Biology subjects

Feng, J.

Publications and source records attributed to Feng, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2022

S-nitrosylation of Aux/IAA protein represses auxin signaling

Auxin plays crucial roles in nearly every aspect of plant growth and development. Auxin signaling activation is mediated through degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) family. Nitric oxide (NO) regulates diverse cellular bioactivities through S-nitrosylation of target protein at specific cysteine residues. NO-auxin interplay has an important role in regulation plant growth. However, little is known about the molecular mechanism of how NO effects Aux/IAA proteins stability. Here we show that NO negatively regulates the IAA17 protein stability to repress auxin signaling. We found that NO directly inhibits IAA17 protein degradation. S-nitrosylation of IAA17 at Cys-70 represses the TIR-IAA17 co-receptor interaction to attenuate auxin responsiveness. Our data suggest a model in which S-nitrosylation of IAA17 at Cys-70 negatively regulates auxin signaling to effect plant development, providing a mechanism for redox-phytohormones networks.

plant biology↗

bioRxiv2022

DeepBIO is an automated and interpretable deep-learning platform for biological sequence prediction, functional annotation, and visualization analysis

Here, we present DeepBIO, the first-of-its-kind automated and interpretable deep-learning platform for high-throughput biological sequence functional analysis. DeepBIO is a one-stop-shop web service that enables researchers to develop new deep-learning architectures to answer any biological question. Specifically, given any biological sequence data, DeepBIO supports a total of 42 state-of-the-art deep-learning algorithms for model training, comparison, optimization, and evaluation in a fully automated pipeline. DeepBIO provides a comprehensive result visualization analysis for predictive models covering several aspects, such as model interpretability, feature analysis, functional sequential region discovery, etc. Additionally, DeepBIO supports 9 base-level functional annotation tasks using deep-learning architectures, with comprehensive interpretations and graphical visualizations to validate the reliability of annotated sites. Empowered by high-performance computers, DeepBIO allows ultra-fast prediction with up to million-scale sequence data in a few hours, demonstrating its usability in real application scenarios. Case study results show that DeepBIO provides an accurate, robust, and interpretable prediction, demonstrating the power of deep learning in biological sequence functional analysis. Overall, we expect DeepBIO to ensure the reproducibility of deep-learning biological sequence analysis, lessen the programming and hardware burden for biologists, and provide meaningful functional insights at both sequence-level and base-level from biological sequences alone. DeepBIO is publicly available at http://inner.wei-group.net/DeepBIO.

bioinformatics↗

bioRxiv2022

Multi-omics data integration via novel interpretable k-hop graph attention network for signaling network inference

With the advent of sequencing technology, large-scale multi-omics data have been generated to understand the diversity and heterogeneity of genetic targets and associated complex signaling pathways at multiple levels in diseases, which are critical targets to guide the development of personalized precision medicine. However, it remains a challenging task to computationally mine a few essential targets and pathways from a large number of variables characterized by the multi-level multi-omics data. In this study, we proposed a novel interpretable k-hop graph attention network model, k-hop GAT, to integrate the multi-omics data to infer the essential targets and related signaling networks. We evaluated the proposed model using the multi-omics data, i.e., genetic mutation, copy number variation, methylation, gene expression data, of 332 cancer lines; and the experimentally identified essential targets. The validation and comparison results indicated that the proposed model outperformed the GAT and graph convolutional network (GCN) models.

systems biology↗

bioRxiv2022

Recombinant protein condensation inside E. coli enables the development of building blocks for bioinspired materials engineering - biomimetic spider silk protein as a case study

Recombinant expression of proteins destined to form biological materials often results in poor production yields or loss of their function due to premature aggregation. Recently, liquid-liquid phase separation has been proposed as a mechanism to control protein solubility during expression and accumulation in the cytoplasm. Here, we investigate this process in vivo during the recombinant overexpression of the spider silk-mimetic mini-spidroin NT2RepCT in Escherichia coli. The protein forms intracellular liquid-like condensates that shift to a solid-like state triggered by a decrease in their microenvironmental pH. These features are also maintained in the purified sample in vitro both in the presence of a molecular crowding agent mimicking the bacterial intracellular environment, and during a biomimetic extrusion process leading to fiber formation. Overall, we demonstrate that characterization of protein condensates inside E. coli could be used as a basis for selecting proteins for both materials applications and their fundamental structure-function studies.

