Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 757 records · Page 42Linked to original sources

bioRxiv2023

Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum

Exceptionally long genes and cis-regulatory enhancers are selectively activated in mammalian brain neurons, and these loci are mutation hotspots in neurological disorders. However, the organization of these large genomic elements at the level of chromosome folding, beyond local enhancer-promoter interactions, remains poorly understood. Here, we report the discovery of a nuclear subcompartment in the mouse cerebellum formed by near-megabase long enhancers and their associated long genes encoding synaptic or signaling proteins. Genomic regions within this subcompartment reside in the outer-half of the nucleus, separated from other transcriptionally active structures. Using an in vivo CRISPR genetic mini-screen, we uncover a specific role for the transcription factor Etv1 in coupling the compartmentalization of neuronal long genes with their expression. Together, our study defines mechanisms that organize transcriptionally active genes across chromosomes in the mammalian brain.

neuroscience↗

bioRxiv2023

Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures

The interactions between nucleic acids and proteins are important in diverse biological processes. The high-quality prediction of nucleic-acid-binding sites continues to pose a significant challenge. Presently, the predictive efficacy of sequence-based methods is constrained by their exclusive consideration of sequence context information, whereas structure-based methods are unsuitable for proteins lacKing Known tertiary structures. Though protein structures predicted by AlphaFold2 could be used, the extensive computing requirement of AlphaFold2 hinders its use for genome-wide applications. Based on the recent breaKthrough of ESMFold for fast prediction of protein structures, we have developed GLMSite, which accurately identifies DNA and RNA-binding sites using geometric graph learning on ESMFold predicted structures. Here, the predicted protein structures are employed to construct protein structural graph with residues as nodes and spatially neighboring residue pairs for edges. The node representations are further enhanced through the pre-trained language model ProtTrans. The networK was trained using a geometric vector perceptron, and the geometric embeddings were subsequently fed into a common networK to acquire common binding characteristics. Then two fully connected layers were employed to learn specific binding patterns for DNA and RNA, respectively. Through comprehensive tests on DNA/RNA benchmarK datasets, GLMSite was shown to surpass the latest sequence-based methods and be comparable with structure-based methods. Moreover, the prediction was shown useful for the inference of nucleic-acid-binding proteins, demonstrating its potential for protein function discovery. The datasets, codes, together with trained models are available at https://github.com/biomed-AI/nucleic-acid-binding.

bioinformatics↗

bioRxiv2023

Predicting Disease-gene Associations through Self-supervised Mutual Infomax Graph Convolution Network

Illuminating associations between diseases and genes can help reveal the pathogenesis of syndromes and contributes to treatments, but a large number of associations still remained unexplored. To identify novel disease-gene association, many computational methods have been developed using disease and gene related prior knowledge. However, these methods remain of relatively inferior performance due to the limited external data sources and the inevitable noise among the prior knowledge. In this study, we have developed a new method, Self-Supervised Mutual Infomax Graph Convolution Network (MiGCN), to predict disease-gene associations under the guidance of external disease-disease and gene-gene collaborative graphs. The noises within the collaborative graphs were eliminated by maximizing the mutual information between nodes and neighbors through a graphical mutual infomax layer. In parallel, the node interactions were strengthened by a novel informative message passing layer to improve the learning ability of graph neural network. The extensive experiments showed that our model achieves performance improvement over the state-of-art method by more than 8% on AUC. The datasets, source codes and trained models of MiGCN are available at https://github.com/biomed-AI/MiGCN.

bioinformatics↗

bioRxiv2023

The canonical single-stranded DNA binding protein SSB is not an essential replication protein but an RNA chaperon in the hyperthermophilic archaeon Saccharolobus islandicus REY15A

