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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 361 records · Page 20Linked to original sources

bioRxiv2016

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion

To identify cell cycle regulators that enable cancer cells to replicate DNA and divide in an unrestricted manner, we performed a parallel genome-wide RNAi screen in normal and cancer cell lines. In addition to many shared regulators, we found that tumor and normal cells are differentially sensitive to loss of the histone genes transcriptional regulator CASP8AP2. In cancer cells, loss of CASP8AP2 leads to a failure to synthesize sufficient amount of histones in the S-phase of the cell cycle, resulting in slowing of individual replication forks. Despite this, DNA replication fails to arrest, and tumor cells progress in an elongated S-phase that lasts several days, finally resulting in death of most of the affected cells. In contrast, depletion of CASP8AP2 in normal cells triggers a response that arrests viable cells in S-phase. The arrest is dependent on p53, and preceded by accumulation of markers of DNA damage, indicating that nucleosome depletion is sensed in normal cells via a DNA-damage-like response that is defective in tumor cells.

Cell Biology↗

bioRxiv2016

Kinetochore Microtubules indirectly link Chromosomes and Centrosomes in C. elegans Mitosis

The mitotic spindle ensures the faithful segregation of chromosomes. To discover the nature of the crucial centrosome-to-chromosome connection during mitosis, we combined the first large-scale serial electron tomography of whole mitotic spindles in early C. elegans embryos with live-cell imaging. Using tomography, we reconstructed the positions of all microtubules in 3D, and identified their plus- and minus-ends. We classified them as kinetochore (KMTs), spindle (SMTs), or astral microtubules (AMTs) according to their positions, and quantified distinct properties of each class. While our light microscopy and mutant studies show that microtubules are nucleated from the centrosomes, we find only a few KMTs are directly connected to the centrosomes. Indeed, by quantitatively analysing several models of microtubule growth, we conclude that minus-ends of KMTs have selectively detached and depolymerized from the centrosome. In toto, our results show that the connection between centrosomes and chromosomes is mediated by an anchoring into the entire spindle network and that any direct connections through KMTs are few and likely very transient.

Cell Biology↗

bioRxiv2016

A novel approach to derive human midbrain-specific organoids from neuroepithelial stem cells

Research on human brain development and neurological diseases is limited by the lack of advanced experimental in vitro models that truly recapitulate the complexity of the human brain. Furthermore, animal models of human neurodegenerative diseases have failed dramatically, and the success rate of clinical trials based on these models has been disappointing. Here, we describe a novel and robust human brain organoid system that is highly specific to the midbrain derived from regionally patterned neuroepithelial stem cells. These human midbrain organoids contain spatially organized groups of dopaminergic neurons, which make them an attractive model to study Parkinsons disease. Midbrain organoids are characterized in detail for neuronal, astroglial and oligodendrocyte differentiation. Furthermore, we show the presence of synaptic connections and electrophysiological activity. The complexity of this model is further highlighted by the myelination of neurites. The present midbrain organoid system has the potential to be used for advanced in vitro disease modeling and therapy development.

Cell Biology↗

bioRxiv2016

The regulatable MAL32 promoter in S. cerevisiae: characteristics and tools to facilitate its use

Here we describe a set of tools to facilitate the use of maltose and the MAL32 promoter for regulated gene expression in yeast, alone or in combination with the GAL1 promoter. Using fluorescent protein reporters we find that under non-inducing conditions the MAL32 promoter exhibits a low basal level of expression, similar to the GAL1 promoter, and that both promoters can be induced independently of each other using the respective sugars, maltose and galactose. While their repression upon glucose addition is immediate and complete, we found that the MAL32 and GAL1 promoter each exhibit distinct induction kinetics. A set of plasmids is available to facilitate the application of the MAL32 promoter for chromosomal modifications using PCR targeting and for plasmid based gene expression.

Cell Biology↗

bioRxiv2016

Hot-wiring clathrin-mediated endocytosis in human cells

Clathrin-mediated endocytosis (CME) is the major route of receptor internalization at the plasma membrane. Analysis of constitutive CME is complicated by the fact that initiation of endocytic events is unpredictable. When and where a clathrin-coated pit will form and what cargo it will contain are difficult to foresee. Here we describe a series of genetically encoded reporters that allow the initiation of CME on demand. This is achieved by inducibly tethering a clathrin \"hook\" to a plasma membrane \"anchor\". Our design incorporates temporal and spatial control of initiation using chemical and optical tools, and the cargo is defined. Since this system bypasses multiple steps in vesicle creation, we term it \"hot-wiring\". In this paper, we use hot-wired endocytosis to define the functional interactions between clathrin and the {beta}2 subunit of the AP2 complex. However, there are numerous applications for this new technology, which we hope will be broadly useful to the field.