synthetic biology↗

bioRxiv2022

Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles

In socially monogamous prairie voles (Microtus ochrogaster), parental behaviors not only occur in mothers and fathers, but also exist in some virgin males. In contrast, the other virgin males display aggressive behaviors towards conspecific pups. However, little is known about the molecular underpinnings of this behavioral dichotomy, such as gene expression changes and their regulatory mechanisms. To address this, we profiled the transcriptome and DNA methylome of hippocampal dentate gyrus of four prairie vole groups, namely attacker virgin males, parental virgin males, fathers, and mothers. While we found a concordant gene expression pattern between parental virgin males and fathers, the attacker virgin males have a more deviated transcriptome. Moreover, numerous DNA methylation changes were found in pair-wise comparisons among the four groups. We found some of these DNA methylation changes correlate with transcription differences, particularly at genes with extreme expression changes. Furthermore, the gene expression changes and methylome alterations are selectively enriched in certain biological pathways, such as Wnt signaling, which suggest a canonical transcription regulatory role of DNA methylation in paternal behavior. Therefore, our study presents an integrated view of prairie vole dentate gyrus transcriptome and epigenome that provides a DNA epigenetic based molecular insight of paternal behavior.

neuroscience↗

bioRxiv2022

Canonical Wnt signaling regulates soft palate development through mediating ciliary homeostasis

Craniofacial morphogenesis requires complex interactions among tissues, signaling pathways, secreted factors, and organelles. The details of these interactions remain elusive. In this study, we analyzed the molecular mechanisms and homeostatic cellular activities governing soft palate development to improve regenerative strategies for cleft palate patients. We have identified canonical Wnt signaling as a key signaling pathway primarily active in cranial neural crest (CNC)-derived mesenchymal cells surrounding soft palatal myogenic cells. Using Osr2-Cre;{beta}-cateninfl/fl mice, we further discovered that Wnt signaling is indispensable for mesenchymal cell proliferation and subsequently myogenesis through mediating ciliogenesis. Specifically, we identified that Wnt signaling directly regulates expression of the ciliary gene Ttll3 through {beta}-catenin/Tcf7l2 complex. Impaired ciliary disassembly leads to differentiation defects of mesenchymal cells and indirectly disrupts myogenesis through decreased expression of Dlk1, a mesenchymal cell-derived pro-myogenesis factor. Moreover, we found that restoring ciliary homeostasis rescues mesenchymal cell proliferation in Osr2-Cre;{beta}-cateninfl/fl samples. This study highlights the role of Wnt signaling in palatogenesis through controlling ciliary homeostasis, which establishes a new mechanism for Wnt-regulated craniofacial morphogenesis.

developmental biology↗

bioRxiv2022

Activation of Keap1 and its isoforms (α and β) inhibits the Nrf2 pathway to affect malignant behaviour of human hepatocellular carcinoma cells

