Biology subjects

Yan, H.

Publications and source records attributed to Yan, H..

At least 181 records · Page 10Linked to original sources

bioRxiv2020

Cross-reactive neutralization of SARS-CoV-2 by serum antibodies from recovered SARS patients and immunized animals

The current COVID-19 pandemic, caused by a novel coronavirus SARS-CoV-2, poses serious threats to public health and social stability, calling for urgent need for vaccines and therapeutics. SARS-CoV-2 is genetically close to SARS-CoV, thus it is important to define the between antigenic cross-reactivity and neutralization. In this study, we firstly analyzed 20 convalescent serum samples collected from SARS-CoV infected individuals during the 2003 SARS outbreak. All patient sera reacted strongly with the S1 subunit and receptor-binding domain (RBD) of SARS-CoV, cross-reacted with the S ectodomain, S1, RBD, and S2 proteins of SARS-CoV-2, and neutralized both SARS-CoV and SARS-CoV-2 S protein-driven infections. Multiple panels of antisera from mice and rabbits immunized with a full-length S and RBD immunogens of SARS-CoV were also characterized, verifying the cross-reactive neutralization against SARS-CoV-2. Interestingly, we found that a palm civet SARS-CoV-derived RBD elicited more potent cross-neutralizing responses in immunized animals than the RBD from a human SARS-CoV strain, informing a strategy to develop a universe vaccine against emerging CoVs. SummarySerum antibodies from SARS-CoV infected patients and immunized animals cross-neutralize SARS-CoV-2 suggests strategies for universe vaccines against emerging CoVs.

microbiology↗

bioRxiv2020

Design of potent membrane fusion inhibitors against SARS-CoV-2, an emerging coronavirus with high fusogenic activity

The coronavirus disease COVID-19, caused by emerging SARS-CoV-2, has posed serious threats to global public health, economic and social stabilities, calling for the prompt development of therapeutics and prophylactics. In this study, we firstly verified that SARS-CoV-2 uses human ACE2 as a cell receptor and its spike (S) protein mediates high membrane fusion activity. Comparing to that of SARS-CoV, the heptad repeat 1 (HR1) sequence in the S2 fusion protein of SARS-CoV-2 possesses markedly increased -helicity and thermostability, as well as a higher binding affinity with its corresponding heptad repeat 2 (HR1) site. Then, we designed a HR2 sequence-based lipopeptide fusion inhibitor, termed IPB02, which showed highly poent activities in inibibiting the SARS-CoV-2 S protein-mediated cell-cell fusion and pseudovirus infection. IPB02 also inhibited the SARS-CoV pseudovirus efficiently. Moreover, the strcuture and activity relationship (SAR) of IPB02 were characterzized with a panel of truncated lipopeptides, revealing the amino acid motifs critical for its binding and antiviral capacities. Therefore, the presented results have provided important information for understanding the entry pathway of SARS-CoV-2 and the design of antivirals that target the membrane fusion step.

microbiology↗

bioRxiv2020

Nucleosome-constrained loop extrusion model for the origin of topologically associating domains

The chromosomes - DNA polymers and their binding proteins - are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood. To gain insight into the structure-dynamics relationship of chromatin, we combine high-precision microscopy in living Schizosaccharomyces pombe cells with systematic genetic perturbations and Rouse- model polymer simulations. We first investigated how the activity of two loop extrusion factors, the cohesin and condensin complexes, influences chromatin dynamics. We observed that deactivating cohesin, or to a lesser extent condensin, increased chromatin mobility, suggesting that loop extrusion constrains rather than agitates chromatin motion. Our corresponding simulations reveal that the introduction of loops is sufficient to explain the constraining activity of loop extrusion factors, highlighting that the conformation adopted by the polymer plays a key role in defining its dynamics. Moreover, we find that the number loops or residence times of loop extrusion factors influences the dynamic behavior of the chromatin polymer. Last, we observe that the activity of the INO80 chromatin remodeler, but not the SWI/SNF or RSC complexes, is critical for ATP-dependent chromatin mobility in fission yeast. Taken together we suggest that thermal and INO80-dependent activities exert forces that drive chromatin fluctuations, which are constrained by the organization of the chromosome into loops.

cell biology↗

bioRxiv2020

DeepTE: a computational method for de novo classification of transposons with convolu-tional neural network

MotivationTransposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE classification has emerged as a new challenge in genomic sequence analysis. ResultsWe developed a novel tool, DeepTE, which classifies unknown TEs using convolutional neural networks. DeepTE transferred sequences into input vectors based on k-mer counts. A tree structured classification process was used where eight models were trained to classify TEs into super families and orders. DeepTE also detected domains inside TEs to correct false classification. An additional model was trained to distinguish between non-TEs and TEs in plants. Given unclassified TEs of different species, DeepTE can classify TEs into seven orders, which include 15, 24, and 16 super families in plants, metazoans, and fungi, respectively. In several benchmarking tests, DeepTE outperformed other existing tools for TE classification. In conclusion, DeepTE successfully leverages convolutional neural network for TE classification, and can be used to precisely identify and annotate TEs in newly sequenced eukaryotic genomes. AvailabilityDeepTE is accessible at https://github.com/LiLabAtVT/DeepTE Contactsongli@vt.edu

bioinformatics↗

bioRxiv2019

Mucin hydrogel glyco-modulation to investigate immune activity of mucin glycans

Mucins are multifunctional glycosylated proteins that are increasingly investigated as building blocks of novel biomaterials. Once assembled into hydrogels (Muc gels), mucins were shown to modulate the recruitment and activation of immune cells and avoid fibrous encapsulation in vivo. However, nothing is known about the early immune response to Muc gels. This study characterizes the response of macrophages, important orchestrators of the material-mediated immune response, over the first 7 days in contact with Muc gels. The role of mucin-bound sialic acid sugar residues was investigated by first enzymatically cleaving the sugar, then assembling the mucin variants into covalently crosslinked hydrogels with rheological and surface nanomechanical properties similar to non-modified Muc gels. Results with THP1 and human primary peripheral blood monocytes-derived macrophages were strikingly consistent and showed that Muc gels transiently activate the expression of both pro-inflammatory and anti-inflammatory cytokines and cell surface markers, with a maximum on the first day and loss of the effect after 7 days. The activation was sialic acid-dependent for a majority of the markers followed. The pattern of gene expression, protein expression, and functional measurements did not strictly correspond to M1 or M2 macrophage phenotypes. This study highlights the complex early events in macrophage activation in contact with mucin materials and the importance of sialic acid residues in such a response. The enzymatic glyco-modulation of Muc gels appears as a useful tool to help understand the biological functions of specific glycans on mucins which can further inform on their use in various biomedical applications.

bioengineering↗

bioRxiv2019

Establishment of morphological atlas of Caenorhabditis elegans embryo with cellular resolution using deep-learning-based 4D segmentation

Cell lineage consists of cell division timing, cell migration and cell fate, which are highly reproducible during the development of some nematode species, including C. elegans. Due to the lack of high spatiotemporal resolution of imaging technique and reliable shape-reconstruction algorithm, cell morphology have not been systematically characterized in depth over development for any metazoan. This significantly inhibits the study of space-related problems in developmental biology, including cell segregation, cell-cell contact and cell shape change over development. Here we develop an automated pipeline, CShaper, to help address these issues. By quantifying morphological parameters of densely packed cells in developing C. elegans emrbyo through segmentation of fluorescene-labelled membrance, we generate a time-lapse framework of cellular shape and migration for C. elegans embryos from 4-to 350-cell stage, including a full migration trajectory, morphological dynamics of 226 cells and 877 reproducible cell-cell contacts. In combination with automated cell tracing, cell-fate associated cell shape change becomes within reach. Our work provides a quantitative resource for C. elegans early development, which is expected to facilitate the research such as signaling transduction and cell biology of division.

developmental biology↗

bioRxiv2019

FvLcp1, a type-D fungal LysM protein with Chitin-binding domains, is a secreted protein involved in host recognition and fumonisin production in Fusarium verticillioides - maize kernel interaction