Cell Biology↗

bioRxiv2016

Palmitoylation of the oncogenic RhoGEF TGAT is dispensable for membrane affinity and consequent activation of RhoA

Rho guanine exchange factors (RhoGEFs) control many aspects of the cellular cytoskeleton, and thereby regulate and control processes such as cell migration, cell adhesion and proliferation. TGAT is a splice variant of the RhoGEF Trio, with oncogenic potential. Whether the subcellular location of TGAT is critical for its activity is unknown. Confocal microscopy of fluorescent protein tagged TGAT revealed co-localization with a Golgi marker. Because plasma membrane localized RhoGEFs are particularly effective at activating RhoA, plasma membrane localization of TGAT was studied. In order to quantitatively measure plasma membrane association we developed a novel, highly sensitive image analysis method. The method requires a cytoplasmic marker and a plasma membrane marker, which are co-imaged with the tagged protein of interest. Linear unmixing is performed to determine the plasma membrane and cytoplasmic component in the fluorescence signal of protein of interest. The analysis revealed that wild-type TGAT is partially co-localized with the plasma membrane. Strikingly, cysteine TGAT-mutants lacking one or more palmitoylation sites in the C-tail, still showed membrane association. In contrast, a truncated variant, lacking the last 15 amino acids, TGAT{Delta}15, lost membrane association. The functional role of membrane localization was determined by measuring TGAT activity in single cells with a RhoA FRET-sensor and F-actin levels. Mutants of TGAT that still maintained membrane association showed similar activity as wild-type TGAT. In contrast, the activity was abrogated for the cytoplasmic TGAT{Delta}15 variant. Synthetic recruitment of TGAT{Delta}15 to membranes confirmed that TGAT effectively activates RhoA at the plasma membrane. Together, these results show that membrane association of TGAT is critical for its activity, but that palmitoylation is dispensable.

Cell Biology↗

bioRxiv2016

Foxc1 Controls Cell Fate Decisions During Transforming Growth Factor β Induced Epithelial to Mesenchymal Transition Through the Regulation of Fibroblast Growth Factor Receptor 1 Expression.

Epithelial to mesenchymal transition (EMT) is an important physiological process that drives tissue formation during development but also contributes to disease pathogenesis including fibrosis and cancer metastasis. The forkhead box transcription factor gene FOXC1 is an important developmental regulator in the generation of mesenchymal cells necessary in the formation of the anterior segment of the eye, the craniofacial skeleton and the meninges. Recently elevated expression of FOXC1 has been detected in several metastatic cancers that have undergone EMT events. We sought to determine the role of FOXC1 in the initiation of EMT events using NMuMG cells treated with TFG{beta}1. We found that although Foxc1 expression was increased following TFG{beta}1 induced EMT, Foxc1 was not required for this induction. Instead we propose that Foxc1 is required for the specification of the mesenchyme cell type, promoting an activated fibroblast phenotype over a myofibroblast phenotype following the initiation of EMT. This cells type specification was achieved through the regulation of Fibroblast growth factor (Fgfr) 1 expression. Using an RNA sequencing approach, we determined that levels of Fgfr1 normally activated upon TFG{beta}1 treatment were reduced in Foxc1-knockdown cells. Through chromatin immunoprecipitation experiments we determined that FOXC1 could bind to an Fgfr1 upstream regulatory region. Furthermore, expression of the myofibroblast marker -smooth muscle actin (SMA) was elevated in Foxc1 knockdown cells. Finally we determined that FGF2 mediated three dimensional migratory ability was greatly impaired in Foxc1-knockdown cells. Together these results define a role for Foxc1 in specifying a mesenchymal cell type following TFG{beta}1 mediated EMT events.