Nrf2 (nuclear factor E2-related factor 2, encoded by Nfe2l2) acts as a master transcriptional regulator in mediating antioxidant, detoxification and cytoprotective responses against oxidative, electrophilic and metabolic stress, but also plays a crucial role in cancer metabolism and multiple oncogenic pathways, whereas the redox sensor Keap1 functions as a predominant inhibitor of Nrf2 and hence changes in its expression abundance directly affect the Nrf2 stability and transcriptional activity. However, nuanced functional isoforms of Keap1 and {beta} have rarely been identified to date. Herein, we have established four distinct cell models stably expressing Keap1-/-, Keap1{beta} (Keap1{Delta}1-31), Keap1-Restored and Keap1-Restored, aiming to gain a better understanding of similarities and differences of two Keap1 isoforms between their distinct regulatory profiles. Our experimental evidence revealed that although Keap1 and its isoforms are still localized in the cytoplasmic compartments, they elicited differential inhibitory effects on Nrf2 and its target HO-1. Furtherly, transcriptome sequencing unraveled that they possess similar but different functions. Such functions were further determined by multiple experiments in vivo (i.e. subcutaneous tumour formation in nude mice) and in vitro (e.g., cell cloning, infection, migration, wound healing, cell cycle, apoptosis, CAT enzymatic activity and intracellular GSH levels). Of note, the results obtained from tumorigenesis experiments in xenograft model mice were verified based on the prominent changes in the PTEN signaling to the PI3K-AKT-mTOR pathways, in addition to substantially aberrant expression patterns of those typical genes involved in the EMT (epithelial-mesenchymal transition), cell cycle and apoptosis.

biochemistry↗

bioRxiv2022

A point mutation in Chl biosynthesis gene Mg-chelatase I subunit influences on leaf color and metabolism in strawberry

Magnesium chelatase catalysis the insertion of magnesium into protoporphyrin IX is a vital step in chlorophyll biogenesis. It consists of three subunits, CHLI, CHLD and CHLH. The CHLI subunit is an ATPase and hydrolysis ATP in the catalysis. However, its key point on influencing flavonoid biosynthesis and chlorophyll accumulation under different light density was still unknown. In this study, we identified an N-Ethyl-N-nitrosourea (ENU) mutant, p240 from strawberry Fragaria pentaphylla that has yellow-green leaves and lower chlorophyll level. We verified the mutation occurs in the 186th amino acid of CHLI subunit, which is conserved in most photosynthetic organism. Mutants generated from RNAi and CRISPR/Cas9 gene editing confirmed this phenotype. In addition, we found that FpCHLI was localized in chloroplast and its subcellular location have not been changed by mutation. Further study showed that the interaction between FpCHLI and FpCHLD were not affected by mutagenesis. In contrast, all types of mutants showed reduced ATPase and magnesium chelatase activity indicating mutagenesis decreased enzymatic activities. Furthermore, mutagenesis suppressed the biosynthesis of Mg-proto IX. Metabolites analysis of gene knock-out mutant and WT revealed that CHLI may help to keep stabilizing the flavonoid level in leaves. Furthermore, both p240 and chli mutants are light sensitive, which has yellow leaves under high light but pale green leaves under poor light. The photosynthesis ability of mutants was also increased under shade. Moreover, stomatal apertures of mutants were wider than WT. Taken together, these results suggest that CHLI plays an important role in both leaf coloration and metabolism.

plant biology↗

bioRxiv2022

MrgprA3-expressing pruriceptors drive pruritogen-induced alloknesis through mechanosensitive Piezo2 channel

Although touch and itch are coded by distinct neuronal populations, light touch also provokes itch in the presence of exogenous pruritogens, resulting in a phenomenon called alloknesis. However, the cellular and molecular mechanisms underlying the initiation of pruritogen-induced mechanical itch sensitization are poorly understood. Here we show that intradermal injections of histamine or chloroquine (CQ) provoke alloknesis through activation of TRPV1- and MrgprA3- expressing prurioceptors, and functional ablation of these neurons reverses pruritogen-induced alloknesis. Moreover, genetic ablation of mechanosensitive Piezo2 channel function from MrgprA3-expressing prurioceptors also dampens pruritogen-induced alloknesis. Mechanistically, histamine and CQ sensitize Piezo2 channel function through activation of the PLC-PKC{delta} signaling. Collectively, our data uncovered a TRPV1+/MrgprA3+ prurioceptor-Piezo2 signaling axis in the initiation of pruritogen-induced mechanical itch sensitization in the skin.

neuroscience↗

bioRxiv2022

PHAT: interpretable prediction of peptide secondary structures using hypergraph multi-head attention network and transfer learning

