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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 721 records · Page 40Linked to original sources

bioRxiv2017

Applying the auxin-inducible degradation (AID) system for rapid protein depletion in mammalian cells

The ability to deplete a protein of interest is critical for dissecting cellular processes. Traditional methods of protein depletion are often slow-acting, which can be problematic when characterizing a cellular process that occurs within a short period of time. Furthermore, these methods are usually not reversible. Recent advances to achieve protein depletion function by inducibly trafficking proteins of interest to an endogenous E3 ubiquitin ligase complex to promote ubiquitination and subsequent degradation by the proteasome. One of these systems, the auxin-inducible degron (AID) system, has been shown to permit rapid and inducible degradation of AID-tagged target proteins in mammalian cells. The AID system can control the abundance of a diverse set of cellular proteins, including those contained within protein complexes, and is active in all phases of the cell cycle. Here we discuss considerations for the successful implementation of the AID system and describe a protocol using CRISPR/Cas9 to achieve bi-allelic insertion of an AID degron in human cells. This method can also be adapted to insert other tags, such as fluorescent proteins, at defined genomic locations.

cell biology↗

bioRxiv2017

The actin cytoskeleton governs apical mitosis and daughter cell dispersion in intestinal epithelia

Cell proliferation is critical for maintaining the absorptive, protective and regenerative functions of the small intestine throughout adulthood. Interphase nuclei are positioned near the basal surface of the intestinal epithelium, but during mitosis, chromosomes are located apically. The molecular basis for apical-basal DNA positioning and its consequences for tissue homeostasis are poorly understood. Here, we image and pharmacologically perturb these behaviors in live murine intestinal organoids. We find that apical and basal DNA movements occur as a result of mitosis-coupled actin rearrangements that alter the basolateral shape of dividing cells, while the apical cell surface remains confined by cell-cell contacts that persist throughout mitosis. Strikingly, these polarized shape changes allow neighboring cells to insert between nascent daughters, intermingling cells of different lineages. In summary, polarized rearrangements of the actin cytoskeleton govern the mitotic behavior of intestinal epithelial cells and lead to interspersion of cell lineages.

cell biology↗

bioRxiv2017

Sox4 drives intestinal secretory differentiation toward tuft and enteroendocrine fates

Background & AimsThe intestinal epithelium is maintained by intestinal stem cells (ISCs), which produce post-mitotic absorptive and secretory epithelial cells. Initial fate specification toward enteroendocrine, goblet, and Paneth cell lineages is dependent on Atoh1, a master regulator of secretory differentiation. However, the origin of tuft cells, which participate in Type II immune responses to parasitic infection, is less clear and appears to occur in an Atoh1-independent manner. Here we examine the role of Sox4 in ISC proliferation and differentiation.\n\nMethodsWe used mice with intestinal epithelial-specific conditional knockout of Sox4 (Sox4fl/fl:vilCre; Sox4cKO) to study the role of Sox4 in the small intestine. Crypt- and single cell-derived organoids were used to assay proliferation and ISC potency between control and Sox4cKO mice. Lineage allocation and genetic consequences of Sox4 ablation were studied by immunofluorescence, RT-qPCR, and RNA-seq. In vivo infection with helminths and in vitro cytokine treatment in primary intestinal organoids were used to assess tuft cell hyperplasia in control and Sox4cKO samples. Atoh1GFP reporter mice and single cell RNA-seq (scRNA-seq) were used to determine co-localization of SOX4 and Atoh1. Wild-type and inducible Atoh1 knockout (Atoh1fl/fl:vilCreER; Atoh1iKO) organoids carrying an inducible Sox4 overexpression vector (Sox4OE) were used to determine the role of Atoh1 in Sox4 driven secretory differentiation.\n\nResultsLoss of Sox4 impairs ISC function and secretory differentiation, resulting in decreased numbers of enteroendocrine and tuft cells. In wild-type mice, SOX4+ cells are significantly upregulated following helminth infection coincident with tuft cell hyperplasia. Sox4 is activated by IL13 in vitro and Sox4cKO knockout mice demonstrate impaired tuft cell hyperplasia and parasite clearance following infection with helminths. A subset of Sox4-expressing cells colocalize with Atoh1 and enteroendocrine markers by scRNA-seq, while Sox4+/Atoh1-cells correlate strongly with tuft cell populations. Gain-of-function studies in primary organoids demonstrate that Sox4 is sufficient to drive both enteroendocrine and tuft cell differentiation, and can do so in the absence of Atoh1.\n\nConclusionOur data demonstrate that Sox4 promotes enteroendocrine and tuft cell lineage allocation independently of Atoh1. These results challenge long-standing views of Atoh1 as the sole regulator of secretory differentiation in the intestine and are relevant for understanding host epithelial responses to parasitic infection.

cell biology↗

bioRxiv2017

Neurochondrin interacts with the SMN protein suggesting a novel mechanism for Spinal Muscular Atrophy pathology.

