Biology subjects

Chen, R.

Publications and source records attributed to Chen, R..

At least 19 recordsLinked to original sources

bioRxiv2018

Centrosome-nuclear envelope tethering and microtubule motor-based pulling forces collaborate in centrosome positioning during mitotic entry

Centrosome positioning relative to the nucleus and cell shape is highly regulated across cell types, during cell migration and during spindle formation in cell division. Across most sexually reproducing animals, centrosomes are provided to the oocyte through fertilization and must be positioned properly to establish the zygotic mitotic spindle. How centrosomes are positioned in space and time through the concerted action of key mitotic entry biochemical regulators including Protein Phosphatase 2A (PP2A-B55/SUR-6), biophysical regulators including Dynein and the nuclear lamina is unclear. Here, we uncover a role for PP2A-B55/SUR-6 in regulating centrosome positioning. Mechanistically, PP2A-B55/SUR-6 regulates nuclear size prior to mitotic entry, in turn affecting nuclear envelope-based Dynein density and motor capacity. Using computational simulations, PP2A-B55/ SUR-6 regulation of nuclear size and nuclear envelope Dynein density were both predicted to be required for proper centrosome positioning. Conversely, compromising nuclear lamina integrity led to centrosome detachment from the nuclear envelope and migration defects. Removal of PP2A-B55/SUR-6 and the nuclear lamina simultaneously further disrupted centrosome positioning, leading to unseparated centrosome pairs dissociated from the nuclear envelope. Taken together, we propose a model in which centrosomes migrate and are positioned through the concerted action of nuclear envelope-based Dynein pulling forces and cen-trosome-nuclear envelope tethering.

cell biology↗

bioRxiv2018

Physical and functional interaction between SET1/COMPASS complex component CFP-1 and a Sin3 HDAC complex

The CFP1 CXXC zinc finger protein targets the SET1/COMPASS complex to non-methylated CpG rich promoters to implement tri-methylation of histone H3 Ly4 (H3K4me3). Although H3K4me3 is widely associated with gene expression, the effects of CFP1 loss depend on chromatin context, so it is important to understand the relationship between CFP1 and other chromatin factors. Using a proteomics approach, we identified an unexpected link between C. elegans CFP-1 and a Rpd3/Sin3 histone deacetylase complex. We find that mutants of CFP-1, SIN-3, and the catalytic subunit SET-2/SET1 have similar phenotypes and misregulate common genes. CFP-1 directly binds SIN-3 through a region including the conserved PAH1 domain and recruits SIN-3 and the HDA-1/HDAC subunit to H3K4me3 enriched promoters. Our results reveal a novel role for CFP-1 in mediating interaction between SET1/COMPASS and a Sin3 HDAC complex at promoters and uncover coordinate regulation of gene expression by chromatin complexes having distinct activities.

genomics↗

bioRxiv2018

Structural and biochemical characterization on the cognate and heterologous interactions of the MazEF-mt9 TA system

The toxin-antitoxin (TA) modules widely exist in bacteria, and their activities are associated with the persister phenotype of the pathogen Mycobacterium tuberculosis (M. tb). M. tb causes Tuberculosis, a contagious and severe airborne disease. There are ten MazEF TA systems in M. tb, which play important roles in stress adaptation. How the antitoxins antagonize toxins in M. tb or how the ten TA systems crosstalk to each other are of interests, but the detailed molecular mechanisms are largely unclear. MazEF-mt9 is a unique member among the MazEF families due to its tRNase activity, which is usually carried out by the VapC family toxins. Here we present the cocrystal structure of the MazEF-mt9 complex at 2.7 [A]. By characterizing the association mode between the TA pairs through various characterization techniques, we found that MazF-mt9 not only bound its cognate antitoxin, but also the non-cognate antitoxin MazE-mt1, a phenomenon that could be also observed in vivo. Based on our structural and biochemical work, we proposed that the cognate and heterologous interactions among different TA systems work together to relieve MazF-mt9s toxicity to M. tb cells, which may facilitate their adaptation to the stressful conditions encountered during host infection.\n\nIMPORTANCETuberculosis (TB) is one of the most severe contagious diseases. Caused by Mycobacterium tuberculosis (M. tb), it poses a serious threat to human health. Additionally, TB is difficult to cure because of the multipledrug-resistant (MDR) and extensively drug-resistant (XDR) M. tb strains. Toxin-antitoxin (TA) systems have been discovered to widely exist in prokaryotic organisms with diverse roles, normally composed of a pair of molecules that antagonize each other. M. tb has ten MazEF systems, and some of them have been proved to be directly associated with the genesis of persisters and drug-resistance of M. tb. We here report the MazEF-mt9 complex structure, and thoroughly characterized the interactions between MazF-mt9 with MazEs within or outside the MazEF-mt9 family. Our study not only revealed the crosstalks between TA families and its significance to M. tb survival but also offers insights into potential anti-TB drug design.