Cell Biology↗

bioRxiv2016

R-spondin1 regulates muscle progenitor cell fusion through control of antagonist Wnt signaling pathways

Tissue regeneration requires the selective activation and repression of specific signaling pathways in stem cells. As such, the Wnt signaling pathways have been shown to control stem cell fate. In many cell types, the R-Spondin (Rspo) family of secreted proteins acts as potent activators of the canonical Wnt/{beta}-catenin pathway. Here, we identify Rspo1 as a mediator of skeletal muscle tissue repair. Firstly we show that Rspo1-null muscles do not display any abnormalities at the basal level. However deletion of Rspo1 results in global alteration of muscle regeneration kinetics following acute injury. We found that muscle stem cells lacking Rspo1 show delayed differentiation. Transcriptome analysis further demonstrated that Rspo1 is required for the activation of Wnt/{beta}-catenin target genes in muscle cells. Furthermore, muscle cells lacking Rspo1 fuse with a higher frequency than normal cells, leading to larger myotubes containing more nuclei both in vitro and in vivo. We found the increase in muscle fusion was dependent on up-regulation of non-canonical Wnt7a/Fzd7/Rac1 signaling. We conclude that antagonistic control of canonical and non-canonical Wnt signaling pathways by Rspo1 in muscle stem cell progeny is important for restitution of normal muscle architecture during skeletal muscle regeneration.

Cell Biology↗

bioRxiv2016

Identification of a novel putative interaction partner of the nucleoporin ALADIN

It has been shown that the nucleoporin ALADIN employs a significant role in the redox homeostasis of the cell but the function in steroidogenesis contributing to adrenal atrophy in triple A syndrome remains largely unknown. In an attempt to identify new interaction partners of ALADIN, co-immunoprecipitation followed by proteome analysis was conducted in different expression models using the human adrenocortical tumour cell line NCI-H295R. Our results suggest an interaction of ALADIN with the microsomal protein PGRMC2. PGRMC2 is shown to be activity regulator of CYP P450 enzymes and therefore, to be a possible target for adrenal dysregulation in triple A syndrome. We show that there is a sexual dimorphism regarding the expression of Pgrmc2 in adrenals and gonads of WT and Aaas KO mice. Female Aaas KO mice are sterile due to delayed oocyte maturation and meiotic spindle assembly. A participation in meiotic spindle assembly confirms the recently investigated involvement of ALADIN in mitosis and emphasises an interaction with PGRMC2 which is a regulator of cell cycle. By identification of a novel interaction partner of ALADIN we provide novel aspects for future research of the function of ALADIN during cell cycle and for new insights into the pathogenesis of triple A syndrome.

Cell Biology↗

bioRxiv2016

An aging-independent replicative lifespan in a symmetrically dividing eukaryote

The replicative lifespan (RLS) of a cell--defined as the number of generations a cell divides before death--has informed our understanding of the molecular mechanisms of cellular aging. Nearly all RLS studies have been performed on budding yeast and little is known about the mechanisms of aging and longevity in symmetrically dividing eukaryotic cells. Here, we describe a multiplexed fission yeast (Schizosaccharomyces pombe) lifespan micro-dissector (FYLM); a microfluidic platform for performing automated micro-dissection and high-content single-cell analysis in well-defined culture conditions. Using the FYLM, we directly observe continuous and robust replication of hundreds of individual fission yeast cells for over seventy-five cell divisions. Surprisingly, cells die without any classic hallmarks of cellular aging such as changes in cell morphology, increased doubling time, or reduced sibling health. Genetic perturbations and longevity-enhancing drugs can further extend the replicative lifespan (RLS) via an aging-independent mechanism. We conclude that despite occasional sudden death of individual cells, fission yeast does not age. These results highlight that cellular aging and replicative lifespan can be uncoupled in a eukaryotic cell.

Cell Biology↗

bioRxiv2016

Toxoplasma gondii establishes an extensive filamentous network consisting of stable F-actin during replication

Apicomplexan actin is well conserved and clearly important during the parasite's life cycle. Several studies assert that its polymerization kinetics are unusual, permitting only short, unstable F-actin filaments. However, it has not been possible to study actin in vivo, so its physiological role has remained obscure. This has led to functional models which are mutually conflicting, incompatible with actin behavior from other eukaryotes, and cannot explain actin's importance during basic processes such as parasite replication and egress. Here we use a chromobody that specifically binds F-actin to demonstrate that Toxoplasma forms stable actin filaments in vivo. F-actin is not only important for parasite replication, but also forms an extensive network that connects individuals both within and between parasitophorous vacuoles, and allows vesicles to be exchanged between parasites within a vacuole. During host cell egress, prior to motility, this network collapses in a calcium-dependent manner. This study demonstrates unexpected roles of Toxoplasma actin during the asexual life cycle, and proves that formation of F-actin depends on a critical concentration of G-actin, implying a polymerization mechanism similar to mammalian actin.\n\nOne Sentence SummaryToxoplasma establishes a stable F-actin network that is essential for replication and material transport between individual parasites.

