Biology subjects

Chen, P.-Y.

Publications and source records attributed to Chen, P.-Y..

31 records · Page 2Linked to original sources

bioRxiv2021

Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles

Newly evolved SARS-CoV-2 variants are driving ongoing outbreaks of COVID-19 around the world. Efforts to determine why these viral variants have improved fitness are limited to mutations in the viral spike (S) protein and viral entry steps using non-SARS-CoV-2 viral particles engineered to display S. Here we show that SARS-CoV-2 virus-like particles can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and rapid dissection of multiple steps in the viral life cycle. Identification of an RNA packaging sequence was critical for engineered transcripts to assemble together with SARS-CoV-2 structural proteins S, nucleocapsid (N), membrane (M) and envelope (E) into non-replicative SARS-CoV-2 virus-like particles (SC2-VLPs) that deliver these transcripts to ACE2- and TMPRSS2-expressing cells. Using SC2-VLPs, we tested the effect of 30 individual mutations within the S and N proteins on particle assembly and entry. While S mutations unexpectedly did not affect these steps, SC2-VLPs bearing any one of four N mutations found universally in more-transmissible viral variants (P199L, S202R, R203M and R203K) showed increased particle production and up to 10-fold more reporter transcript expression in receiver cells. Our study provides a platform for rapid testing of viral variants outside a biosafety level 3 setting and identifies viral N mutations and viral particle assembly as mechanisms to explain the increased spread of current viral variants, including Delta (N:R203M). One-Sentence SummaryR203M substitution within SARS-CoV-2 N, found in delta variant, improves RNA packaging into virus-like particles by 10-fold.

microbiology↗

bioRxiv2021

Multi-omics approach to identify bacterial polyynes and unveil their antifungal mechanism against Candida albicans

Bacterial polyynes are highly active natural products with a broad-spectrum of antimicrobial activities. However, their detailed mechanism of action remains unclear. Through integrating comparative genomics, transcriptomics, functional genetics, and metabolomics analysis, we identified a unique polyyne resistance gene, masL (encoding acetyl-CoA acetyltransferase), from the biosynthesis gene cluster (BGC) dominant for the production of antifungal polyynes (massilin A, massilin B, collimonin C, and collimonin D) in Massilia sp. YMA4. Phylogenic and chemotaxonomic analyses characterized the core architecture of bacterial polyyne BGC. The crystallographic analysis of the MasL-collimonin C complex indicated that bacterial polyynes serve as a covalent inhibitor of acetyl-CoA acetyltransferase. Moreover, we confirmed that the bacterial polyynes disrupted cell membrane integrity and inhibited cell viability of Candida albicans by targeting ERG10 (homolog of MasL). Overall, understanding of the antifungal mechanism of bacterial polyynes presented herein will be useful for the development of polyynes for fungal infections.

microbiology↗

bioRxiv2020

The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron retention of ABA-responsive genes

Histone deacetylases (HDAs) play an important role in transcriptional regulation involved in multiple biological processes. In this study, we investigate the function of HDA15 in abscisic acid (ABA) responses. Immunopurification coupled with mass spectrometry-based proteomics was used to identify the HDA15 interacting proteins. We found that HDA15 can interact with the core subunits of MOS4-Associated Complex (MAC), MAC3A and MAC3B. In addition, ABA enhances the interaction of HDA15 with MAC3B. hda15 and mac3a/mac3b mutants are ABA-insensitive in seed germination and hyposensitive to salinity. RNA sequencing (RNA-seq) analysis demonstrate that HDA15 and MAC3A/MAC3B not only affect the expression of ABA-related genes, but also regulate ABA-responsive intron retention (IR). Furthermore, HDA15 and MAC3A/MAC3B reduce the histone acetylation level of the genomic regions near ABA-responsive IRs. Our studies uncovered the role of histone deacetylation in ABA-mediated splicing regulation and identified that HDA15-MAC3A/MAC3B acts as an important regulation module to mediate splicing of introns in ABA responses. One Sentence SummaryHDA15 and MAC3A/MAC3B coregulate intron retention and reduce the histone acetylation level of the genomic regions near ABA-responsive retained introns.

plant biology↗

bioRxiv2020

Multimodal Brain Age Gap as a Mediating Indicator in the Relation between Modifiable Dementia Risk Factors and Cognitive Functioning

IntroductionAs a structural proxy for evaluating brain health, neuroimaging-based brain age gap (BAG) is presumed to link the dementia risks to cognitive changes in the premorbid phase, but this remains unclear. MethodsBrain age prediction models were constructed and applied to a population-based cohort (N=371) to estimate their BAG. Further, structural equation modeling was employed to investigate the mediation effect of BAG between risk levels (assessed by 2 dementia-related risk scores) and cognitive changes (examined by 4 cognitive assessments). ResultsA higher burden of modifiable dementia risk factors was causally associated with a greater cognitive decline, and this was significantly mediated (P=0.017) by a larger multimodal BAG, which indicated an older brain. Moreover, a steeper slope (P=0.020) of association between cognitive decline and multimodal BAG was observed when individuals had higher dementia risks. DiscussionMultimodal BAG is a potential mediating indicator to reflect the changes in the pathophysiological mechanism of cognitive aging.