Single-stranded DNA binding proteins (SSBs) have been regarded as indispensable factors in all three domains of life since they play vital roles in DNA replication. Herein, we report that genes coding for the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in the hyperthermophilic archaeon Saccharolobus islandicus REY15A can both be deleted. The growth is not affected, and the cell cycle progression and genome stability of the deletion strains is not impaired, suggesting that SisSSB and SisDBP are not essential for cell viability. Interestingly, at a lower temperature (55{degrees}C), the protein level of SisSSB increases [~]1.8 fold in the wild type and the growth of {Delta}Sisssb and {Delta}Sisssb{Delta}Sisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and unwinding RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of the cold shock proteins CspABGE in E. coli, suggesting that SisSSB functions as RNA chaperon. We show that a two-fold overexpression of SisSSB is beneficial to the cell growth at lower temperature, but it has detrimental effect on the cell growth and cell cycle progression at normal growth temperature, which differs from bacterial Csp proteins. Importantly, these in vitro and in vivo activities are conserved in SSB subtype SSB-1 in Crenarchaeota species that lack bacterial Csp homologs. Overall, we have clarified the function of the archaeal canonical SSB which does not function as a DNA processing factor, but plays a role in processes requiring dsRNA or DNA/RNA hybrid unwinding.

microbiology↗

bioRxiv2023

Cholinergic stimulation increases cortical spine formation via local inhibitory circuit

Basal forebrain (BF) cholinergic projections densely innervate the neocortex, releasing acetylcholine (ACh) to modulate neuronal excitability, thereby influencing sensory processing and cognitive functions. However, the synaptic basis of such ACh-induced effects in vivo remains elusive. To investigate how ACh release from BF regulates synaptic dynamics in the neocortex, we selectively stimulated BF cholinergic neurons in mice, and used two-photon microscopy to track structural changes of dendritic spines on cortical pyramidal neurons. We found that optogenetic and chemogenetic stimulation of BF cholinergic neurons rapidly induced spine formation in layer 5 pyramidal neurons in the auditory cortex and the posterior parietal cortex. Selective blockage of ACh receptors (AChRs) demonstrated that nicotinic AChRs are required for the ACh-induced spine formation. We also found that Ach-induced spine formation of pyramidal neurons requires the activity of cortical somatostatin-expressing inhibitory interneurons. Together, our study revealed ACh-induced synaptic plasticity in the cortical microcircuit in vivo, providing a synaptic mechanism for cortical neuronal plasticity and functional changes associated with BF ACh release.

neuroscience↗

bioRxiv2023

Aberrant regulation of the Rap1 small GTPase in response to escalating, intermittent stress produces hippocampal synaptic and cognitive dysfunction

The effects of repeated stress on cognitive impairment are thought to be mediated, at least in part, by reductions in the stability of dendritic spines in brain regions critical for proper learning and memory, including the hippocampus. Small GTPases are particularly potent regulators of dendritic spine formation, stability, and morphology in hippocampal neurons. Through the use of small GTPase protein profiling in mice, we identify increased levels of synaptic Rap1 in the hippocampal CA3 region in response to escalating, intermittent stress. We then demonstrate that increased Rap1 in the CA3 is sufficient in and of itself to produce stress-relevant dendritic spine and cognitive phenotypes. Further, using super-resolution imaging, we investigate how the pattern of Rap1 trafficking to synapses likely underlies its effects on the stability of select dendritic spine subtypes. These findings illuminate the involvement of aberrant Rap1 regulation in the hippocampus in contributing to the psychobiological effects of stress.

neuroscience↗

bioRxiv2023

Human Th17- and IgG3-associated autoimmunity induced by a translocating gut pathobiont

