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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2017

The spatial position of budding yeast chromosomes affects gene expression

The three-dimensional organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remains debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modelling and single cell imaging to determine chromosome position and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in expression of genes near fusion sites. Modeling suggests that this is due to both disruption of telomere-associated silencing and the displacement of genes relative to the nuclear periphery. A 10% decrease in the predicted time a gene spends near the nuclear periphery is associated with a 10% increase in expression. These data suggest that basal transcriptional activity is sensitive to radial changes on gene position, and provide insight into the functional relevance of budding yeast chromosome-level three-dimensional organization in gene expression.

cell biology↗

bioRxiv2017

RAB-35 and ARF-6 GTPases Mediate Engulfment and Clearance Following Linker Cell-Type Death

Clearance of dying cells is essential for development and homeostasis. Conserved genes mediate apoptotic cell removal, but whether these genes also control non-apoptotic cell removal is a major open question. Linker cell-type death (LCD) is a prevalent non-apoptotic developmental cell death process with features conserved from C. elegans to vertebrates. Using microfluidics-based long-term in vivo imaging, we show that unlike apoptotic cells, the C. elegans linker cell, which dies by LCD, is competitively phagocytosed by two neighboring cells, resulting in cell splitting. Subsequent cell elimination does not require apoptotic engulfment genes. Rather, we find that RAB-35 GTPase is a key coordinator of competitive phagocytosis onset and linker cell degradation. RAB-35 binds CNT-1, an ARF-6 GTPase activating protein; removes ARF-6, a degradation inhibitor, from phagosome membranes; and recruits RAB-5 and RAB-7 GTPases for phagolysosome maturation. We propose that RAB-35 and ARF-6 drive an evolutionarily conserved program eliminating cells dying by LCD.

cell biology↗

bioRxiv2017

A Testis ER Chaperone Marks Mature Olfactory and Vomeronasal Sensory Neurons

The proper folding of most secreted and membrane proteins involves interaction with endoplasmic reticulum-resident, glycan-binding chaperones. Some of these chaperones, such as Calreticulin and Calnexin, are nearly ubiquitous, while others are found only in specific cell types, presumably reflecting a role in biosynthesis of proteins specific to those cells. Herein, I have identified Calmegin (Clgn), a chaperone required for fertile spermatogenesis, as a marker of mature neurons in the olfactory system. CLGN was expressed by olfactory marker protein (OMP)-positive neurons in both the main olfactory epithelium (MOE) and the vomeronasal organ (VNO). CLGN was detected both in the perinuclear ER network and in axons. Finally expression of Atf5, a transcription factor required for OSN and VSN development, was both required and sufficient for robust CLGN expression in OSNs and VSNs. Together these findings establish that an ER chaperone required for sperm fertility is developmentally regulated in olfactory neurons, provide a novel marker of mature olfactory neurons, and suggest common mechanisms of secretory protein biogenesis in these cell types.

cell biology↗

bioRxiv2018

A quantitative map of human Condensins provides new insights into mitotic chromosome architecture

The two Condensin complexes in human cells are essential for mitotic chromosome structure. We used homozygous genome editing to fluorescently tag Condensin I and II subunits and mapped their absolute abundance, spacing and dynamic localization during mitosis by fluorescence correlation spectroscopy-calibrated live cell imaging and super-resolution microscopy. While [~]35,000 Condensin II complexes are stably bound to chromosomes throughout mitosis, [~]195,000 Condensin I complexes dynamically bind in two steps, in prometaphase and early anaphase. The two Condensins rarely co-localize at the chromatid axis, where Condensin II is centrally confined but Condensin I reaches [~]50% of the chromatid diameter from its center. Based on our comprehensive quantitative data, we propose a three-step hierarchical loop model of mitotic chromosome compaction: Condensin II initially fixes loops of a maximum size of [~]450 kb at the chromatid axis whose size is then reduced by Condensin I binding to [~]90 kb in prometaphase and [~]70 kb in anaphase, achieving maximum chromosome compaction upon sister chromatid segregation.