Cell Biology↗

bioRxiv2016

Bright photoactivatable fluorophores for single-molecule imaging

Small molecule fluorophores are important tools for advanced imaging experiments. The development of self-labeling protein tags such as the HaloTag and SNAP-tag has expanded the utility of chemical dyes in live-cell microscopy. We recently described a general method for improving the brightness and photostability of small, cell-permeable fluorophores, resulting in the novel azetidine-containing \"Janelia Fluor\" (JF) dyes. Here, we refine and extend the utility of the JF dyes by synthesizing photoactivatable derivatives that are compatible with live-cell labeling strategies. These compounds retain the superior brightness of the JF dyes once activated, but their facile photoactivation also enables improved single-particle tracking and localization microscopy experiments.

Cell Biology↗

bioRxiv2016

Polo kinase phosphorylation determines C. elegans centrosome size and density by biasing SPD-5 toward an assembly-competent conformation

Centrosomes are major microtubule-organizing centers composed of centrioles surrounded by an extensive proteinacious layer called the pericentriolar material (PCM). In C. elegans embryos, the mitotic PCM expands by Polo-kinase (PLK-1) phosphorylation-accelerated assembly of SPD-5 molecules into supramolecular scaffolds. However, how PLK-1 phosphorylation regulates SPD-5 assembly is not known. We found that a mutant version of SPD-5 that is insensitive to PLK-1 phosphorylation (SPD-54A) could localize to PCM but was unable to rescue the reduction in PCM size and density when wild-type SPD-5 levels were decreased. In vitro, purified SPD-54A self-assembled into functional supramolecular scaffolds over long time scales, suggesting that phosphorylation only controls the rate of SPD-5 scaffold assembly. Furthermore, the SPD-5 scaffold, once assembled, remained intact and supported microtubule nucleation in the absence of PLK-1 activity in vivo. We conclude that Polo Kinase is required for rapid assembly of the PCM scaffold but not for scaffold maintenance or function. Based on this idea, we developed a theoretical model that adequately predicted PCM growth rates in different mutant conditions in vivo. We propose that PLK-1 phosphorylation-dependent conversion of SPD-5 into an assembly-competent form underlies PCM formation in vivo and that the rate of this conversion determines final PCM size and density.

Cell Biology↗

bioRxiv2016

Experimental Reconstitution of Chronic ER Stress in the Liver Reveals Feedback Suppression of Bip mRNA Expression

ER stress is implicated in many chronic diseases, but very little is known about how the unfolded protein response (UPR) responds to persistent ER stress in vivo. Here, we experimentally reconstituted chronic ER stress in the mouse liver, using repeated injection of a low dose of the ER stressor tunicamycin. Paradoxically, this treatment led to feedback-mediated suppression of a select group of mRNAs, including those encoding the ER chaperones BiP and GRP94. This suppression was due to both silencing of the ATF6a pathway of UPR-dependent transcription and enhancement of mRNA degradation, most likely via regulated IRE1-dependent decay (RIDD). The suppression of Bip mRNA was phenocopied by ectopic overexpression of BiP protein, and was also observed in obese mice. Our findings suggest that persistent cycles of UPR activation and deactivation create an altered, quasi-stable setpoint for UPR-dependent transcriptional regulation--an outcome that could be relevant to conditions such as metabolic syndrome.