Spinal Muscular Atrophy (SMA) is an inherited neurodegenerative condition caused by reduction in functional Survival Motor Neurones Protein (SMN). SMN has been implicated in transport of mRNA in neural cells for local translation. We previously identified microtubule-dependant mobile vesicles rich in SMN and the splicing factor SmB, a member of the Sm protein family, in neural cells. By comparing the proteome of SmB to that of SmN, a neural-specific Sm protein, we now show that the essential neural protein neurochondrin (NCDN) interacts with Sm proteins and SMN in the context of mobile vesicles in neurites. NCDN has roles in protein localisation in neural cells, and in maintenance of cell polarity. NCDN is required for the correct localisation of SMN, suggesting they may both be required for formation and transport of trafficking vesicles. NCDN provides a potential therapeutic target for SMA together with, or in place of, those targeting SMN expression.

cell biology↗

bioRxiv2017

Chaperone AMPylation modulates aggregation and toxicity of neurodegenerative disease-associated polypeptides

Proteostasis is critical to maintain organismal viability, a process counteracted by aging-dependent protein aggregation. Chaperones of the heat shock protein (HSP) family help control proteostasis by reducing the burden of unfolded proteins. They also oversee the formation of protein aggregates. Here, we explore how AMPylation - a post-translational protein modification that has emerged as a powerful modulator of HSP70 activity - influences the dynamics of protein aggregation. We find that adjustments of cellular AMPylation levels in C.elegans directly affect aggregation properties and associated toxicity of amyloid-{beta} (A{beta}), of a polyglutamine (polyQ)- extended polypeptide and of -synuclein (-syn). Expression of a constitutively active C. elegans AMPylase Fic-1(E274G) under its own promoter expedites aggregation of A{beta} and -syn, and drastically reduces their toxicity. A deficiency in AMPylation decreases the cellular tolerance for aggregation-prone polyQ proteins and alters their aggregation behavior. Over-expression of Fic-1(E274G) interferes with cell survival and larval development, underscoring the need for tight control of AMPylase activity in vivo. We thus define a link between HSP70 AMPylation and the dynamics of protein aggregation in neurodegenerative disease models. Our results are consistent with a cyto-protective, rather than a cytotoxic role for such protein aggregates.

cell biology↗

bioRxiv2017

Protective effect of estrogen against intervertebral disc degeneration is attenuated by miR-221 through targeting estrogen receptor

Intervertebral disc degeneration (IDD) is a multifactorial disease that associates apoptosis, senescence and calcification of cartilage cells, inflammatory response and alterations in the extracellular matrix. Previous documents imply that estrogen and miR-221 may be involved in IDD. This study further investigated their regulatory mechanisms underlying IDD. Normal and degenerated cartilaginous endplates (CEP) tissues were isolated surgically from juvenile patients with idiopathic scoliosis and adult patients with IDD, respectively. PCR and western blot assays showed decreased aggrecan, Col2A1, TGF-{beta} and estrogen receptor (ER) levels in CEP, but increased MMP-3, adamts-5, IL-1{beta}, TNF-, IL-6 and miR-221 levels. CEP cells were harvested from degenerated CEP tissues and treated with doses of 17{beta}-E2. 17{beta}-E2 increased expression of aggrecan and Col2A1 levels in endplate chondrocytes and secretion of TGF-{beta}, but decreased IL-6 secretion. Moreover, 17{beta}-E2 inhibited the apoptosis and cell-cycle arrest in G0/G1, improving the cell viability. These data indicated estrogen confers protective effect against IDD. However, we found that ER was a target of miR-221 via luciferase assay. miR-221 up-regulation via the mimics or ER knockdown attenuated these protective effects conferred by estrogen, while intervention of miR-221 via the inhibitors promoted the protective effects. This study provided novel evidence that estrogen confers protective effects of CEP against IDD, however, up-regulated miR-221 in degenerated CEP decreased the protective effects via targeting ER, thus it may be an important cause for IDD.

cell biology↗

bioRxiv2017

Fibroblast-derived HGF drives acinar lung cancer cell polarization through integrin-dependent RhoA-ROCK1 inhibition.