cell biology↗

bioRxiv2017

Comprehensive Cell Type Specific Transcriptomics of the Human Kidney

The human kidney is a complex organ composed of specialized cell types. To better define this cellular complexity, we profiled the individual transcriptomes of 22,469 normal human kidney cells, identifying 27 cell types. We describe three distinct endothelial cell populations, a novel subset of intercalated cells, interstitial macrophage and dendritic cells, and identify numerous novel cell-type-specific markers, many validated using imaging mass cytometry and immunohistochemistry. Receptor-ligand analysis revealed previously unknown intercalated-endothelial and intercalated-distal nephron interactions, suggesting a role in maintenance of vascular integrity and intercalated cell survival. Notably, kidney disease-associated genes were largely expressed in proximal tubules, podocytes, endothelial and myeloid cells, highlighting an underappreciated role for endothelial cells in kidney pathologies. Our analysis also provides a resource of cell type enriched markers, solute carriers, channels and lncRNAs. In summary, this cell-type-specific transcriptome resource provides the foundation for a comprehensive understanding of kidney function and dysfunction at single cell resolution.

cell biology↗

bioRxiv2017

Mathematical models for cell migration with real-time cell cycle dynamics

Fluorescent ubiquitination-based cell cycle indicator, also known as FUCCI, allows the visualisation of the G1 and S/G2/M cell cycle phases of individual cells. FUCCI consists of two fluorescent probes, so that cells in the G1 phase fluoresce red and cells in the S/G2/M phase fluoresce green. FUCCI reveals real-time information about cell cycle dynamics of individual cells, and can be used to explore how the cell cycle relates to the location of individual cells, local cell density, and different cellular microenvironments. In particular, FUCCI is used in experimental studies examining cell migration, such as malignant invasion and wound healing. Here we present new mathematical models which can describe cell migration and cell cycle dynamics as indicated by FUCCI. The fundamental model describes the two cell cycle phases, G1 and S/G2/M, which FUCCI directly labels. The extended model includes a third phase, early S, which FUCCI indirectly labels. We present experimental data from scratch assays using FUCCI-transduced melanoma cells, and show that the predictions of spatial and temporal patterns of cell density in the experiments can be described by the fundamental model. We obtain numerical solutions of both the fundamental and extended models, which can take the form of travelling waves. These solutions are mathematically interesting because they are a combination of moving wavefronts and moving pulses. We derive and confirm a simple analytical expression for the minimum wave speed, as well as exploring how the wave speed depends on the spatial decay rate of the initial condition.

cell biology↗

bioRxiv2017

The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation

There is growing appreciation of the importance of the mechanical properties of the tumor microenvironment on disease progression. However, the role of extracellular matrix (ECM) stiffness and cellular mechanotransduction in epithelial ovarian cancer (EOC) is largely unknown. Here, we investigated the effect of substrate rigidity on various aspects of SKOV3 human EOC cell morphology and migration. Youngs modulus values of normal mouse peritoneum, a principal target tissue for EOC metastasis, were determined by atomic force microscopy (AFM) and hydrogels were fabricated to mimic these values. We find that cell spreading, focal adhesion formation, myosin light chain phosphorylation, and cellular traction forces all increase on stiffer matrices. Substrate rigidity also positively regulates random cell migration and, importantly, directional increases in matrix tension promote SKOV3 cell durotaxis. Matrix rigidity also promotes nuclear translocation of YAP1, an oncogenic transcription factor associated with aggressive metastatic EOC. Furthermore, disaggregation of multicellular EOC spheroids, a behavior associated with dissemination and metastasis, is enhanced by matrix stiffness through a mechanotransduction pathway involving ROCK, actomyosin contractility, and FAK. Finally, this pattern of mechanosensitivity is maintained in highly metastatic SKOV3ip.1 cells. These results establish that the mechanical properties of the tumor microenvironment may play a role in EOC metastasis.

cell biology↗

bioRxiv2017

Building a 3D Integrated Cell

We present a conditional generative model for learning variation in cell and nuclear morphology and predicting the location of subcellular structures from 3D microscopy images. The model generalizes well to a wide array of structures and allows for a probabilistic interpretation of cell and nuclear morphology and structure localization from fluorescence images. We demonstrate the effectiveness of the approach by producing and evaluating photo-realistic 3D cell images using the generative model, and show that the conditional nature of the model provides the ability to predict the localization of unobserved structures, given cell and nuclear morphology. We additionally explore the models utility in a number of applications, including cellular integration from multiple experiments and exploration of variation in structure localization. Finally, we discuss the model in the context of foundational and contemporary work and suggest forthcoming extensions.