biochemistry↗

bioRxiv2018

Epigenomic Profiling and Single-Nucleus-RNA-Seq Reveal Cis-Regulatory Elements in Human Retina, Macula and RPE and Non-Coding Genetic Variation.

Cis-regulatory elements (CREs) orchestrate the dynamic and diverse transcriptional programs that assemble the human central nervous system (CNS) during development and maintain its function throughout life. Genetic variation within CREs plays a central role in phenotypic variation in complex traits including the risk of developing disease. However, the cellular complexity of the human brain has largely precluded the identification of functional regulatory variation within the human CNS. We took advantage of the retina, a well-characterized region of the CNS with reduced cellular heterogeneity, to establish a roadmap for characterizing regulatory variation in the human CNS. This comprehensive resource of tissue-specific regulatory elements, transcription factor binding, and gene expression programs in three regions of the human visual system (retina, macula, retinal pigment epithelium/choroid) reveals features of regulatory element evolution that shape tissue-specific gene expression programs and defines the regulatory elements with the potential to contribute to mendelian and complex disorders of human vision.

neuroscience↗

bioRxiv2018

in vitro egg production by the human parasite Schistosoma mansoni

Schistosomes infect over 200 million people. The prodigious egg output of these parasites is the sole driver of pathology due to infection, yet our understanding of their sexual reproduction is limited because egg production is not sustained for more than a few days in vitro. Here, we describe culture conditions that support schistosome sexual development and sustained egg production in vitro. Female schistosomes rely on continuous pairing with male worms to fuel the maturation of their reproductive organs. Exploiting these new culture conditions, we explore the process of male-stimulated female maturation and demonstrate that physical contact with a male worm, and not insemination, is sufficient to induce female development and the production of viable parthenogenetic haploid embryos. We further report the characterization of a novel nuclear receptor, that we call vitellogenic factor 1, that is essential for female sexual development following pairing with a male worm. Taken together, these results provide a platform to study the fascinating sexual biology of these parasites on a molecular level, illuminating new strategies to control schistosome egg production.

microbiology↗

bioRxiv2018

PHASE TRANSITIONED NUCLEAR OSKAR PROMOTES CELL DIVISION OF DROSOPHILA PRIMORDIAL GERM CELLS

Germ granules are non-membranous ribonucleoprotein granules deemed the hubs for post-transcriptional gene regulation and functionally linked to germ cell fate across species. Little is known about the physical properties of germ granules and how these relate to germ cell function. Here we study two types of germ granules in the Drosophila embryo: cytoplasmic germ granules that instruct primordial germ cells (PGCs) formation and nuclear germ granules within early PGCs with unknown function. We show that cytoplasmic and nuclear germ granules are phase transitioned condensates nucleated by Oskar protein that display liquid as well as hydrogel-like properties. Focusing on nuclear granules, we find that Oskar drives their formation in heterologous cell systems. Multiple, independent Oskar protein domains synergize to promote granule phase separation. Deletion of Oskars nuclear localization sequence specifically ablates nuclear granules in cell systems. In the embryo, nuclear germ granules promote germ cell divisions thereby increasing PGC number for the next generation.

cell biology↗

bioRxiv2018

Effective principal components analysis of SNP data

PCA is frequently used to display and discover patterns in SNP data from humans, animals, plants, and microbes--especially to elucidate population structure. Given the popularity of PCA, one might expect that PCA is understood well and applied effectively. However, our literature survey of 125 representative articles that apply PCA to SNP data shows that three choices have usually been made poorly: SNP coding, PCA variant, and PCA graph. Accordingly, we offer several simple recommendations for effective PCA analysis of SNP data. The ultimate benefit from informed and optimal choices of SNP coding, PCA variant, and PCA graph is expected to be discovery of more biology, and thereby acceleration of medical, agricultural, and other vital applications.