O_LIFusarium verticillioides is one of the key maize ear rot pathogens and produces fumonisins, a group of mycotoxins detrimental to humans and animals. Unfortunately, our understanding on how this fungus interacts with maize kernels to trigger mycotoxin biosynthesis is very limited.\nC_LIO_LIWe performed a systematic computational network-based analysis of large-scale F. verticillioides RNA-seq datasets to identify potential gene subnetwork modules that are associated with virulence and fumonisin regulation.\nC_LIO_LIAmong the highly discriminative subnetwork modules, we identified a putative hub gene FvLCP1, which encodes a putative a type-D fungal LysM protein with a signal peptide, three LysM domains, and two chitin binding domains. FvLcp1 is a unique protein that harbors these domains amongst five representative Fusarium species.\nC_LIO_LIFvLcp1 is a secreted protein important for fumonisin production with LysM domain playing acritical role. Chitin-binding domain was essential for in vitro chitin binding.\nC_LIO_LIUsing rice blast fungus, we learned that FvLcp1 accumulates in appressoria, a key infection structure, suggesting that FvLcp1 could be involved in host recognition and infection. Also, full length FvLcp1 was able to suppress the BAX triggered plant cell death in Nicotiana benthamiana.\nC_LIO_LIThis is the first report where a unique type-D LysM secreted protein with chitin-binding domain in mycotoxigenic fungus F. verticillioides was shown to be potentially involved in suppressing host cell death and promoting fumonisins biosynthesis while the pathogen colonizes maize kernels.\nC_LI

microbiology↗

bioRxiv2019

Characterization of non-canonical G beta-like protein FvGbb2 and its relationship with heterotrimeric G proteins in Fusarium verticillioides

Fusarium verticillioides is a fungal pathogen that is responsible for maize ear rot and stalk rot diseases worldwide. The fungus also produces carcinogenic mycotoxins, fumonisins, on infested maize. Unfortunately, we still lack clear understanding of how the pathogen responds to host and environmental stimuli to trigger fumonisin biosynthesis. The heterotrimeric G protein complex, consisting of canonical G, G{beta}, and G{gamma} subunits, is involved in transducing signals from external stimuli to regulate downstream signal transduction pathways. Previously, we demonstrated that G{beta} protein FvGbb1 has direct impact on fumonisin regulation but no other physiological aspects in F. verticillioides. In this study, we identified and characterized a putative receptor for activated C kinase 1 (RACK1) homolog FvGbb2 as a putative G{beta}-like protein in F. verticillioides. The mutant exhibited severe defects not only in fumonisin biosynthesis but also vegetative growth and conidiation. FvGbb2 was positively associated with carbon source utilization and stress agents but negatively regulated general amino acid control. While FvGbb2 does not interact with canonical G protein subunits, it may interact with diverse proteins in the cytoplasm to regulate vegetative growth, virulence, fumonisin biosynthesis, and stress response in F. verticillioides.

microbiology↗

bioRxiv2019

Stress generation, relaxation and size control in confined tumor growth

Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Stress release experiments show that nonuniform anisotropic elastic stresses can be distributed throughout. The elastic stresses are maintained by structural proteins and adhesive molecules, and can be actively relaxed by a variety of biophysical processes. In this paper, we present a new continuum model to investigate how the growth-induced elastic stresses and active stress relaxation, in conjunction with cell size control feedback machinery, regulate the cell density and stress distributions within growing tumors as well as the tumor sizes in the presence of external physical confinement and gradients of growth-promoting chemical fields. We introduce an adaptive reference map that relates the current position with the reference position but adapts to the current position in the Eulerian frame (lab coordinates) via relaxation. This type of stress relaxation is similar to but simpler than the classical Maxwell model of viscoelasticity in its formulation. By fitting the model to experimental data from two independent studies of tumor spheroid growth and their cell density distributions, treating the tumors as incompressible, neo-Hookean elastic materials, we find that the rates of stress relaxation of tumor tissues can be comparable to volumetric growth rates. Our study provides insight on how the biophysical properties of the tumor and host microenvironment, mechanical feedback control and diffusion-limited differential growth act in concert to regulate spatial patterns of stress and growth. When the tumor is stiffer than the host, our model predicts tumors are more able to change their size and mechanical state autonomously, which may help to explain why increased tumor stiffness is an established hallmark of malignant tumors. Author summaryThe mechanical state of cells can modulate their growth and division dynamics via mechanotransduction, which affects both the cell size distribution and the tissue size as a whole. Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Besides external confinement and compression on the tumor border, a heterogeneous stress field can be generated inside the tumor by nutrient-driven differential growth. Such growth-induced mechanical stresses can be relaxed by tissue rearrangement, which happens during cell neighbor exchanges, cell divisions, and extracellular matrix renewal. In this study, we have developed a continuum model that describes the above mechanical interactions and the dynamics of tissue rearrangement explicitly. Motivated by published experimental data, we consider mechanotransduction where the local compressive stress slows down cell growth and cell size reduction limits cell division. We have analyzed how external mechanical stimuli and internal processes influence the outcome of cell-and-tissue sizes and spatial patterns of cell density and mechanical stress in growing tumors.

