Biology subjects

Guo, T.

Publications and source records attributed to Guo, T..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v1, a previous pan-human library built from 1096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying 10,943 proteins. However, a major limitation of DPHL v1 is the lack of semi-tryptic peptides and protein isoforms, which are abundant in clinical specimens. Here, we generated DPHL v2 from 1608 DDA-MS data acquired using Orbitrap mass spectrometers. The data included 586 DDA-MS newly acquired from 17 tissue types, while 1022 files were derived from DPHL v1. DPHL v2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v2 to include semi-tryptic peptides and protein isoforms. DPHL v2 was then applied to a publicly available colorectal cancer dataset with 286 DIA-MS files. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v1. Our findings show that the increased human proteome coverage of DPHL v2 provides larger pools of potential protein biomarkers.

bioinformatics↗

bioRxiv2022

Immortalized bovine satellite cells for cultured meat applications

For cultured meat to succeed at scale, muscle cells from food-relevant species must be expanded in vitro in a rapid and reliable manner to produce millions of metric tons of biomass annually. Toward this goal, genetically immortalized cells offer substantial benefits over primary cells, including rapid growth, escape from cellular senescence, and consistent starting cell populations for production. Here, we develop genetically immortalized bovine satellite cells (iBSCs) via constitutive expression of bovine Telomerase reverse transcriptase (TERT) and Cyclin-dependent kinase 4 (CDK4). These cells achieve over 120 doublings at the time of publication and maintain their capacity for myogenic differentiation. They therefore offer a valuable tool to the field, enabling further research and development to advance cultured meat.

cell biology↗

bioRxiv2022

Activin receptor ALK4 promotes adipose tissue hyperplasia by suppressing differentiation of adipocyte precursors

Adipocyte hyperplasia and hypertrophy are the two main processes contributing to adipose tissue expansion, yet the mechanisms that regulate and balance their involvement in obesity are incompletely understood. Activin B/GDF-3 receptor ALK7 is expressed in mature adipocytes, and promotes adipocyte hypertrophy upon nutrient overload by suppressing adrenergic signaling and lipolysis. In contrast, the role of ALK4, the canonical pan-activin receptor, in adipose tissue is unknown. Here we report that, unlike ALK7, ALK4 is preferentially expressed in adipocyte precursors, where it suppresses differentiation, allowing proliferation and adipose tissue expansion. ALK4 expression in adipose tissue increases upon nutrient overload and positively correlates with fat depot mass and body weight, suggesting a role in adipose tissue hyperplasia during obesity. Mechanistically, ALK4 signaling suppresses expression of CEBP and PPAR{gamma}, two master regulators of adipocyte differentiation. Conversely, ALK4 deletion enhances CEBP/PPAR{gamma} expression and induces premature adipocyte differentiation, which can be rescued by CEBP knock-down. These results clarify the function of ALK4 in adipose tissue and highlight the contrasting roles of the two activin receptors in the regulation of adipocyte hyperplasia and hypertrophy during obesity.

physiology↗

bioRxiv2022

Regulation of adventitial interstitial fluid circulation by heartbeat and respiration

Converging studies showed interstitial fluid (ISF) adjacent to blood vessels flows along adventitia of vasculature into heart and lungs. We aim to reveal circulatory pathways and regulatory mechanism of such adventitial ISF flow in rat model. By MRI, real-time fluorescent imaging, micro-CT and histological analysis, ISF was found to flow in adventitial matrix surrounded by fascia and along systemic vessels into heart, then flow into lungs via pulmonary arteries and back to heart via pulmonary veins, which was neither perivascular tissues nor blood or lymphatic vessels. Under physiological conditions, speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, became pulsative during heavy breathing. During cardiac or respiratory cycle, each dilation or contraction of heart or lungs can generate to-and-fro adventitial ISF flow along femoral veins. Discovered regulatory mechanisms of adventitial ISF flow along vasculature by heart and lungs will revolutionize understanding of cardiovascular system. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/512678v3_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1d29c16org.highwire.dtl.DTLVardef@583f5org.highwire.dtl.DTLVardef@1a551eorg.highwire.dtl.DTLVardef@ca4780_HPS_FORMAT_FIGEXP M_FIG Graphic abstract of adventitial interstitial fluid cycle by heartbeat and respiration.The heart and lungs can work together to regulate the ISF (green arrow) adjacent to blood vessels to flow centripetally in an adventitial pathway along the major arteries and veins of the systemic vasculature to the epicardium and myocardium, then flow into the lungs via the pulmonary arteries and back to the heart via the pulmonary veins, forming an adventitial ISF circulatory network. Under physiological conditions, the speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, and became pulsative during heavy breathing. During respiratory cycle, each expansion of the lungs during inflation generates a centrifugal flow of adventitial ISF along the systemic veins, while each contraction of the lungs during deflation generates a centripetal adventitial ISF flow. During cardiac cycle, each dilation of atria or ventricles generates a centripetal flow of adventitial ISF along the systemic veins, while each contraction of atria or ventricles generates a centrifugal adventitial ISF flow. C_FIG

physiology↗

bioRxiv2022

Selection and validation of internal control genes for quantitative real-time RT-qPCR normalization of Phlebopus portentosus gene expression under different conditions