cell biology↗

bioRxiv2017

Tension-dependent regulation of mammalian Hippo signaling through LIMD1

Hippo signaling is regulated by biochemical and biomechanical cues that influence the cytoskeleton, but the mechanisms that mediate this have remained unclear. We show that all three mammalian Ajuba family proteins - AJUBA, LIMD1, and WTIP - exhibit tension-dependent localization to adherens junctions, and that both Lats family proteins, LATS1 and LATS2, exhibit an overlapping tension-dependent junctional localization. This localization of Ajuba and Lats family proteins is also influenced by cell density, and by Rho activation. We establish that junctional localization of Lats kinases requires LIMD1, and that LIMD1 is also specifically required for the regulation of Lats kinases and YAP by Rho. Our results identify a biomechanical pathway that contributes to regulation of mammalian Hippo signaling, establish that this occurs through tension-dependent LIMD1-mediated recruitment and inhibition of Lats kinases in junctional complexes, and identify roles for this pathway in both Rho-mediated and density-dependent regulation of Hippo signaling.

cell biology↗

bioRxiv2017

Hepatic NF-kB-inducing Kinase (NIK) Suppresses Liver Regeneration in Chronic Liver Disease

Hepatocyte replication maintains liver homeostasis and integrity. It is impaired in chronic liver disease, promoting disease progression. Herein, we have identified NF-kB-inducing kinase (NIK) as an unrecognized suppressor of hepatocyte replication. Hepatic NIK was aberrantly activated in chronic liver disease. Hepatocyte-specific deletion of NIK or its downstream mediator IKK substantially accelerated hepatocyte proliferation and liver regeneration following partial hepatectomy. Mechanistically, NIK and IKK suppressed the mitogenic JAK2/STAT3 pathway, thereby inhibiting hepatocyte cell cycle progression. Remarkably, inactivation of hepatic NIK largely reversed suppression of the hepatic JAK2/STAT3 pathway, hepatocyte replication, and liver regeneration induced by either chronic liver injury or metabolic stress. Our data suggest that hepatic NIK acts as a rheostat for liver regeneration to restrain liver overgrowth. Pathologic activation of hepatic NIK blocks hepatocyte replication, likely contributing to liver disease progression.

cell biology↗

bioRxiv2017

CYRI1-mediated inhibition of RAC1 signalling restricts Salmonella Typhimurium infection

Salmonella presents a global public health concern. Central to Salmonella pathogenicity is an ability to subvert host defence mechanisms through bacterial effectors that target key host proteins implicated in restricting infection. Thus, to gain insight into host-pathogen interactions governing Salmonella infection, a thorough understanding of host defence mechanisms is needed. To tackle this, we performed an in vivo genome-wide ENU mutagenesis screen to uncover novel host defence proteins. Through this screen we identified an uncharacterised protein, which we name CYRI1 (CYFIP-related RAC1 Interacting protein 1) that serves as a Salmonella resistance factor. We show that CYRI1 binds to the small GTPase RAC1 through a conserved domain present in CYFIP proteins, which are known RAC1 effectors that stimulate actin polymerisation. However, unlike CYFIP proteins, CYRI1 negatively regulates RAC1-driven actin cytoskeleton remodelling, thereby attenuating processes such as phagocytosis and cell migration. This, in turn, enables CYRI1 to counteract Salmonella at various stages of infection, including bacterial entry into epithelial cells, internalisation into myeloid-derived phagocytes as well as phagocyte-mediated bacterial dissemination. Together, this outlines a novel host defence mechanism that is crucial for determining bacterial fate.

cell biology↗

bioRxiv2018

Olfactory and Vomeronasal Receptor Feedback Employ Divergent Mechanisms of PERK Activation