Extraintestinal autoimmune diseases are multifactorial with translocating gut pathobionts implicated as instigators and perpetuators in mice. However, the microbial contributions to autoimmunity in humans remain largely unclear, including whether specific pathological human adaptive immune responses are triggered by such pathobionts. We show here that the translocating pathobiont Enterococcus gallinarum induces human IFN{gamma}+ Th17 differentiation and IgG3 subclass switch of anti-E. gallinarum RNA and correlating anti-human RNA autoantibody responses in patients with systemic lupus erythematosus and autoimmune hepatitis. Human Th17 induction by E. gallinarum is cell-contact dependent and involves TLR8-mediated human monocyte activation. In murine gnotobiotic lupus models, E. gallinarum translocation triggers IgG3 anti-RNA autoantibody titers that correlate with renal autoimmune pathophysiology and with disease activity in patients. Overall, we define cellular mechanisms of how a translocating pathobiont induces human T- and B-cell-dependent autoimmune responses, providing a framework for developing host- and microbiota-derived biomarkers and targeted therapies in extraintestinal autoimmune diseases. One Sentence SummaryTranslocating pathobiont Enterococcus gallinarum promotes human Th17 and IgG3 autoantibody responses linked to disease activity in autoimmune patients.

immunology↗

bioRxiv2023

Personalized connectivity-based network targeting model of TMS for treatment of psychiatric disorders: computational feasibility and reproducibility

Consider the limited clinical efficacy of transcranial magnetic stimulation (TMS) due to heterogeneity in treatment outcomes, the utilization of individual functional connectivity (FC) can enhance the prediction accuracy in the network targeting model. However, the low signal-to-noise ratio (SNR) of FC poses a challenge when utilizing individual resting-state FC (rsFC). To overcome this challenge, proposed solutions include increasing the scan duration and employing clustering approaches to enhance the stability of FC. In this study, we aimed to evaluate the stability of a personalized functional-based network targeting model in individuals with major depressive disorder (MDD) and schizophrenia with auditory verbal hallucinations (AVH). Using resting-state functional magnetic resonance imaging (rsfMRI) data from the Human Connectome Project (HCP), we assessed the models stability and employed longer scan durations (7 minutes, 14 minutes, 21 minutes, 28 minutes) and clustering methodologies to improve the precision of identifying optimal individual sites. Our findings demonstrate that a scan duration of 28 minutes and the utilization of the clustering approach lead to stable identification of individual sites, as evidenced by the intraindividual distance falling below the [~]1cm spatial resolution of TMS. These findings contribute to the understanding of individualized TMS targeting and have implications for improving treatment outcomes in psychiatric disorders.

neuroscience↗

bioRxiv2023

Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins

Prokaryotic Argonaute (pAgo) proteins, a class of DNA/RNA-guided programmable endonucleases, have been extensively utilized in nucleic acid biosensors. The specific binding and cleavage of nucleic acids by pAgo proteins, which are crucial processes for their applications, are dependent on the presence of Mn2+ bound in the pockets, as verified through X-ray crystallography. However, a comprehensive understanding of how dissociated Mn2+ in the solvent affects the catalytic cycle, and its underlying regulatory role in this structure-function relationship, remains underdetermined. By combining experimental and computational methods, this study reveals that unbound Mn2+ in solution enhances the flexibility of diverse pAgo proteins. This increase in flexibility through decreasing the number of hydrogen bonds, induced by Mn2+, leads to higher affinity for substrates, thus facilitating cleavage. More importantly, Mn2+-induced structural flexibility increases the mismatch tolerance between guide-target pairs by increasing the conformational states, thereby enhancing the cleavage of mismatches. Further simulations indicated that the enhanced flexibility in linkers triggers conformational changes in the PAZ domain for recognizing various lengths of nucleic acids. Additionally, Mn2+-induced dynamic alterations of the protein cause a conformational shift in the N domain and catalytic sites towards their functional form, resulting in a decreased energy penalty for target release and cleavage. These findings demonstrate that the dynamic conformations of pAgo proteins, resulting from the presence of the unbound Mn2+ in solution, significantly promote the catalytic cycle of endonucleases and the tolerance of cleavage to mismatches. This flexibility enhancement mechanism serves as a general strategy employed by Ago proteins from diverse prokaryotes to accomplish their catalytic functions and provide useful information for Ago-based precise molecular diagnostics.

biophysics↗

bioRxiv2023

Variations in Homoeologous Dosage and Epigenomics Mark the Early Evolution of Synthetic Brassica Tetraploids