Accurately predicting peptide secondary structures remains a challenging task due to the lack of discriminative information in short peptides. In this study, we propose PHAT, a deep graph learning framework for the prediction of peptide secondary structures. The framework includes a novel interpretable deep hypergraph multi-head attention network that uses residue-based reasoning for structure prediction. Our algorithm can incorporate sequential semantic information from large-scale biological corpus and structural semantic information from multi-scale structural segmentation, leading to better accuracy and interpretability even with extremely short peptides. Our interpretable models are able to highlight the reasoning of structural feature representations and the classification of secondary substructures. We further demonstrate the importance of secondary structures in peptide tertiary structure reconstruction and downstream functional analysis, highlighting the versatility of our models. To facilitate the use of our model, we establish an online server which is accessible via http://inner.wei-group.net/PHAT/. We expect our work to assist in the design of functional peptides and contribute to the advancement of structural biology research.

bioinformatics↗

bioRxiv2022

The immunogenomic landscape of cattle

Here, we report the de novo assembly of a cattle genome using ultra-long-read nanopore sequencing in conjunction with other advanced technologies. The assembled genome contains only 145 contigs (N50 [~] 74.0 Mb). Compare to the current reference cattle genome ARS-UCD1.2, 154 gaps are closed, and 467 scaffolds are further placed in our assembly. Importantly, except two remained gaps in the T-cell receptor /{delta} (TRA/TRD) region, the gene loci of other TRs and immunoglobulins (IGs) are seamlessly assembled and exquisitely annotated. With the characterization of 258 IG genes and 626 TR genes that distributed in seven genomic loci, we illustrate the highest immune gene diversity in mammals to our knowledge. Moreover, the gene structures of major histocompatibility complex (MHC) are integrally depicted with properly phased haplotypes. Thus, our work not only reports a cattle genome with the most continuity and completeness, but also provide a comprehensive view of the complex immune- genome.

genomics↗

bioRxiv2022

Adverse PFAS effects on mouse oocyte in vitro maturation are associated with carbon-chain length and inclusion of a sulfonate group

Per- and polyfluoroalkyl substances (PFAS) are man-made chemicals that are used in products such as non-stick cookware, stain-resistant coating, and food packaging. PFAS are characterized by their fluorinated carbon chains that make them hard to degrade and bioaccumulate in human and animals. Toxicological studies have shown PFAS toxic effects: cytotoxicity, immunotoxicity, neurotoxicity, and reproductive toxicity. Two major categories of PFAS are perfluoroalkyl carboxylic acid (PFCA) and perfluoroalkyl sulfonic acid (PFSA). In this study, we used a mouse-oocyte-in-vitro-maturation (IVM) system to study how the structures of PFAS, such as carbon-chain length and functional groups, determine their reproductive toxicity. We found the toxicity of PFAS is elevated with increasing carbon-chain length and the inclusion of the sulfonate group. Specifically, at 600 {micro}M, perfluorohexanesulfonic acid (PFHxS) and perfluorooctanesulfonic acid (PFOS) reduced the rates of both germinal vesicle breakdown (GVBD) and polar body extrusion (PBE) as well as induced the formation of relatively large polar bodies. However, the shorter PFSA, perfluorobutanesulfonic acid (PFBS), and all PFCA did not show similar adverse cytotoxicity. We further examined mitochondria and cytoskeleton, two essential factors for cell division, in PFOS- and PFHxS-treated oocytes. We found that 600 {micro}M PFHxS and PFOS exposure induced excess reactive oxygen species (ROS) and decreased mitochondrial membrane potential (MMP). Cytoskeleton analysis revealed that PFHxS and PFOS exposure induced chromosome misalignment, abnormal F-actin organization, elongated the spindle formation, and symmetric division in the treated oocytes. Together, our study provides new information on the structure-toxicity relationship of PFAS. SynopsisReproductive toxicity of PFAS, a group of persistent organic pollutants, is determined by their chemical structures.

pharmacology and toxicology↗

bioRxiv2022

BEN: a generalizable Brain Extraction Net for multimodal MRI data from rodents, nonhuman primates, and humans