The formation of lumens in epithelial tissues requires apical-basal polarization of cells, and the co-ordination of this individual polarity collectively around a contiguous lumen. Signals from the Extracellular Matrix (ECM) instruct epithelia as to the orientation of where basal, and thus consequently apical, surfaces should be formed. We report that this pathway is normally absent in Calu-3 human lung adenocarcinoma cells in 3-Dimensional culture, but that paracrine signals from MRC5 lung fibroblasts can induce correct orientation of polarity and acinar morphogenesis. We identify HGF, acting through the c-Met receptor, as the key polarity-inducing morphogen, which acts to activate {beta}1-integrin-dependent adhesion. HGF and ECM-derived integrin signals co-operate via a c-Src-dependent inhibition of the RhoA-ROCK1 signalling pathway via p190A RhoGAP. This occurred via controlling localization of these signalling pathways to the ECM-abutting surface of cells in 3-Dimensional culture. Thus, stromal derived signals can influence morphogenesis in epithelial cells by controlling activation and localization of cell polarity pathways.

cell biology↗

bioRxiv2017

Dynamic Spatiotemporal Organization of Exocytosis During Cellular Shape Change

Morphological elongation of developing neurons requires plasmalemma expansion, hypothesized to occur primarily via exocytosis. We posited that exocytosis in developing neurons and non-neuronal cells exhibit distinct spatiotemporal organization. We exploited TIRF microscopy to image VAMP-pHluorin mediated exocytosis in murine embryonic cortical neurons and interphase melanoma cells, and developed computer-vision software and statistical tools to uncover spatiotemporal aspects of exocytosis. Vesicle fusion behavior differed between vesicle types, cell types, developmental stage, and extracellular environment. Experiment-based mathematical calculations indicated that VAMP2-mediated vesicle fusion supplied excess material for the plasma membrane expansion that occurred early in neuronal morphogenesis, which was balanced in part by clathrin-mediated endocytosis. Spatial statistics uncovered distinct spatiotemporal regulation of exocytosis in the soma and neurites of developing neurons that was modulated by developmental stage, exposure to the guidance cue netrin-1, and the brain-enriched ubiquitin ligase TRIM9. In melanoma cells, exocytosis occurred less frequently with distinct spatial clustering patterns.

cell biology↗

bioRxiv2017

CDK1 and PLK1 co-ordinate the disassembly and re-assembly of the Nuclear Envelope in vertebrate mitosis.

Micronuclei (MN) arise from chromosomes or fragments that fail to be incorporated into the primary nucleus after cell division. These structures are a major source of genetic instability caused by DNA repair and replication defects coupled to aberrant Nuclear Envelope (NE). These problems ultimately lead to a spectrum of chromosome rearrangements called chromothripsis, a phenomenon that is a hallmark of several cancers. Despite its importance, the molecular mechanism at the origin of this instability is still not understood. Here we show that lagging chromatin, although it can efficiently assemble Lamin A/C, always fails to recruit Nuclear Pore Complexes (NPCs) proteins and that Polo-Like Kinase (PLK1) negatively regulates the NPC assembly. We also provide evidence for the requirement of PLK1 activity for the disassembly of NPCs, but not Lamina (A/C), at mitotic entry. Altogether this study reveals the existence of independent regulatory pathways for Lamin A/C and NPC reorganization during mitosis where Lamin A targeting to the chromatin is controlled by CDK1 activity (a clock-based model) while the NPC loading is also spatially monitored by PLK1.

cell biology↗

bioRxiv2017

HiCTMap: Detection and Analysis of Chromosome Territory Structure and Position by High-throughput Imaging