Polyploidization is important in plant evolution and is becoming increasingly important in crop breeding and material creation. Studies have provided evidence for structural variations and epigenomic repatterning in synthetic polyploidizations, but the relationships between structural and epigenomic variations, as well as their effects on gene expression and phenotypic variations are unknown. Here, we investigated the genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics, in the leaf organ as a representative, of progenies from eight generations that derived from the synthetic tetraploidization between Brassica rapa and Brassica oleracea. We found that half or complete deletion/duplication of fragments ranging in size from 400 kb to 65.85 Mb, with a mean size of 5.70 Mb, occurred frequently from the first generation of selfing and thereafter. The genes located in these DelDups expressed at levels expected for a positive dosage effect, as indicated by the positive association between expression and the copy number of these genes. Plants containing these DelDups also showed distinct phenotypic variations. The whole genome methylation level experienced significant fluctuations in different generations and eventually decreased in the latter generations. Moreover, the DelDups did not show methylation changes from other individuals of the same generation, and the local regions with methylation alterations did not affect gene expression. Our findings provide new insights into the early evolution of polyploid genomes and guide the use of synthetic polyploidizations in breeding.

genomics↗

bioRxiv2023

Uncovering Ghost Introgression Through Genomic Analysis of a Distinct East Asian Hickory Species

Although the possibility of introgression from ghost lineages (all unsampled extant and extinct taxa) is now widely recognized, detecting and characterizing ghost introgression remains a challenge. Here, we propose a combined use of the popular D-statistic method, which tests for the presence of introgression, and the full-likelihood method BPP, which determines which of the possible gene-flow scenarios, including ghost introgression, is truly responsible. We illustrate the utility of this approach by investigating the reticulation and bifurcation history of the genus Carya (Juglandaceae), including the beaked hickory Carya sinensis. To achieve this goal, we generated two chromosome-level reference genomes respectively for C. sinensis and C. cathayensis. Furthermore, we re-sequenced the whole genomes of 43 individuals from C. sinensis and one individual from each of the 11 diploid species of Carya. The latter dataset with one individual per species is used to reconstruct the phylogenetic networks and estimate the divergence time of Carya. Our results unambiguously demonstrate the presence of ghost introgression from an extinct lineage into the beaked hickory, dispelling certain misconceptions about the phylogenetic history of C. sinensis. We also discuss the profound implications of ghost introgression into C. sinensis for the historical biogeography of hickory species. [BPP; Carya; D-statistic; gene flow; ghost introgression]

evolutionary biology↗

bioRxiv2023

IQCH regulates spermatogenesis by interacting with CaM to promote RNA-binding proteins' expression

IQ motif-containing proteins can be recognized by calmodulin (CaM) and are essential for many biological processes. However, the role of IQ motif-containing proteins in spermatogenesis is largely unknown. In this study, we identified a loss-of-function mutation in the novel gene IQ motif-containing H (IQCH) in a Chinese family with male infertility characterized by a cracked flagellar axoneme and abnormal mitochondrial structure. To verify the function of IQCH, Iqch knockout (KO) mice were generated via CRISPR-Cas9 technology. As expected, the Iqch KO male mice exhibited impaired fertility, which was related to deficient acrosome activity and abnormal structures of the axoneme and mitochondria, mirroring the patient phenotypes. Mechanistically, IQCH can bind to CaM and subsequently regulate the expression of RNA-binding proteins (especially HNRPAB), which are indispensable for spermatogenesis. Overall, this study revealed the function of IQCH, expanded the role of IQ motif-containing proteins in reproductive processes, and provided important guidance for genetic counseling and genetic diagnosis of male infertility.

genetics↗

bioRxiv2023

A pseudovirus-based method to dynamically mimic SARS-CoV-2-associated cell-to-cell fusion and transmission