neuroscience↗

bioRxiv2020

Mycena genomes resolve the evolution of fungal bioluminescence

Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life, yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. We sequenced the genomes and transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. Two species with haploid genome assemblies [~]150Mb are amongst the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. Luciferase cluster members were co-expressed across developmental stages, with highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species. SignificanceWe present the genomes of five new bonnet mushroom Mycena species, formerly the last fungal bioluminescent lineage lacking reference genomes. These genome-scale datasets allowed us to construct an evolutionary model pinpointing all possible changes in the luciferase cluster across all fungi and additional genes involved in bioluminescence. We show that luciferase clusters were differentially lost in different fungal lineages and in particular a substantial loss was observed in the Mycena lineage. This can be attributed to genome regions of Mycena underwent different evolutionary dynamics. Our findings offer insights into the evolution of how a gene cluster that emerged 160 million years ago and was frequently lost or maintained due to differences in genome plasticity.

genomics↗

bioRxiv2019

Artificial intelligence method to design and fold alpha-helix structural proteins from the primary amino acid sequence

The development of rational techniques to discover new proteins for use in variety of applications ranging from agriculture to biotechnology remains an outstanding materials design problem. The key barrier is to design a sequence to fold into a predictable structure to achieve a certain material function. Focused on alpha-helical proteins, we report a Multi-scale Neighborhood-based Neural Network (MNNN) model to learn how a specific amino acid sequence folds into a protein structure. The algorithm predicts the protein structure without using a template or co-evolutional information at a maximum error of 2.1 [A]. We find that the prediction accuracy is higher than other models and the prediction consumes less than six orders of magnitude time than ab initio folding methods. We demonstrate that MNNN can predict the structure of an unknown protein that agrees with experiments, and our model hence shows a great advantage in the rational design of de novo proteins.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC=\"FIGDIR/small/660639v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (66K):\norg.highwire.dtl.DTLVardef@8771fcorg.highwire.dtl.DTLVardef@4c7255org.highwire.dtl.DTLVardef@e63f1eorg.highwire.dtl.DTLVardef@39e4ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

Glia-derived exosomal miR-274 targets Sprouty in trachea and synaptic boutons to modulate growth and responses to hypoxia

Secreted exosomal miRNAs mediate inter-organ/tissue communication by downregulating gene expression, thereby modulating developmental and physiological functions. However, the source, route, and function have not been formally established for specific miRNAs. Here, we show that glial miR-274 non-cell autonomously modulates the growth of synaptic boutons and tracheal branches. Whereas precursor miR-274 was expressed in glia, mature miR-274 was secreted. miR-274 secretion to circulating hemolymph was detected in exosomes, a process requiring ESCRT components in exosome biogenesis and Rab11 and Syx1A in exosome release. miR-274 downregulated Sprouty to activate MAPK in synaptic boutons and tracheal branches, thereby promoting their growth. Expression of miR-274 solely in glia of a mir-274 null mutant reset normal levels of Sprouty and MAPK, and hemolymphatic exosomal miR-274. mir-274 mutant larvae were hypersensitive to hypoxia, which was suppressed by increasing tracheal branches. Thus, glia-derived miR-274 coordinates growth of synaptic boutons and tracheal branches to modulate larval hypoxia responses.

developmental biology↗

bioRxiv2019

Assessing chromatin accessibility in maize using ATAC-seq

Background: Maize is an important crop that has a complex genome. A better understanding of maize chromatin architecture provides great opportunities for crop improvement, because chromatin accessibility influences gene expression, thereby affecting agricultural traits. The newly developed method for chromatin profiling, Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq), has been developed to investigate chromatin accessibility. Result: We adapt this method by testing parameters of several key steps and generate the first ATAC-seq protocol for maize. We demonstrate that purification of maize nuclei to eliminate organelles can be achieved without the need for cell sorting, and that only a standard bench-top centrifuge is required for sample preparation. Finally, our sequence analyses confirm that our protocol of ATAC-seq can be successfully used to assess the chromatin landscape in maize. Conclusion: The ATAC-seq provides a useful technique to study the chromatin accessibility. Given the parameters tested in our study, it can be a simple and practical method for maize and may be a foundation for similar studies in other crop species.

genomics↗

bioRxiv2019

Glial response to hypoxia in trachealess mutants induces synapse remodeling.