Accurate brain tissue extraction on magnetic resonance imaging (MRI) data is crucial for analyzing brain structure and function. While several conventional tools have been optimized to handle human brain data, there have been no generalizable methods to extract brain tissues for multimodal MRI data from rodents, nonhuman primates, and humans. Therefore, developing a flexible and generalizable method for extracting whole brain tissue across species would allow researchers to analyze and compare experiment results more efficiently. Here, we propose a domain-adaptive and semi-supervised deep neural network, named the Brain Extraction Net (BEN), to extract brain tissues across species, MRI modalities, and MR scanners. We have evaluated BEN on 18 independent datasets, including 783 rodent MRI scans, 246 nonhuman primate MRI scans, and 4,601 human MRI scans, covering five species, four modalities, and six MR scanners with various magnetic field strengths. Compared to conventional toolboxes, the superiority of BEN is illustrated by its robustness, accuracy, and generalizability. Our proposed method not only provides a generalized solution for extracting brain tissue across species but also significantly improves the accuracy of atlas registration, thereby benefiting the downstream processing tasks. As a novel fully automated deep-learning method, BEN is designed as an open-source software to enable high-throughput processing of neuroimaging data across species in preclinical and clinical applications.

neuroscience↗

bioRxiv2022

TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development

The communication between myogenic cells and their surrounding connective tissues is indispensable for muscle morphogenesis. During late embryonic development in mice, myogenic progenitors migrate to discrete sites to form individual muscles. The detailed mechanism of this process remains unclear. Using levator veli palatini (LVP) development as a model, we systematically investigated how a distinct connective tissue subpopulation, perimysial fibroblasts, communcates with myogenic cells to regulate mouse pharyngeal myogenesis. Using single-cell RNAseq data analysis, we identified that TGF-{beta} signaling is a key regulator for the perimysial fibroblasts. Loss of TGF-{beta} signaling led to defects in perimysial fibroblasts and subsequently muscle formation in Osr2-Cre;Alk5fl/fl mice. In particular, a perimysial fibroblast-specific regulator, Creb5, interacts with TGF-{beta} signaling to enable specific activation of perimysial fibroblast-derived signals such as Fgf18. Moreover, Fgf18 supports pharyngeal muscle development in vivo and its exogenous expression can partially rescue myogenic cell numbers in Osr2-Cre;Alk5fl/fl samples, illustrating that TGF-{beta}-regulated Fgf18 signaling is required for LVP development. Collectively, our findings revealed the mechanism by which TGF-{beta} signaling achieves its specificity in defining the perimysial-to-myogenic signals for pharyngeal myogenesis.

developmental biology↗

bioRxiv2022

Nrf1 is an indispensable redox-determining factor for mitochondrial homeostasis by integrating multi-hierarchical regulatory networks

To defend a vast variety of challenges in the oxygenated environments, all life forms have been evolutionally established a set of antioxidant, detoxification and cytoprotective systems during natural selection and adaptive survival, in order to maintain cell redox homeostasis and organ integrity in the healthy development and growth. Such antioxidant defense systems are predominantly regulated by two key transcription factors Nrf1 and Nrf2, but the underlying mechanism(s) for their coordinated redox control remains elusive. Here, we found that loss of full-length Nrf1 led to a dramatic increase in reactive oxygen species (ROS) and oxidative damages in Nrf1-/- cells, and this increase was not eliminated by drastic elevation of Nrf2, even though the antioxidant systems were also substantially enhanced by hyperactive Nrf2. Further studies revealed that the increased ROS production in Nrf1-/- resulted from a striking impairment in the mitochondrial oxidative respiratory chain and its gene expression regulated by nuclear respiratory factors, called PalNRF1 and GABPNRF2. In addition to antioxidant capacity of cells, glycolysis was greatly augmented by aberrantly-elevated Nrf2, so to partially relieve the cellular energy demands, but aggravate its mitochondrial stress. The generation of ROS was also differentially regulated by Nrf1 and Nrf2 through miR-195 and/or mIR-497-mediated UCP2 pathway. Consequently, the epithelial-mesenchymal transformation (EMT) of Nrf1-/- cells was activated by putative ROS-stimulated signaling via MAPK, HIF1, NF-kB, PI3K and AKT, all players involved in cancer development and progression. Taken together, it is inferable that Nrf1 acts as a potent integrator of redox regulation by multi-hierarchical networks.