genomics↗

bioRxiv2018

A circuit motif in the songbird basal ganglia for computing predicted performance quality

Ventral tegmental area (VTA) dopamine neurons signal prediction error, the difference between actual and predicted outcome, but it remains unclear how error is computed. Here we identify in songbirds a ventral basal ganglia (vBG) region that is required for song learning and that sends prediction error signals to VTA. During singing, vBG neurons heterogeneously encoded song timing, auditory error, predicted error, and the difference between the two (prediction error). Viral tracing revealed inputs to vBG from auditory and vocal motor thalamus, auditory and vocal motor cortex, and VTA. Our findings reveal a classic actor-critic circuit motif in which a ventral critic learns the prediction component of a prediction error signal that is relayed by VTA to a dorsal actor (the vocal motor BG nucleus Area X). A circuit motif for computing reward prediction error can compute predicted performance quality during motor sequence learning.

neuroscience↗

bioRxiv2018

Vesicular delivery of the antifungal antibiotics of Lysobacter enzymogenes C3

Lysobacter enzymogenes C3 is a predatory strain of gram-negative gliding bacteria that produces antifungal antibiotics by the polyketide synthetic pathway. Outer membrane vesicles (OMV) are formed as a stress response and can deliver virulence factors to host cells. The production of OMV by C3 and their role in antifungal activity are reported here. Vesicles in the range of 130-150 nm in diameter were discovered in the cell-free supernatants of C3 cultures. These OMV contain molecules characteristic of bacterial outer membranes, such as lipopolysaccharide and phospholipids. In addition, they contain chitinase activity and essentially all of the heat stable antifungal activity in cell supernatants. We show here that C3 OMV can directly inhibit growth of the yeast Saccharomyces cerevisiae as well as the filamentous fungus Fusarium subglutinans. The activity is dependent on physical contact between OMV and the cells. Furthermore, fluorescent lipid labeling of C3 OMV demonstrated transfer of the membrane-associated probe to yeast cells, suggesting the existence of a mechanism of delivery for membrane-associated molecules. Mass spectrometric analysis of C3 OMV extracts indicates the presence of molecules with molecular weights identical to some of the previously identified antifungal products of C3. These data together suggest that OMV act as an important remote mobile component of predation by Lysobacter.\n\nImportanceThe data presented here suggest a newly discovered function of outer membrane vesicles (OMV) that are produced from the outer membrane of the bacterial species Lysobacter enzymogenes C3. We show that these OMV can be released from the surface of the cells to deliver antibiotics to target fungal organisms as a mechanism of killing or growth inhibition. Understanding the role of OMV in antibiotic delivery can generally lead to improved strategies for dealing with antibiotic-resistant organisms. These results also add to the evidence that some bacterially produced antibiotics can be discovered and purified using methods designed for isolation of nanoscale vesicles. Information on these systems can lead to better identification of active molecules or design of delivery vehicles for these molecules.

microbiology↗

bioRxiv2018

Tissue-specific Gene Expression Prediction Associates Vitiligo with SUOX through an Active Enhancer

Vitiligo is an autoimmune disease featuring destruction of melanocytes, which results in patchy depigemtation of skin and hair; two vitiligo GWAS studies identified multiple significant associations, including SNPs in 12q13.2 region. But one study ascribed the association to IKZF4 because it encodes a regulator of T cell activation and is associated with two autoimmune diseases; while the other study ascribed the association to PMEL because it encodes melanocyte protein and has the strongest differential expression between vitiligo lesions and perilesional normal skins. Here we show that vitiligo associated gene in 12q13.2 region is SUOX. Reanalyzing one GWAS dataset, we predicted tissue-specific gene-expression by leveraging Genotype-Tissue Expression (GTEx) datasets, and performed association mapping between the predicted gene-expressions and vitiligo status. SUOX expression is significantly associated with vitiligo in both Nerve (tibia) and Skin (sun exposed) tissues. Epigenetic marks encompass the most significant eQTL of SUOX in both nerve and skin tissues suggest a putative enhancer 3Kb downstream of SUOX. We silenced the putative enhancer using the CRISPR interference system and observed 50% decrease in SUOX expression in K562 cells, a cell line that has similar DNase hypersensitive sites and gene expression pattern to the skin tissue at SUOX locus. Our work provided an example to make sense GWAS hits through examining factors that affect gene expression both computationally and experimentally.