Cell Biology↗

bioRxiv2016

GTSE1 tunes microtubule stability for chromosome alignment and segregation through MCAK inhibition

The dynamic regulation of microtubules during mitosis is critical for accurate chromosome segregation and genome stability. Cancer cell lines with hyperstabilized kinetochore microtubules have increased segregation errors and elevated chromosomal instability (CIN), but the genetic defects responsible remain largely unknown. The microtubule depolymerase MCAK can influence CIN through its impact on microtubule stability, but how its potent activity is controlled in cells remains unclear. Here we show that GTSE1, a protein found overexpressed in aneuploid cancer cell lines and tumours, regulates microtubule stability during mitosis by inhibiting MCAK microtubule depolymerase activity. Cells lacking GTSE1 have defects in chromosome alignment and spindle positioning due to microtubule instability caused by excess MCAK activity. Reducing GTSE1 levels in CIN cancer cell lines reduces chromosome missegregation defects, while artificially inducing GTSE1 levels in chromosomally stable cells elevates chromosome missegregation and CIN. Thus GTSE1 inhibition of MCAK activity regulates the balance of microtubule stability that determines the fidelity of chromosome alignment, segregation, and chromosomal stability.

Cell Biology↗

bioRxiv2016

Adverse effects of culture media on human pluripotent stem cells

Culture conditions play an important role in regulating the genomic integrity of HPSCs. We report that HPSCs cultured in Essential 8 (E8) and mTeSR, two widely used media for off-feeder culturing of HPSCs, had many fold higher levels of ROS and higher mitochondrial potential than cells cultured in KSR containing media. HPSCs also exhibited increased levels of 8-hydroxyguanosine, phospho-histone-H2A.X and p53, as well as increased sensitivity to {gamma}-irradiation in these two media. HPSCs in E8 and mTeSR had increased incidence of alterations in their DNA sequence, reflecting genotoxic stress, in addition to changes in nucleolar morphology and number. Supplementing E8 and mTeSR with antioxidants provided only a partial rescue. Our results suggest that it is essential to determine cellular ROS levels in designing culture media as it affects the genomic integrity of HPSCs and will limit their use in studying development and in regenerative medicine.\n\nHighlightsO_LICulture media can dramatically alter nuclear and nucleolar morphology\nC_LIO_LIHPSCs in E8 and mTeSR media have increased ROS levels and mitochondrial potential\nC_LIO_LIThere is increased nuclei acid damage in HPSCs cultured in E8 and mTeSR media\nC_LIO_LINucleolar morphology of HPSCs can act as a \"stress reporter\"\nC_LI

Cell Biology↗

bioRxiv2016

An RNA-binding tropomyosin recruits kinesin-1 dynamically to oskar mRNPs

Localization and local translation of oskar mRNA at the posterior pole of the Drosophila oocyte directs abdominal patterning and germline formation in the embryo. The process requires recruitment and precise regulation of motor proteins to form transport-competent mRNPs. We show that the posterior-targeting kinesin-1 is loaded upon nuclear export of oskar mRNPs, prior to their dynein-dependent transport from the nurse cells into the oocyte. We demonstrate that kinesin-1 recruitment requires the DmTropomyosin1-I/C isoform, an atypical RNA-binding tropomyosin that binds directly to dimerizing oskar 3UTRs. Finally, we show that a small but dynamically changing subset of oskar mRNPs gets loaded with inactive kinesin-1 and that the motor is activated during mid-oogenesis by the functionalized spliced oskar RNA localization element. This inefficient, dynamic recruitment of Khc decoupled from cargo-dependent motor activation constitutes an optmized, coordinated mechanism of mRNP transport, by minimizing interference with other cargo-transport processes and between the cargo associated dynein and kinesin-1.

Cell Biology↗

bioRxiv2016

Excitability in the p53 network mediates robust signaling with tunable activation thresholds in single cells

Cellular signaling systems precisely transmit information in the presence of molecular noise while retaining flexibility to accommodate the needs of individual cells. To understand design principles underlying such versatile signaling, we analyzed the response of the tumor suppressor p53 to varying levels of DNA damage in hundreds of individual cells and observed a switch between distinct signaling modes characterized by isolated pulses and sustained oscillations of p53 accumulation. Guided by dynamic systems theory we show that this requires an excitable network structure comprising positive feedback and provide experimental evidence for its molecular identity. The resulting data-driven model reproduced all features of measured signaling responses and is sufficient to explain their heterogeneity in individual cells. We present evidence that heterogeneity in the levels of the feedback regulator Wip1 sets cell-specific thresholds for p53 activation, providing means to modulate its response through interacting signaling pathways. Our results demonstrate how excitable signaling networks can provide high specificity, sensitivity and robustness while retaining unique possibilities to adjust their function to the physiology of individual cells.

Cell Biology↗