Mutually-exclusive chemoreceptor expression in olfactory and vomeronasal sensory neurons (OSNs and VSNs) enables odorant discrimination. This configuration involves chemoreceptor mediated activation of the endoplasmic reticulum (ER)-resident kinase PERK. PERK drives translation of the transcription factor ATF5 to preclude additional chemoreceptor expression. ATF5 translation is transient in OSNs but persistent in VSNs, suggesting chemoreceptor-specific modes of PERK activation. Herein, we showed that the ER-lumenal domain (LD) of PERK recognized vomeronasal receptor (VR)-derived peptides, suggesting direct PERK activation drives persistent ATF5 translation in VSNs. In contrast, PERK LD did not recognize olfactory receptor (OR)-derived peptides in vitro, and facilitating OR maturation in vivo prevented PERK activation, suggesting that ORs activate PERK indirectly through a failure to exit the ER. Importantly, impairing or prolonging ATF5 expression drove specific chemoreceptor repertoire biases. Together, these results demonstrate mechanistic divergence in chemoreceptor feedback and establish that differences in PERK activation promote qualitatively different gene regulatory results.

cell biology↗

bioRxiv2017

In vivo imaging of radial spoke proteins reveals independent assembly and turnover of the spoke head and stalk

Radial spokes (RSs) are multiprotein complexes regulating dynein activity. In the cell body and ciliary matrix, RS proteins are present in a 12S precursor, which is converted into axonemal 20S spokes consisting of a head and stalk. To study RS assembly in vivo, we expressed fluorescent protein (FP)-tagged versions of the head protein RSP4 and the stalk protein RSP3 to rescue the corresponding Chlamydomonas mutants pfl, lacking spoke heads, and pf14, lacking RSs entirely. RSP3 and RSP4 mostly co-migrated by intraflagellar transport (IFT). Transport was elevated during ciliary assembly. IFT of RSP4-FP depended on RSP3. To study RS assembly independently of ciliogenesis, strains expressing FP-tagged RS proteins were mated to untagged cells with, without, or with partial RSs. RSP4-FP is added a tip-to-base fashion to preexisting pf1 spoke stalks while de novo RS assembly occurred lengthwise. In wild-type cilia, the exchange rate of head protein RSP4 exceeded that of the stalk protein RSP3 suggesting increased turnover of spoke heads. The data indicate that RSP3 and RSP4 while transported together separate inside cilia during RS repair and maintenance. The 12S RS precursor encompassing both proteins could represent transport form of the RS ensuring stoichiometric delivery by IFT. (196 of 200)

cell biology↗

bioRxiv2017

An ordered pattern of Ana2 phosphorylation by Plk4 is required for centriole assembly

Polo-like kinase 4 (Plk4) initiates an early step in centriole assembly by phosphorylating Ana2/STIL, a structural component of the procentriole. Here, we show that Plk4 binding to the central coiled-coil (CC) of Ana2 is a conserved event, involving Polo-box 3 and a previously unidentified putative CC located adjacent to the kinase domain. Ana2 binding stimulates Plk4 kinase activity in vitro, and, in turn, is phosphorylated along its length. Previous studies showed that Plk4 phosphorylates the C-terminal STAN domain of Ana2/STIL, triggering binding and recruitment of the cartwheel protein Sas6 to the procentriole assembly site. However, the physiological relevance of N-terminal phosphorylation was unknown. We found that Plk4 first phosphorylates the extreme N-terminus of Ana2 which is critical for subsequent STAN domain modification. Phosphorylation of the central region then breaks the Plk4-Ana2 interaction. This phosphorylation pattern is important for centriole assembly and integrity because replacement of endogenous Ana2 with phospho-Ana2 mutants disrupts distinct steps in Ana2 function and inhibits centriole duplication.

cell biology↗

bioRxiv2017

Short-term hyperglycaemia induces motor defects in C. elegans.