genetics↗

bioRxiv2018

Let-7i-5p regulation of cell morphology and migration through distinct signaling pathways in normal and pathogenic fibroblasts from urethra

Pelvic fracture urethral distraction defects (PFUDD) is a common disease that could severely affect patients life quality, yet little is known about the molecular mechanism associated with pathogenic fibrosis in PFUDD. In this study, we found that let-7i-5p could regulate different cellular events in normal and pathogenic fibroblasts through three distinct signaling pathways. Interestingly, those regulations are compromised during the translation from mRNA to protein, and partially based on pathogenic status of the fibroblasts. By analyzing the molecular mechanism associated with its function, we conclude that let-7i-5p plays an essential role in regulating cell shape and tissue elasticity, cell migration, cell morphology and cytoskeleton, and could serve as a potential target for clinical treatment of urethral stricture patients.

molecular biology↗

bioRxiv2018

A computational model of task allocation in social insects: ecology and interactions alone can drive specialisation

Social insect colonies are capable of allocating their workforce in a decentralised fashion; addressing a variety of tasks and responding effectively to changes in the environment. This process is fundamental to their ecological success, but the mechanisms behind it remain poorly understood. While most models focus on internal and individual factors, empirical evidence highlights the importance of ecology and social interactions. To address this gap we propose a game theoretical model of task allocation. Individuals are characterised by a trait that determines how they split their energy between two prototypical tasks: foraging and regulation. To be viable, a colony needs to learn to adequately allocate its workforce between these two tasks. We study two different processes: individuals can learn relying exclusively on their own experience, or by using the experiences of others via social learning. We find that social organisation can be determined by the ecology alone, irrespective of interaction details. Weakly specialised colonies in which all individuals tend to both tasks emerge when foraging is cheap; harsher environments, on the other hand, lead to strongly specialised colonies in which each individual fully engages in a single task. We compare the outcomes of self-organised task allocation with optimal group performance. Counter to intuition, strongly specialised colonies perform suboptimally, whereas the group performance of weakly specialised colonies is closer to optimal. Social interactions lead to important differences when the colony deals with dynamic environments. Colonies whose individuals rely on their own experience are more exible when dealing with change. Our computational model is aligned with mathematical predictions in tractable limits. This different kind of model is useful in framing relevant and important empirical questions, where ecology and interactions are key elements of hypotheses and predictions.

ecology↗

bioRxiv2018

Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1

A central goal of HIV-1-vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion-stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryo-electron microscopy structures of these antibodies revealed fusion peptide-conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses suggesting translatability. The N terminus of the HIV-1-fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.

immunology↗

bioRxiv2018

NRG1-mediated recognition of HopQ1 reveals a link between PAMP and Effector-triggered Immunity.

O_LIMembers of the hopQ1/XopQ family of effectors are conserved amongst pathogenic bacteria suggesting an important function in virulence. Therefore, the identification of R proteins recognising members of this family is potentially of high value to achieve broad-spectrum resistance in crops.\nC_LIO_LIRecent studies demonstrated that HopQ1/XopQ recognition is EDS1-dependant and is mediated by the TIR-NB-LRR protein Roq1. Using our recently described R gene RNAi library, we have investigated the mechanism of HopQ1 recognition and the other components of its signalling network.\nC_LIO_LIWe show that silencing of the CCR-NB-LRR helper protein N Requirement Gene 1 (NRG1) prevents HopQ1 recognition in N. benthamiana and that NRG1 expression confers recognition of HopQ1 and restricts Pto DC3000 proliferation in the otherwise susceptible host Arabidopsis. Moreover NRG1 expression is briefly but strongly induced at a very early stage of the plant innate response, establishing a strong dependency link between PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI).\nC_LIO_LIOverall we demonstrate that in addition to Roq1, HopQ1 recognition in N. benthamiana requires the CCR-NB-LRR protein NRG1 and propose a model based on the dual requirement of a CCR-NB-LRR and a TIR-NB-LRR that could extend beyond HopQ1 detection and possibly be used to recognize other pathogen effectors.\nC_LI

plant biology↗

bioRxiv2018

Task activations produce spurious but systematic inflation of task functional connectivity estimates