SARS-CoV-2 has caused the global tremendous loss and continues to evolve to generate variants. Entry of SARS-CoV-2 into the host cells is primarily mediated by Spike (S), which binds to the host receptor hACE2 and initiates virus-cell membrane fusion. Cell fusion contributes to viral entry, cell-to-cell transmission and tissue damage in COVID-19 patients. Many reporter assays have been developed to study S-mediated cell fusion by equally coculturing S-expressing cells and hACE2-positive cells. However, these strategies cannot fully simulate cell-to-cell fusion and transmission of SARS-CoV-2 infection, in which virions from a single target cell transmit to the neighbor cells and induce syncytia formation. Here, we design a pseudovirus-based method to dynamically mimic cell-to-cell fusion and transmission of SARS-CoV-2. We coculture a small number of pseudovirus-producing 293FT cells and a large number of hACE2-expressing 293T cells, and demonstrate that a single cell producing S-pseudotyped virions can induce significant syncytia of hACE2-positive cells. This pseudovirus-based method is a powerful tool to screen and estimate potential inhibitors of S-driven syncytia. Moreover, this strategy can also be utilized to explore fusogenic ability of SARS-CoV-2 variants. Together, the pseudovirus-based method we report here will be beneficial to drug screening and scientific research against SARS-CoV-2 or future emerging coronavirus.

microbiology↗

bioRxiv2023

Se-Glargine II. Native Function of a Basal Insulin Analog Stabilized by an Internal Diselenide Bridge

Insulin glargine, the active component of basal clinical pharmaceutical formulations Lantus(R) and Toujeo(R) (Sanofi), provides a model for principles of therapeutic protein design. Formulated in solution at pH 4, insulin glargine exhibits a shifted isoelectric point (from pH 5.3 to neutral pH) due to a basic dipeptide B-chain extension (ArgB31-ArgB32). In the first article in this series, we described pairwise substitution of CysA6 and CysA11 by seleno-cysteine (Sec; the 21st encoded amino acid) by solid-phase peptide synthesis. 1H-2H amide proton exchange, as monitored by 1H-NMR spectroscopy, provides evidence that substitution of internal cystine A6-A11 by a diselenide bridge stabilizes the protein and damps segmental conformational fluctuations. Further, this analog and its major metabolites M1 and M2 (respectively denoting proteolytic derivatives lacking ArgB31-ArgB32 or ThrB30-ArgB31-ArgB32) exhibit native hormonal activity in mammalian cell-based assays measuring dose-dependent autophosphorylation of the insulin receptor (pIR/IR ratio) and metabolic gene regulation in human liver-derived HepG2 cells. The internal diselenide bridge also did not alter respective baseline mitogenicities of insulin glargine or its proteolytic products as evaluated by a qPCR-based assay of the balance between proliferative and antiproliferative cyclin gene expression; the assays employed L6 myoblasts over-expressing mitogenic IR isoform A. Given such native function, shelf life--and hence global access to insulin in the developing world--may be enhanced by stabilizing diselenide chemistry.

biochemistry↗

bioRxiv2023

Molecular pathway of mitochondrial preprotein import through the TOM-TIM23

Most mitochondrial proteins need to be imported from the cytosol. Over half of mitochondrial proteins are imported through the pre-sequence pathway that is controlled by the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. It is unclear on the molecular level how proteins cross the mitochondrial double membranes through the TOM and TIM23 complexes. Here, we report the assembly of the active TOM-TIM23 supercomplex with translocating polypeptide substrates captured in the import pathway. Electron cryo-microscopy (Cryo-EM) analyses reveal that during translocation across the outer membrane, the polypeptide substrates pass through the center of the Tom40 channel while interacting with a glutamine-rich patch in the inner wall of Tom40. Structural and biochemical analyses show that the TIM23 complex contains a heterotrimer of the subunits Tim23, Tim17, and Mgr2 in the inner membrane. Tim17 and Mgr2 shield the polypeptide substrates from the lipid environment. The import pathway consists of two highly conserved residue patches of Tim17, one negatively charged patch at the entrance and one hydrophobic patch in the middle of the pathway. These data reveal an unexpected pre-sequence pathway mediated by the TOM-TIM23 supercomplex for facilitating protein import across the double membranes of mitochondria.