Hyperglycaemia causes various intracellular changes resulting in oxidative stress leading to loss of integrity and cell death. While cellular effects of hyperglycaemia have been reported extensively there is no clarity on whether the cellular changes translate into alterations in behaviour. Study of behavioural alterations also provides a sublime top-down approach to dapple the putative systems affected due to hyperglycaemic stress. Hence, this aspect of effect of hyperglycaemia deserves attention as it could be an early indicator of neurodegenerative changes. Caenorhabditis elegans is an excellent model to address these questions since it has a simple nervous system and the ability to respond to various cues.\n\nWe have investigated alteration in behaviour which involves various motor and sensory function of the C. elegans nervous system under hyperglycaemia. Exposure of C. elegans to 400 mM glucose for 4hr did not kill the worm but gave rise to decreased number of progeny, exhibiting other aberrant behaviours. This dosage was considered to cause hyperglycaemic stress and used further in the studies. Various assays that quantified behaviour, such as feeding (pharyngeal pumping/min), locomotion (distance travelled by the worms/min), olfactory response towards Butanol (response index) and gustatory response NaCl (response index) were conducted under both normal and hyperglycaemic conditions. The behavioural alterations were validated by scrutinizing changes in level of Acetylchloine which regulates motor behaviour and morphology of chemosensory neurons. Our results indicate that hyperglycaemia alters motor behaviour of the worm which was validated by a reduction in ACh levels. However, chemosensory systems were robust enough to resist reduction in neuronal integrity due to hyperglycaemic assault.

cell biology↗

bioRxiv2017

Multiple Determinants and Consequences of Cohesion Fatigue in Mammalian Cells

Cells delayed in metaphase with intact mitotic spindles undergo cohesion fatigue, where sister chromatids separate asynchronously, while cells remain in M phase. Cohesion fatigue requires release of sister chromatid cohesion. However, the pathways necessary to breach sister chromatid cohesion during cohesion fatigue remain unknown. Using a regulated protein heterodimerization system to lock different cohesin interfaces at specific times in mitosis, we show that the prophase pathway of Cohesin release is not required for cohesion fatigue. By manipulating microtubule stability and Cohesin complex integrity in cell lines with varying sensitivity to cohesion fatigue, we show that rates of cohesion fatigue reflect a dynamic balance between spindle pulling forces and resistance to separation by interchromatid cohesion. Cohesion fatigue that results in complete chromatid separation may be an unrecognized but common source of chromosome instability. Here, we extend the significance of cohesion fatigue by showing that even limited delays at metaphase lead to partial centromere separation and predispose cells to chromosome missegregation.

cell biology↗

bioRxiv2017

Scaling of G1 duration with population doubling time by a cyclin in Saccharomyces cerevisiae

The longer cells stay in particular phases of the cell cycle, the longer it will take these cell populations to increase. However, the above qualitative description has very little predictive value, unless it can be codified mathematically. A quantitative relation that defines the population doubling time (Td) as a function of the time eukaryotic cells spend in specific cell cycle phases would be instrumental for estimating rates of cell proliferation and for evaluating introduced perturbations. Here, we show that in human cells the length of the G1 phase (TG1) regressed on Td with a slope of {approx}0.75, while in the yeast Saccharomyces cerevisiae the slope was slightly smaller, at {approx}0.60. On the other hand, cell size was not strongly associated with Td or TG1 in cell cultures that were proliferating at different rates. Furthermore, we show that levels of the yeast G1 cyclin Cln3p were positively associated with rates of cell proliferation over a broad range, at least in part through translational control mediated by a short uORF in the CLN3 transcript. Cln3p was also necessary for the proper scaling between TG1 and Td. In contrast, yeast lacking the Whi5p transcriptional repressor maintained the scaling between TG1 and Td. These data reveal fundamental scaling relations between the duration of eukaryotic cell cycle phases and rates of cell proliferation, point to the necessary role of Cln3p in these relations in yeast and provide a mechanistic basis linking Cln3p levels to proliferation rates and the scaling of G1 with doubling time.

cell biology↗

bioRxiv2017

The Transcriptional Program of Regeneration in the Giant Single Cell, Stentor coeruleus

The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis at the level of a single cell. Stentor are polarized cells with a complex subcellular architecture. The anterior of the cell is marked by an array of cilia, known as the oral apparatus. This feeding organelle can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. We used RNAseq to assay the dynamic changes in Stentos transcriptome during regeneration with high temporal resolution, allowing us to identify five distinct waves of gene expression. We show that the oral apparatus is a model for organelle regeneration, as well as for centriole assembly and ciliogenesis as many conserved genes involved in those processes are induced. Additionally, we find genes involved in signaling, cell cycle regulation, transcription, and RNA binding to be expressed at distinct stages of organelle regeneration, suggesting that the morphological steps of regeneration are driven by a complex regulatory system.

cell biology↗