biophysics↗

bioRxiv2019

Glucocorticoids Induce the Expansion of an Immature Human CFU-E Population

Despite effective clinical use, the mechanistic bases for the regulation of human erythropoiesis by glucocorticoids remain poorly understood. Here, we employed an erythroid culture system to differentiate primary human CD34+ cells isolated from control peripheral blood, cord blood and patients with Diamond Blackfan anemia (DBA), as model of an erythropoietic disorder treated with glucocorticoids. We found that the response to Dexamethasone is dependent on the developmental origin of the source of CD34+ cells, specifically increasing the expansion of CD34+ cells from peripheral blood but not cord blood. We also demonstrated that Dex treatment leads to the expansion of a novel immature colony-forming unit-erythroid (CFU-E) population in peripheral blood which is uniquely responsible for the proliferative effects observed during human adult erythropoiesis. Dex treatment of peripheral blood CFU-E cells also induced p57Kip2 expression while patients with DBA resistant to steroids had altered p57Kip2 expression that did not increase with Dex. Furthermore, shRNA knockdown of p57Kip2 reduced proliferation and abrogated the effects of Dex. Finally, proteomics of Dex-treated CFU-E from peripheral blood and cord blood additionally revealed novel Dex targets in the erythroid system. Altogether, these results provide novel insights into the regulation of human erythropoiesis by glucocorticoids.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC=\"FIGDIR/small/722850v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@c5c076org.highwire.dtl.DTLVardef@dec2f9org.highwire.dtl.DTLVardef@d27737org.highwire.dtl.DTLVardef@190c795_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2019

Heterozygous variants in the mechanosensitive ion channel TMEM63A result in transient hypomyelination during infancy

Mechanically activated (MA) ion channels convert physical forces into electrical signals. Despite the importance of this function, the involvement of mechanosensitive ion channels in human disease is poorly understood. Here we report heterozygous missense mutations in the gene encoding the MA ion channel TMEM63A that result in an infantile disorder resembling a hypomyelinating leukodystrophy. Four unrelated individuals presented with congenital nystagmus, motor delay, and deficient myelination on serial scans in infancy, prompting the diagnosis of Pelizaeus-Merzbacher (like) disease. Genomic sequencing revealed all four individuals carry heterozygous missense variants in the pore-forming domain of TMEM63A. These variants were confirmed to have arisen de novo in three of the four individuals. While the physiological role of TMEM63A is incompletely understood, it is highly expressed in oligodendrocytes and it has recently been shown to be a mechanically activated (MA) ion channel. Using patch clamp electrophysiology, we demonstrated that each of the modelled variants results in strongly attenuated stretch-activated currents when expressed in naive cells. Unexpectedly, the clinical evolution of all four individuals has been surprisingly favorable, with substantial improvements in neurological signs and developmental progression. In the three individuals with follow-up scans after four years of age, the myelin deficit had almost completely resolved. Our results suggest a previously unappreciated role for mechanosensitive ion channels in myelin development.

genomics↗

bioRxiv2019

Prenatal Diagnosis of Fetuses with Increased Nuchal Translucency by Genome Sequencing Analysis

BackgroundIncreased Nuchal Translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single nucleotide variants to those affecting millions of base-pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA), however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT.\n\nMethodsWe retrospectively applied GS (>30-fold) for fetuses with increased NT ([≥]3.5-mm), who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy-number variants and structural rearrangements was performed simultaneously and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available.\n\nResultsOverall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a 2-fold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion which disrupted an OMIM autosomal dominant disease-causing gene at the inserted site.\n\nConclusionsOur study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turn-around-time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.

genomics↗

bioRxiv2019

Fusarium verticillioides SNARE protein FvSyn1 harbors two key functional motifs that play selective roles in fungal development and virulence

