depend on cortical polarization directed by chromosomes, which are positioned near the cortex to allow the asymmetric cell division. Thus, selfish meiotic drivers exploit the asymmetry inherent in female meiosis to bias their transmission.

cell biology↗