Phlebopus portentosus (Berk. and Broome) Boedijin is an attractive edible mushroom and considered as the unique bolete to have achieved artificial cultivation in vitro. Gene expression analysis has become widely used in researches of edible fungi and is important to uncover the functions of genes involved in complex biological processes. Selecting appropriate reference genes is crucial to ensuring reliable results of gene expression analysis by RT-qPCR. In our study, a total of 12 candidate control genes were selected from 25 traditional housekeeping genes based on the expression stability in 9 transcriptomes of 3 developmental stages. These genes were further evaluated using geNorm, NormFinder and RefFinder under different conditions and developmental stages. The results revealed that MSF1-domain-containing protein (MSF1), synaptobrevin (SYB), mitogen-activated protein kinase genes (MAPK), TATA binding protein 1 (TBP1) and SPRY domain protein (SPRY) were the most stable reference genes in all sample treatments, while elongation factor 1-alpha (EF1), Actin and ubiquitin-conjugating enzyme (UBCE) were the most unstably expressed. The gene SYB was selected based on the transcriptome results and was identified as a novel reference gene in P. portentosus. This is the first detailed study for identification reference genes in this fungus and may provide new insights into selecting genes and quantifying gene expression.

microbiology↗

bioRxiv2022

Magnesium modulates Bacillus subtilis cell division frequency

By chance, we discovered a window of extracellular magnesium (Mg2+) availability that modulates Bacillus subtilis division frequency without affecting growth rate. In this window, cells grown with excess Mg2+ produce shorter cells than those grown in unsupplemented medium. The Mg2+-responsive adjustment in cell length occurs in both rich and minimal media and in domesticated and undomesticated strains. Of other divalent cations tested, manganese (Mn2+) and zinc (Zn2+) also resulted in cell shortening, but only at concentrations that affected growth. Cell length decreased proportionally with increasing Mg2+ from 0.2 mM to 2.0 mM, with little or no detectable change in labile, intracellular Mg2+ based on a riboswitch reporter. Cells grown in excess Mg2+ had fewer nucleoids and possessed more FtsZ-rings per unit cell length, consistent with increased division frequency. Remarkably, when shifting cells from unsupplemented to supplemented medium, more than half of the cell length decrease occurred in the first 10 min, consistent with rapid division onset. Relative to unsupplemented cells, cells growing at steady-state with excess Mg2+ showed enhanced expression of a large number of SigB-regulated genes and activation of the Fur, MntR, and Zur regulons. Thus, by manipulating the availability of one nutrient, we were able to uncouple growth rate from division frequency and identify transcriptional changes suggesting cell division is accompanied by oxidative stress and an enhanced demand to sequester and/or increase uptake of iron, Mn2+, and Zn2+. IMPORTANCEThe signals cells use to trigger cell division are unknown. Although division is often considered intrinsic to the cell-cycle, microorganisms can continue to grow and repeat rounds of DNA replication without dividing, indicating cycles of division can be skipped. Here we show that by manipulating a single nutrient, Mg2+, cell division can be uncoupled from growth rate. This finding can be applied to investigate the nature of the cell division signal(s).

microbiology↗

bioRxiv2022

COVIDpro: Database for mining protein dysregulation in patients with COVID-19

BackgroundThe ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers. MethodsWe built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers. FindingsWe built and maintain a web server COVIDpro (https://www.guomics.com/covidPro/) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80. InterpretationCOVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients. FundingNational Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504) Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAlthough an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the diseases mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets. Added value of this studyWe integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples. Implications of all the available evidenceCOVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.

systems biology↗

bioRxiv2022

Dear-DIAXMBD: deep autoencoder for data-independent acquisition proteomics

Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition (DDA) data represents a promising direction. In this paper, we proposed an untargeted analysis method, Dear-DIAXMBD, for direct analysis of DIA data. Dear-DIAXMBD first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms, then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes, and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides, and between fragments and peptides. We show that Dear-DIAXMBD performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms. Dear-DIAXMBD is publicly available at https://github.com/jianweishuai/Dear-DIA-XMBD.

bioinformatics↗

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

Proteomic Dynamics of Breast Cancers Identifies Potential Therapeutic Protein Targets