Most neuroscientific studies have focused on task-evoked activations (activity amplitudes at specific brain locations), providing limited insight into the functional relationships between separate brain locations. Task-state functional connectivity (FC) - statistical association between brain activity time series during task performance moves beyond task-evoked activations by quantifying functional interactions during tasks. However, many task-state FC studies do not remove the first-order effect of taskevoked activations prior to estimating task-state FC. It has been argued that this results in the ambiguous inference \"likely active or interacting during the task\", rather than the intended inference \"likely interacting during the task\". Utilizing a neural mass computational model, we verified that task-evoked activations substantially and inappropriately inflate task-state FC estimates, especially in functional MRI (fMRI) data. Various methods attempting to address this problem have been developed, yet the efficacies of these approaches have not been systematically assessed. We found that most standard approaches for fitting and removing mean task-evoked activations were unable to correct these inflated correlations. In contrast, methods that flexibly fit mean task-evoked response shapes effectively corrected the inflated correlations without reducing effects of interest. Results with empirical fMRI data confirmed the models predictions, revealing activation-induced task-state FC inflation for both Pearson correlation and psychophysiological interaction (PPI) approaches. These results demonstrate that removal of mean task-evoked activations using an approach that flexibly models task-evoked response shape is an important preprocessing step for valid estimation of task-state FC.\n\nHighlightsO_LIComputational model shows task inflation of functional connectivity estimates\nC_LIO_LIHemodynamic responses cause task activations to further inflate estimates\nC_LIO_LIStandard approaches to remove task activations leave many false positives\nC_LIO_LIMethods that flexibly fit hemodynamic response shape effectively correct inflation\nC_LIO_LICorrection of functional connectivity inflation verified with empirical fMRI data\nC_LI

neuroscience↗

bioRxiv2018

Chromatin accessibility dynamics across C. elegans development and ageing

An essential step for understanding the transcriptional circuits that control development and physiology is the global identification and characterization of regulatory elements. Here we present the first map of regulatory elements across the development and ageing of an animal, identifying 42,245 elements accessible in at least one C. elegans stage. Based on nuclear transcription profiles, we define 15,714 protein-coding promoters and 19,231 putative enhancers, and find that both types of element can drive orientation-independent transcription. Additionally, hundreds of promoters produce transcripts antisense to protein coding genes, suggesting involvement in a widespread regulatory mechanism. We find that the accessibility of most elements is regulated during development and/or ageing and that patterns of accessibility change are linked to specific developmental or physiological processes. The map and characterization of regulatory elements across C. elegans life provides a platform for understanding how transcription controls development and ageing.

genomics↗

bioRxiv2018

The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice

Accumulated genetic evidences indicate that the contactin associated protein-like (CNTNAP) family is implicated in autism spectrum disorders (ASD). In this study, we identified genetic mutations in the CNTNAP3 gene from Chinese Han ASD cohorts and Simons Simplex Collections. We found that CNTNAP3 interacted with synaptic adhesion proteins Neuroligin1 and Neuroligin2, as well as scaffolding proteins PSD95 and Gephyrin. Significantly, we found that CNTNAP3 played an opposite role in controlling the development of excitatory and inhibitory synapses in vitro and in vivo, in which ASD mutants exhibited loss-of-function effects. In this study, we showed that Cntnap3-null mice exhibited deficits in social interaction, spatial learning and prominent repetitive behaviors. These evidences elucidate the pivotal role of CNTNAP3 in synapse development and social behaviors, providing the mechanistic insights for ASD.

neuroscience↗

bioRxiv2017

The segregation of vocal circuits solves a credit assignment problem associated with multi-objective reinforcement learning

Motor circuits vary in topographic organization, ranging from a coarse relationship between neuron location and function to highly localized regions controlling specific behaviors. For unclear reasons, vocal learning circuits lie at this second extreme: they repeatedly evolved to be spatially segregated from other parts of the motor system. Here we show that spatially segregated motor circuits can solve a specific problem that arises when an animal tries to learn two things at once. We trained songbirds in vocal and place learning paradigms with brief strobe light flashes and noise bursts. Strobe light negatively reinforced place learning but did not affect song syllable learning. Noise bursts positively reinforced place preference but negatively reinforced syllable learning. These double dissociations indicate that vocalization-related reinforcement signals specifically target the vocal motor system, while place-related reinforcement signals specifically target the navigation system. Non-global, target-specific reinforcement signals have established utility in machine implementation of multi-objective learning. In vocal learners, such signals could enable an animal to practice vocalizing as it does other things such as forage for food or learn to walk.

neuroscience↗