Fusarium verticillioides is one of the key fungal pathogens responsible for maize stalk rots. While stalk rot pathogens are prevalent worldwide, our understanding of stalk rot virulence mechanism in pathogenic fungi is still very limited. We previously identified F. verticillioides FvSYN1 gene, which was demonstrated to plays an important role in maize stalk rot virulence. FvSyn1 belongs to a family of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins that play critical roles in a variety of developmental processes. In this study, we further characterized the cellular features of FvSyn1 protein motifs in F. verticillioides development and virulence. We generated FvSyn1 motif-specific deletion mutants to further investigate how different motifs contribute to development and virulence. Microscopic observation showed that {Delta}fvsyn1 mutant exhibits rough and hyper-branched hyphae when compared to the wild type progenitor. Moreover, {Delta}fvsyn1 mutant was sensitive to cell wall stress agents resulting in vegetative growth reduction. We showed that FvSyn1::GFP protein is associated with endomembrane but this outcome did not clarify why the deletion of this protein led to stress sensitivity and aberrant hyphal development. Characterization of FvSyn1 domains indicated that both Syntaxin N-terminus (SynN) domain and SNARE C-terminus domain play distinct roles in fungal development but collectively function in virulence. We also determined that two domains in FvSyn1 is not required for fumonisin production. Interestingly, these two domains were involved in carbon nutrient utilization including pectin, starch and sorbitol. This study further characterized the role of FvSyn1 in hyphal growth, localization, cell wall stress response and virulence in F. verticillioides.\n\nHighlights{blacktriangleright} F. verticillioides SNARE protein FvSYN1 is important for vegetative growth and virulence.\n\n {blacktriangleright}FvSYN1 deletion mutant performed better under cell wall stressors.\n\n {blacktriangleright}Dissecting of two domains and investigate the roles.

molecular biology↗

bioRxiv2019

A Rab GTPase protein FvSec4 is necessary for fumonisin B1 biosynthesis and virulence in Fusarium verticillioides

Rab GTPases are responsible for a variety of membrane trafficking and vesicular transportation in fungi. But the role of Rab GTPases in Fusarium verticillioides, one of the key corn pathogens worldwide, remains elusive. These Small GTPases in fungi, particularly those homologous to Saccharomyces cerevisiae Sec4, are known to be associated with protein secretion, vesicular trafficking, secondary metabolism and pathogenicity. Here, we characterized the molecular functions of FvSec4 by generating a null mutant and learned that it is important for vegetative growth, hyphal branching, and conidiation. Interestingly, the mutation did not impair the expression of key conidiation-related genes. Meanwhile, the mutant did not show any defect in sexual development, including perithecia production. GFP-FvSec4 localized to growing hyphal tips, and raised the possibility that FvSec4 is involved in protein trafficking and endocytosis. The mutant exhibited defect in corn stalk rot virulence and also significant alteration of fumonisn B1 production. The mutation led to more sensitivity to oxidative and cell wall stress agents, and defects in carbon utilization. Gene complementation fully restored the defects in the mutant demonstrating that FvSec4 plays important role in these functions. Taken together, our data indicate that FvSec4 plays important roles in F. verticillioides hyphal development, virulence, mycotoxin production and stresses response. Further study is needed to characterize whether the mutation in FvSec4 leads to altered vesicle trafficking and protein secretion, which ultimately impact F. verticillioides physiology and virulence.

microbiology↗

bioRxiv2019

Immune-informed mucin hydrogels evade fibrotic foreign body response in vivo

The immune-mediated foreign body response to biomaterial implants can trigger the formation of insulating fibrotic capsules that can compromise implant function. To address this challenge, we leverage the intrinsic bioactivity of the mucin biopolymer, a heavily glycosylated protein that forms the protective mucus gel covering mucosal epithelia. By using a bioorthogonal inverse electron demand Diels-Alder reaction, we crosslink mucins into implantable hydrogels. We show that mucin hydrogels (Muc-gels) modulate the immune response driving biomaterial-induced fibrosis. Muc-gels did not elicit fibrosis 21 days after implantation in the peritoneal cavity of C57Bl/6 mice, whereas medical-grade alginate hydrogels (Alg-gels) were covered by fibrous tissues. Further, Muc-gels dampened the recruitment of innate and adaptive immune cells to the gel and triggered a pattern of very mild activation marked by a noticeably low expression of the fibrosis-stimulating TGF-{beta}1 cytokine. With this advance in mucin materials, we provide an essential tool to better understand mucin bioactivities and to initiate the development of new mucin-based and mucin-inspired immune-informed materials for implantable devices subject to fibrotic encapsulation.

bioengineering↗

bioRxiv2018

WBC-Profiler: an Unsupervised Feature Learning System for Leukocytes Characterization and Classification