Treatment and relevant targets for breast cancer (BC) remain limited, especially for triple-negative BC (TNBC). We quantified the proteomes of 76 human BC cell lines using data independent acquisition (DIA) based proteomics, identifying 6091 proteins. We then established a 24-protein panel distinguishing TNBC from other BC types. Integrating prior multi-omics datasets with the present proteomic results to predict the sensitivity of 90 drugs, we found that proteomics data improved drug sensitivity predictions. The sensitivity of the 90 drugs was mainly associated with cell cytoskeleton, signal transduction and mitochondrial function. We next profiled the proteome changes of nine cell lines (five TNBC cell lines, four non-TNBC cell lines) perturbated by EGFR/AKT/mTOR inhibitors. In the TNBC cell lines, metabolism pathways were dysregulated after EGFR/mTOR inhibitors treatment, while RNA modification and cell cycle pathways were dysregulated after AKT inhibitor treatment. Our study presents a systematic multi-omics and in-depth analysis of the proteome of BC cells. This work aims to aid in prioritization of potential therapeutic targets for TNBC as well as to provide insight into adaptive drug resistance in TNBC.

systems biology↗

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

A common mechanism of temperature-sensing in thermoTRP channels

Detecting temperature is crucial for the survival of living organisms. Though the thermo transient receptor potential (thermoTRP) channels, such as TRPV1 or TRPM8, have been identified as prototypic heat or cold sensors, respectively, how they detect temperature remains elusive. Here we first identified groups of clustered residues in these channels that undergo burial/exposure conformational rearrangements during temperature activation by analyzing available protein structures or hydroxyl radical footprinting-mass spectroscopy (HRF-MS). By systematically perturbing water-protein interactions at these residues, we found that the temperature sensitivity in these channels were modulated in accordance with the sidechain hydrophobicity. The changes in energy associated with changes in water-protein interactions were sufficient for thermo activation. Therefore, our study has established that the water-protein interactions as a common mechanism underlying temperature sensing in TRPM8 and TRPV1.

biophysics↗

bioRxiv2022

Combined omics unravels the molecular mechanism of golden-leaf coloration in Koelreuteria paniculata 'jinye'

Koelreuteria paniculata is widely distributed in Asia and introduced to Europe and North America. K. paniculata jinye is a mutant variety used in landscaping that has a golden leaf color phenotype. Although similar leaf color variants occur in plants, little is known of the underlying mechanism. We performed physiological, anatomical, microRNA sequencing, transcriptomic, and metabolomic analyses of the golden leaf variation in the mutant. Compared with the original green cultivar, the golden leaf mutant exhibited 76.05% and 44.32% decreased chlorophyll a (Chl a) and chlorophyll b (Chl b) contents, respectively, and significantly increased carotenoid content. Analysis of leaf ultrastructure revealed an abnormal chloroplast morphology and fewer lamellae in the mutant. Fifty-nine differentially expressed genes (DEGs), forty transcription factors (TFs) and forty-nine differentially expressed miRNAs (DEmiRs) involved in pigment metabolism, chloroplast development, and photosynthesis were identified. The GLK and petC genes were downregulated and are involved in chloroplast development and chlorophyll synthesis, respectively. The upregulated PSY and PDS genes, and the downregulated NCED gene promote carotenoid accumulation. A variety of chalcones and flavonols were upregulated in the mutant. Consequently, the carotenoid to chlorophyll ratio increased by more than 75%, and the accumulation of chalcones and flavonols was responsible for the golden leaf phenotype of the mutant K. paniculata.

molecular biology↗

bioRxiv2022

Downregulating PTBP1 fails to convert astrocytes into hippocampal neurons and to alleviate symptoms in Alzheimer's mouse models

Conversion of astroglia into functional neurons has been considered as a promising therapeutic strategy for neurodegenerative diseases. Recent studies reported that downregulation of the RNA binding protein, PTBP1, converts astrocytes into neurons in situ in multiple mouse brain regions, consequently improving pathological phenotypes associated with Parkinsons disease, RGC loss, and aging. Here, we demonstrate that PTBP1 downregulation using antisense oligonucleotides or an astrocyte specific AAV-mediated shRNA system fails to convert hippocampal astrocytes into neurons in WT, and {beta}-amyloid (5xFAD) and tau (PS19) Alzheimers disease (AD) mouse models, and fails to reverse synaptic/cognitive deficits and AD-associated pathology. Similarly, PTBP1 downregulation cannot convert astrocytes into neurons in the striatum and substantia nigra. Together, our study suggests that cell fate conversion strategy for neurodegenerative disease therapy through manipulating one single gene, such as PTBP1, warrants more rigorous scrutiny.