Synaptic structure and activity are sensitive to environmental alterations. Modulation of synaptic morphology and function is often induced by signals from glia. However, the process by which glia mediate synaptic responses to environmental perturbations such as hypoxia remains unknown. Here, we report that, in the Drosophila trachealess (trh) mutant, smaller synaptic boutons form clusters named bunch boutons appear at larval neuromuscular junctions (NMJs), which is induced by the reduction of internal oxygen levels due to defective tracheal branches. Thus, the bunch bouton phenotype in the trh mutant is suppressed by hyperoxia, and recapitulated in wild-type larvae raised under hypoxia. We further show that hypoxia-inducible factor (HIF)-1/Similar (Sima) is critical in mediating hypoxia-induced bunch bouton formation. Sima upregulates the level of the Wnt/Wingless (Wg) signal in glia, leading to reorganized microtubule structures within presynaptic sites. Finally, hypoxia-induced bunch boutons maintain normal synaptic transmission at the NMJs, which is crucial for coordinated larval locomotion. Author summaryOxygen is essential for animals to maintain their life such as growth, metabolism, responsiveness, and movement. It is therefore important to understand how animal cells trigger hypoxia response and adapt to hypoxia thereafter. Both mammalian vascular and insect tracheal branches are induced to enhance the oxygen delivery. However, the study of hypoxia response in the nervous system remains limited. In this study, we assess the morphology of Drosophila neuromuscular junctions (NMJs), a model system to study development and function of synapses, in two hypoxia conditions, one with raising wild-type larvae in hypoxia, and the other in the trachealess (trh) mutant in which the trachea is defective, causing insufficient oxygen supply. Interestingly, glia, normally wrapping the axons of NMJs, invade into synapse and trigger Wg signals to reconstitute the synaptic structure under hypoxia. This synaptic remodeling maintains the synaptic transmission of synapse, which associate the locomotor behavior of larvae.

genetics↗

bioRxiv2019

Dominant coral bacterium Endozoicomonas acroporae metabolizes DMSP

Dominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase--a dddD gene homolog found in all E. acroporae strains--and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

ecology↗

bioRxiv2018

Dynamic Network Analysis of the 4D Nucleome

MotivationFor many biological systems, it is essential to capture simultaneously the function, structure, and dynamics in order to form a comprehensive understanding of underlying phenomena. The dynamical interaction between 3D genome spatial structure and transcriptional activity creates a genomic signature that we refer to as the four-dimensional organization of the nucleus, or 4D Nucleome (4DN). The study of 4DN requires assessment of genome-wide structure and gene expression as well as development of new approaches for data analysis.\n\nResultsWe propose a dynamic multilayer network approach to study the co-evolution of form and function in the 4D Nucleome. We model the dynamic biological system as a temporal network with node dynamics, where the network topology is captured by chromosome conformation (Hi-C), and the function of a node is measured by RNA sequencing (RNA-seq). Network-based approaches such as von Neumann graph entropy, network centrality, and multilayer network theory are applied to reveal universal patterns of the dynamic genome. Our model integrates knowledge of genome structure and gene expression along with temporal evolution and leads to a description of genome behavior on a system wide level. We illustrate the benefits of our model via a real biological dataset on MYOD1-mediated reprogramming of human fibroblasts into the myogenic lineage. We show that our methods enable better predictions on form-function relationships and refine our understanding on how cell dynamics change during cellular reprogramming.\n\nAvailability: The software is available upon request.\n\nContactindikar@umich.edu\n\nSupplementary informationSee Supplementary Material.

bioinformatics↗

bioRxiv2018

A Model for Resource Competition in CRISPR-Mediated Gene Repression

CRISPR-mediated gene regulation is known for its ability to control multiple targets simultaneously due to its modular nature: the same dCas9 effector can target different genes simply by changing the associated gRNA. However, multiplexing requires the sharing of limited amounts of dCas9 proteins among multiple gRNAs, leading to resource competition. In turn, competition between gRNAs for the same resource may hamper network function. In this work, we develop a general model that takes into account the sharing of a limited amount of dCas9 protein for arbitrary CRISPR-mediated gene repression networks. We demonstrate that, as a result of resource competition, hidden interactions appear, that modify the intended network regulations. As a case study, we analyze the effects of these hidden interactions in repression cascades. In particular, we illustrate that perfect adaptation to resource fluctuations can be achieved in cascades with an even number of repressors. In contrast, cascades with an odd number of repressors are substantially impacted by resource competition.

synthetic biology↗

bioRxiv2017

Genome Architecture Leads a Bifurcation in Cell Identity

Genome architecture is important in transcriptional regulation and study of its features is a critical part of fully understanding cell identity. Altering cell identity is possible through overexpression of transcription factors (TFs); for example, fibroblasts can be reprogrammed into muscle cells by introducing MYOD1. How TFs dynamically orchestrate genome architecture and transcription as a cell adopts a new identity during reprogramming is not well understood. Here we show that MYOD1-mediated reprogramming of human fibroblasts into the myogenic lineage undergoes a critical transition, which we refer to as a bifurcation point, where cell identity definitively changes. By integrating knowledge of genome-wide dynamical architecture and transcription, we found significant chromatin reorganization prior to transcriptional changes that marked activation of the myogenic program. We also found that the local architectural and transcriptional dynamics of endogenous MYOD1 and MYOG reflected the global genomic bifurcation event. These TFs additionally participate in entrainment of biological rhythms. Understanding the system-level genome dynamics underlying a cell fate decision is a step toward devising more sophisticated reprogramming strategies that could be used in cell therapies.

cell biology↗