molecular biology↗

bioRxiv2023

Tumor-derived exosomal miR-222-3p induce cancer-associated fibroblasts activation to foster progression of renal cancer

The interaction between tumor-derived exosomes and stroma is crucial for tumor progression. However, the mechanisms by which tumor cells influence stromal changes are not yet fully understood. Our study revealed that high-metastatic renal cancer cells are more effective in converting normal fibroblasts into cancer-associated fibroblasts (CAFs) compared to low-metastatic renal cancer cells. Meanwhile, high-metastatic renal cancer cells secrete more exosomal miR-222-3p, which can directly target PANK3, activate NF-kB signaling pathway in fibroblasts and induce intracellular metabolic reprogramming to produce more lactic acid through Warburg effect. The activated CAFs further promote renal cancer progression by secreting lactic acid and inflammatory cytokines, including IL-6 and IL-8. Patients with renal cancer who have high levels of serum exocrine miR-222-3p are more likely to experience progression. These findings suggest that the intercellular communication between renal cancer cells and fibroblasts is facilitated by tumor exosomes. Targeting this communication may hold promise for the prevention and treatment of renal cancer.

cancer biology↗

bioRxiv2023

Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning

Phage tailspike proteins are depolymerases that target diverse bacterial surface glycans with high specificity, determining the host-specificity of numerous phages. To address the challenge of identifying tailspike proteins due to their sequence diversity, we developed SpikeHunter, an approach based on the ESM-2 protein language model. Using SpikeHunter, we successfully identified 231,965 tailspike proteins from a dataset comprising 8,434,494 prophages found within 165,365 genomes of five common pathogens. Among these proteins, 143,035 tailspike proteins displayed strong associations with serotypes. Moreover, we observed highly similar tailspike proteins in species that share closely related serotypes. We found extensive domain swapping in all five species, with the C-terminal domain being significantly associated with host serotype highlighting its role in host range determination. Our study presents a comprehensive cross-species analysis of tailspike protein to serotype associations, providing insights applicable to phage therapy and biotechnology.

bioinformatics↗

bioRxiv2023

Rictor induces AKT signaling to regulate lymphatic valve formation

Lymphatic valves are specialized structures of the collecting lymphatic vessels and are crucial for preventing retrograde lymph flow. Mutations in valve-forming genes have been clinically implicated in the pathology of congenital lymphedema. Lymphatic valves form when oscillatory shear stress (OSS) from lymph flow signals through the PI3K/AKT pathway to promote the transcription of valve-forming genes that trigger the growth and maintenance of lymphatic valves throughout life. Conventionally, in other tissue types, AKT activation requires dual kinase activity and the mammalian target of rapamycin complex 2 (mTORC2) commands this process by phosphorylating AKT at Ser473. Here we showed that embryonic and postnatal lymphatic deletion of Rictor, a critical component of mTORC2, led to a significant decrease in lymphatic valves and prevented the maturation of collecting lymphatic vessels. RICTOR knockdown in human lymphatic endothelial cells (hdLECs) not only significantly reduced the level of activated AKT and the expression of valve-forming genes under no-flow conditions, but also abolished the upregulation of AKT activity and valve-forming genes in response to flow. We further showed that the AKT target, FOXO1, a repressor of lymphatic valve formation, had increased nuclear activity in Rictor knockout mesenteric LECs, in vivo. Deletion of Foxo1 in Rictor knockout mice restored the number of valves to control levels in both mesenteric and ear lymphatics. Our work revealed a novel role of RICTOR signaling in the mechanotransduction signaling pathway, wherein it activates AKT and prevents the nuclear accumulation of the valve repressor, FOXO1, which ultimately allows the formation and maintenance of a normal lymphatic valve.

developmental biology↗