neuroscience↗

bioRxiv2022

Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy

BackgroundQuantitative systems pharmacology (QSP) modeling of the host-immune response against Mtb can inform rational design of host-directed therapies (HDTs). We aimed to develop a QSP framework to evaluate the effects of metformin-associated autophagy-induction in combination with antibiotics. MethodsA QSP framework for autophagy was developed by extending a model for host-immune response to include AMPK-mTOR-autophagy signalling. This model was combined with pharmacokinetic-pharmacodynamic models for metformin and antibiotics against Mtb. We compared the model predictions to mice infection experiments, and derived predictions for pathogen and host-associated dynamics in humans treated with metformin in combination with antibiotics. ResultsThe model adequately captured the observed bacterial load dynamics in mice Mtb infection models treated with metformin. Simulations for adjunctive metformin therapy in newly diagnosed patients suggested a limited yet dose-dependent effect of metformin on reducing the intracellular bacterial load and selected pro-inflammatory cytokines. Our predictions suggest that metformin may provide beneficiary effects when overall bacterial load, or extracellular-to-intracellular bacterial ratio is low, either early after infection or late during antibiotic treatment. ConclusionsWe present the first QSP framework for HDTs against Mtb, linking cellular-level autophagy effects to disease progression. This framework may be extended to guide design of HDTs against Mtb.

systems biology↗

bioRxiv2022

Complex genetic architecture underlying the plasticity of maize agronomic traits

Phenotypic plasticity is the property of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant for future agriculture under changing climate. Here, we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a maize diverse population, planted at five sites with distinct environmental conditions and genotyped with ~ 6.60 million SNPs. We found that altitude-related environmental factors were main drivers for across site variation in flowering time traits but not plant architecture and yield traits. For 23 traits, we detected 109 QTLs, of which 29 was for mean, 66 was for plasticity, and 14 for both parameters, besides, 80% of the QTLs were interreacted with the environment. The effects of several QTLs changed in magnitude or sign, driving variation in phenotype plasticity, and we further experimentally validated one plastic gene ZmTPS14.1 whose effect was likely mediated by the compensation effect of ZmSPL6 which was from the downstream pathway probably. By integrating genetic diversity, environmental variation, and their interaction in a joint model, we could provide site-specific predictions with increased accuracy by as much as 15.5%, 3.8%, and 4.4% for DTT, PH, and EW, respectively. Overall, we revealed a complex genetic architecture involving multiallelic, pleiotropy, and genotype by environment interaction underlying maize complex trait mean and plasticity variation. Our study thus provided novel insights into the dynamic genetic architectures of agronomic traits in response to changing environments, paving a practical route to precision agriculture.

genetics↗

bioRxiv2021

Single chain models illustrate the 3D RNA folding shape during translation

The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell. We developed TRIP; Three-dimensional RNA Illustration Program, to model the three-dimensional RNA folding shape based on single-chain models. We identified the angle restriction of each bead component from previously reported single-molecule FISH experimental data. This simulation method was able to recapitulate the mRNA conformation change of the translation activity and three-dimensional positional interaction between organelle and its localized mRNAs. Within the analyzed cases base-pairing interactions only have minor effects on the three-dimensional mRNA conformation, and instead single-chain polymer characteristics have a more significant impact on the conformation. This method will be used to predict the aggregation mechanism of mRNA and long noncoding RNA in specific cellular conditions such as nucleolus and phase-separated granules.

biophysics↗

bioRxiv2021

Kdm6b confers Tfdp1 with the competence to activate p53 signalling in regulating palatogenesis

Epigenetic regulation plays extensive roles in diseases and development. Disruption of epigenetic regulation not only increases the risk of cancer, but can also cause various developmental defects. However, it is still unclear how epigenetic regulators coordinate with tissue-specific regulatory factors during morphogenesis of specific organs. Using palatogenesis as a model, we reveal the functional significance of Kdm6b, a H3K27me3 demethylase, in regulating embryonic development. Our study shows that Kdm6b plays an essential role in neural crest development, and loss of Kdm6b disturbs p53 pathway-mediated activity, leading to complete cleft palate along with cell proliferation and differentiation defects. Furthermore, activity of H3K27me3 on the promoter of p53 is precisely controlled by Kdm6b, and Ezh2 in regulating p53 expression in cranial neural crest cells. More importantly, Kdm6b renders chromatin accessible to the transcription factor Tfdp1, which binds to the promoter of p53 along with Kdm6b to specifically activate p53 expression during palatogenesis. Collectively our results highlight the important role of the epigenetic regulator Kdm6b and how it cooperates with Tfdp1 to achieve its functional specificity in regulating p53 expression, and further provide mechanistic insights into the epigenetic regulatory network during organogenesis.

developmental biology↗