The spatial organization of chromosomes in the nuclear space is an extensively studied field that relies on measurements of structural features and 3D positions of chromosomes with high precision and robustness. However, no tools are currently available to image and analyze chromosome territories in a high-throughput format. Here, we have developed High-throughput Chromosome Territory Mapping (HiCTMap), a method for the robust and rapid analysis of 2D and 3D chromosome territory positioning in mammalian cells. HiCTMap is a high-throughput imaging-based chromosome detection method which enables routine analysis of chromosome structure and nuclear position. Using an optimized FISH staining protocol in a 384-well plate format in conjunction with a bespoke automated image analysis workflow, HiCTMap faithfully detects chromosome territories and their position in 2D and 3D in a large population of cells per experimental condition. We apply this novel technique to visualize chromosomes 18, X, and Y in male and female primary human skin fibroblasts, and show accurate detection of the correct number of chromosomes in the respective genotypes. Given the ability to visualize and quantitatively analyze large numbers of nuclei, we use HiCTMap to measure chromosome territory area and volume with high precision and determine the radial position of chromosome territories using either centroid or equidistant-shell analysis. The HiCTMap protocol is also compatible with RNA FISH as demonstrated by simultaneous labeling of X chromosomes and Xist RNA in female cells. We suggest HiCTMap will be a useful tool for routine precision mapping of chromosome territories in a wide range of cell types and tissues.

cell biology↗

bioRxiv2017

Src42A required for collective border cell migration in vivo

The tyrosine kinase Src is over-expressed in numerous human cancers and is associated with poor prognosis. While Src has been extensively studied, its contributions to collective cell migration in vivo remain incompletely understood. Here we show that Src42A, but not Src64, is required for the specification and migration of the border cells in the Drosophila ovary, a well-developed and genetically tractable in vivo cell migration model. We found active Src42A enriched at border cell/nurse cell interfaces, where E-cadherin is less abundant, and depleted from border cell/border cell and border cell/polar cell junctions where E-cadherin is more stable, whereas total Src42A protein co-localizes with E-cadherin. Over-expression of wild type Src42A mislocalized Src activity and prevented border cell migration. Constitutively active or kinase dead forms of Src42A also impeded border cells. These findings establish border cells as a model for investigating the mechanisms of action of Src in cooperative, collective, cell-on-cell migration in vivo.

cell biology↗

bioRxiv2017

Inferring parameters for a lattice-free model of cell migration and proliferation using experimental data

Collective cell spreading takes place in spatially continuous environments, yet it is often modelled using discrete lattice-based approaches. Here, we use data from a series of cell proliferation assays, with a prostate cancer cell line, to calibrate a spatially continuous individual based model (IBM) of collective cell migration and proliferation. The IBM explicitly accounts for crowding effects by modifying the rate of movement, direction of movement, and the rate of proliferation by accounting for pair-wise interactions. Taking a Bayesian approach we estimate the free parameters in the IBM using rejection sampling on three separate, independent experimental data sets. Since the posterior distributions for each experiment are similar, we perform simulations with parameters sampled from a new posterior distribution generated by combining the three data sets. To explore the predictive power of the calibrated IBM, we forecast the evolution of a fourth experimental data set. Overall, we show how to calibrate a lattice-free IBM to experimental data, and our work highlights the importance of interactions between individuals. Despite great care taken to distribute cells as uniformly as possible experimentally, we find evidence of significant spatial clustering over short distances, suggesting that standard mean-field models could be inappropriate.

cell biology↗

bioRxiv2017

Comparative Analysis Of Cell Ultrastructure With Evidences Of Programmed Death In Tissue Cultures Of Cereals

Degrading cells of wheat and barley callus have all known ultrastructural features, which are characteristic for apoptotic cells: intense vacuolization, increasing the size of the nucleus, cupped invaginations of plastids, mitochondria saving until the last stages of cell degradation and the formation of vesicles, similar to apoptotic bodies. It is the first showed that degrading cells in embryogenic callus are characterized with the destruction of the nuclear membrane and the allocated substances of fibrillar nature in the periplasmic space and on the surface of cells.

cell biology↗

bioRxiv2017

A genome-wide RNAi screen identifies MASK as a positive regulator of cytokine receptor stability