molecular biology↗

bioRxiv2022

Genomic insights into present local adaptation and future climate change vulnerability of a keystone forest tree species in East Asian

Rapid global climate change is posing a huge threat to biodiversity. Assessments of the adaptive capacity for most taxa is usually performed on the species as a whole, but fails to incorporate intraspecific adaptive variation that may play a fundamental role in buffering future shifting climates. Here we generate a chromosome-scale genome assembly for Populus koreana, a pioneer and keystone tree species in East Asia temperate forests. We also obtain whole-genome sequences of 230 individuals collected from 24 natural populations. An integration of population genomics and environmental variables was performed to reveal the genomic basis of local adaptation to diverse climate variable. We identify a set of climate-associated single nucleotide polymorphisms (SNPs), insertions-deletions (Indels) and structural variations (SVs), in particular numerous adaptive non-coding variants distributed across the genome of P. koreana. We incorporate these variants into an environmental modelling scheme to predict spatiotemporal responses of P. koreana to future climate change. Our results highlight the insights that the integration of genomic and climate data can shed on the future evolutionary adaptive capacities of a species to changing environmental conditions.

evolutionary biology↗

bioRxiv2022

Transcriptional circuitry of NKX2-1 and SOX1 defines an unrecognized lineage subtype of small cell lung cancer

RationaleThe current molecular classification of small cell lung cancer (SCLC) based on expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. ObjectivesTo refine the current SCLC classification with epigenomic profiles and to identify features of the re-defined SCLC subtypes. MethodsWe performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance was evaluated by cell growth, apoptosis and xenograft using CRISPR-Cas9-mediated deletion. The specific cistromic profiles by ChIP-seq and its functional transcriptional partners using co-immunoprecipitation followed by mass spectrometry were determined. Rb1fl/flTrp53fl/fl and Rb1fl/flNkx2-1fl/fl mouse models were engineered to explore the function of Nkx2-1 in tumor initiation and differentiation. H3K27ac profiles were analyzed to reveal 6 human SCLC specimen and 20 mice tumors epigenomic landscapes. Measurements and Main ResultsWe identified an epigenomic subclusters of the major SCLC-A subtype, named SCLC-A and SCLC-A{sigma}. SCLC-A was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-A. We further found maintenance of this neural identity in SCLC-A is mediated by collaborative transcriptional activity with another neuronal transcriptional factor SOX1. ConclusionsWe comprehensively describe an additional epigenomic heterogeneity of the major SCLC-A subtype, and define SCLC-A subtype by the core regulatory circuitry representing NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.

molecular biology↗

bioRxiv2022

Development and evaluation of a loop-mediated isothermal amplification (LAMP) method for detection of the potato wart pathogen Synchytrium endobioticum

Potato (Solanum tuberosum) wart, caused by the biotrophic fungal pathogen Synchytrium endobioticum, is a serious disease of cultivated potatoes. A rapid and accurate method for wart diagnosis is needed. In this study, we described the development and evaluation of a loop-mediated isothermal amplification (LAMP) method for the detection of S. endobioticum. Four sets of LAMP primers were designed. Their sensitivity was tested on a gBlock and the specificity of the most sensitive primer set (LAMP1) was verified by in silico analysis and on DNA of non-target species. The LAMP1 primer set showed a detection limit at 7-8 gBlock DNA molecules per reaction. On sensitivity, the LAMP was comparable to qPCR (SYBR green- and probe-based) and about 10 times more sensitive than conventional PCR. Considering the convenience of operation, the LAMP protocol is accurate and robust and should be recommended for the routine lab testing for potato wart.

microbiology↗