The characterization and classification of white blood cells (WBC) is critical for the diagnosis of anemia, leukemia and many other hematologic diseases. We developed WBC-Profiler, an unsupervised feature learning system for quantitative analysis of leukocytes. We demonstrate that WBC-Profiler enables automatic extraction of complex signatures from microscopic images without human-intervention and thereafter effective construction of leukocytes profiles, which decouples large scale complex leukocytes characterization from limitations in both human-based feature engineering/optimization and the end-to-end solutions provided by modern deep neural networks, and therefore has the potential to provide new opportunities towards meaningful studies/applications with scientific and/or clinical impact

bioinformatics↗

bioRxiv2018

Ezh2-dependent epigenetic reprogramming controls a developmental switch between modes of gastric neuromuscular regulation

Physiological interconversion between specialized cell types has only been described in a few mammalian tissues and the mechanisms remain obscure. Using genetic lineage tracing during postnatal development and in-vitro models we demonstrate conversion of gastric interstitial cells of Cajal (ICC), regulatory cells that electrically pace phasic contractions and mediate nitrergic and cholinergic neural control of smooth muscle cells, into phenotypically distinct \"fibroblast-like\" interstitial cells (FLC), which only mediate purinergic signaling. Mechanistically, we find this transition to be epigenetically governed by H3K27 trimethylation of cell identity-related promoters whose susceptibility to repression is predicted by H3K27 acetylation patterns in ICC. The phenotypic switch was reversible by inhibition, knockdown or in-vivo genomic inactivation of the polycomb H3K27 methyl-transferase Ezh2. These results demonstrate a role for Ezh2-mediated epigenetic repression in physiological mammalian transdifferentiation and identify FLC as a reserve from which ICC can potentially be restored in common gastrointestinal disorders where ICC are depleted.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC=\"FIGDIR/small/486423v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (38K):\norg.highwire.dtl.DTLVardef@e12f42org.highwire.dtl.DTLVardef@1e5c7beorg.highwire.dtl.DTLVardef@9cbc21org.highwire.dtl.DTLVardef@34f28_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGastric pacemaker cells (ICC) transdifferentiate into quiescent cells (FLC) in vivo\nC_LIO_LIICC-to-FLC shift switches neural control from nitrergic/cholinergic to purinergic\nC_LIO_LIEzh2-mediated H3K27me3 represses cell-identity genes during ICC-to-FLC transition\nC_LIO_LIEzh2 inhibition restores ICC numbers, phenotype and function\nC_LI\n\neTOC BLURBSyed et al. find aging to cause transdifferentiation of gastric pacemaker cells (interstitial cells of Cajal, ICC), which also communicate cholinergic and nitrergic neurotransmission to smooth muscle cells, into quiescent \"fibroblast-like cells\" (FLC), which only mediate purinergic signals. This switch is governed by Ezh2, whose inhibition can reverse ICC depletion.

molecular biology↗

bioRxiv2018

Characterization of the Rosa roxbunghii Tratt transcriptome and analysis of MYB genes

Rosa roxbunghii Tratt belongs to the Rosaceae family, and the fruit is flavorful, economic, and highly nutritious, providing health benefits. MYB proteins play key roles in R. roxbunghii fruit development and quality. However, the available genomic and transcriptomic information are extremely deficient. Here, a normalized cDNA library was constructed using five tissues, stem, leaf, flower, young fruit, and mature fruit, with three repetitions, and sequenced using the Illumina HiSeq 2500 platform. De novo assembly was performed, and 470.66 million clean reads were obtained. In total, 63,727 unigenes, with an average GC content of 42.08%, were determined and 59,358 were annotated. In addition, 9,354 unigenes were assigned the Gene Ontology category, and 20,202 unigenes were assigned to 25 Eukaryotic Ortholog Groups. Additionally, 19,507 unigenes were classified into 140 pathways of the Kyoto Encyclopedia of Genes and Genomes database. Using the transcriptome, 18 candidate MYB genes that were significantly expressed in mature fruit, compared with other tissues, were obtained. Among them, 10 R2R3 MYB and 1 R1 MYB were identified. The expression levels of 12 MYB genes randomly selected for qRT-PCR analysis were consistent with the RNA-seq results. A total of 37,545 microsatellites were detected, with an average EST--SSR frequency of 0.59 (37,545/63,727). This transcriptome data will be valuable for identifying genes of interest and studying their expression and evolution.

bioinformatics↗