In order for cells to sense and thus respond to their environment, they require transmembrane receptors, which bind extracellular ligands and then transduce this signal within the cell. A subset of receptors, with single-pass transmembrane domains are known as cytokine receptors and act via the Janus Kinase and Signal Transducer and Activator of Transcription (JAK/STAT) pathway. These receptors are essential for processes such as haematopoiesis, immune responses and tissue homeostasis. In order to transduce ligand activation, cytokine receptors must dimerise. However, mechanisms regulating their dimerisation are largely unknown. In order to better understand the processes regulating cytokine receptor levels, activity and dimerisation, we used the highly conserved JAK/STAT pathway in Drosophila, which acts via a single receptor, known as Domeless. We have performed a genome-wide RNAi screen in Drosophila cells, identifying MASK as a positive regulator of Domeless dimerisation and protein levels. We show that MASK is able to regulate JAK/STAT signalling both in vitro and in vivo. We go on to show that MASK is able to bind to Domeless via its Ankyrin repeat domains and alters the stability of the receptor. Finally, we extend our observations to the human homologue, ANKHD1, and demonstrate functional conservation, with ANKHD1 able to regulate JAK/STAT signalling and the levels of a subset of pathway receptors in human cells. Taken together, we have identified MASK as a conserved regulator of cytokine receptor levels, which may have implications for human health.

cell biology↗

bioRxiv2017

Lipid droplet and peroxisome biogenesis occur at the same ER subdomains.

Nascent lipid droplet (LD) formation occurs in the ER membrane1-4. It is not known whether LD biogenesis occurs stochastically in the ER or at subdomains with unique protein and lipid composition. We previously identified ER subdomains in S. cerevisiae that contain Pex30, a reticulon-like ER-resident membrane protein5. There are ~25 Pex30-containing puncta in the ER per cell. These sites are regions where preperoxisomal vesicles (PPVs) are generated5. Here we show that Pex30 subdomains are also the location where most nascent LDs form. Mature LDs remain associated with Pex30 subdomains and the same Pex30 subdomain can simultaneously associate with a LD and a PPV. Pex30 subdomains become highly enriched in diacylglycerol (DAG) during LD biogenesis, indicating they have a unique lipid composition. We find that in higher eukaryotes multiple C2 domain containing transmembrane protein (MCTP2) is the functional homologue of Pex30; MCTP2 resides in ER subdomains where most nascent LD biogenesis occurs and that are often associated with peroxisomes. Together, these findings indicate that most LDs and PPVs form and remain associated with conserved ER subdomains and suggest a link between LD and peroxisome biogenesis.

cell biology↗

bioRxiv2017

Cell size and growth rate are modulated by TORC2-dependent signals

The size of all cells, from bacteria to vertebrates, is proportional to the growth rate set by nutrient availability, but the underlying mechanisms are unknown. Here, we show that nutrients modulate TORC2 signaling, and that cell size is proportional to TORC2 signaling in budding yeast. The TORC2 network controls production of ceramide lipids, which play roles in signaling. We discovered that ceramide-dependent signals control both growth rate and cell size. Thus, cells that can not make ceramides fail to modulate their growth rate or size in response to changes in nutrients. PP2A associated with the Rts1 regulatory subunit (PP2ARts1) is embedded in a feedback loop that controls TORC2 signaling and plays an important role in mechanisms that modulate TORC2 signaling in response to nutrients. Together, the data suggest a model in which growth rate and cell size are mechanistically linked by ceramide-dependent signals arising from the TORC2 network.

cell biology↗

bioRxiv2017

Regulator of calcineurin-2 is a ciliary protein with a role in cilia length control.

Almost every cell in the human body extends a primary cilium. Defective cilia function leads to a set of disorders known as ciliopathies characterised by debilitating developmental defects affecting many tissues. Here we report a new role for regulator of calcineurin 2, RCAN2, in primary cilia function. It localises to centrioles and the basal body and is required to maintain normal cilia length. RCAN2 was identified as the most strongly upregulated gene from a comparative RNAseq analysis of cells in which expression of the Golgi matrix protein giantin had been abolished by gene editing. In contrast to previous work where we showed that depletion of giantin by RNAi results in defects in ciliogenesis and in cilia length control, giantin knockout cells generate normal cilia on serum withdrawal. Furthermore, giantin knockout zebrafish show increased expression of RCAN2. Importantly, suppression of RCAN2 expression in giantin knockout cells results in the same defects in cilia length control seen on RNAi of giantin itself. Together these data define RCAN2 as a regulator of cilia function that can compensate for loss of giantin function.

cell biology↗

bioRxiv2017

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains

Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the sub-megabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is however missing, as visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only below 550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ, and provides important biophysical parameters to understand general principles of chromatin organization.

cell biology↗