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Chai, Y.

Publications and source records attributed to Chai, Y..

At least 37 records · Page 2Linked to original sources
bioRxiv2025

Toti: an integrated multi-omics database to decipher the epigenetic regulation of gene expression in totipotent stem cells

Totipotent cells (TSCs), the origin of mammalian life and foundation to early mammalian embryogenesis, are characterized by the highest differentiation capacity and extensive developmental potential. However, none of the existing embryonic databases have provided epigenetic and transcriptomic resources on totipotency, greatly limiting our understanding of the mechanisms governing the establishment and exit of totipotency. Here, we present Toti, a pioneering multi-omics database exclusively developed for totipotency, covering in vivo, in vitro and genome-edited human and mouse embryonic TSCs, TSC-like cells, pluripotent cells (PSCs), and embryos spanning preimplantation stages, with a total of 8,265 samples. Toti facilitates an in-depth exploration of the molecular mechanisms underlying totipotency by offering Search, Browse and Analysis modules available at http://toti.zju.edu.cn/.

developmental biology↗
bioRxiv2024

Expression and characterization of the complete cyanophage genome PP in the heterologous host Synechococcus elongatus PCC 7942

Cyanophages are considered a promising biological management option for treating cyanobacterial blooms. Broadening the host range of cyanophages and/or shortening the lysis cycle by designing and synthesizing artificial cyanophages are potential strategies to enhance their effectiveness and efficiency. However, the rescue of artificial cyanophage genomes remains unexplored. In this study, we achieved the integration of a full-length cyanophage genome, PP, which originally infects Plectonema boryanum FACHB-240, into the model cyanobacterium Synechococcus elongatus PCC 7942. Since the integration of these large fragments ([~]42 kb) into cyanobacteria depended on conjugation via Escherichia coli, the toxic open reading frames (ORFs) of PP to E. coli were first identified, leading to the identification of toxic ORF6, ORF11, and ORF22. The original PP genome was then rearranged, and the three toxic ORFs were controlled using a tandem induction switch. The full length of the PP genome was integrated into the genome of S. elongatus PCC 7942 via two rounds of homologous recombination. Interestingly, compared to the control strain, the integration of the PP genome decreased photosynthesis and carbon fixation in S. elongatus PCC 7942, exhibiting cyanophage-like behavior. Transcriptomic analysis revealed that 32 of the 41 ORFs of the PP genome were transcribed in S. elongatus PCC 7942, significantly altering the energy metabolism and carbon fixation pathways. These influences were further demonstrated using metabolomics. This study provides a comprehensive approach for the artificial design and integration of cyanophage genomes in cyanobacteria, laying the foundation for their real rescue in the future.

synthetic biology↗
bioRxiv2024

PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development

Spliceosomopathies, which are a group of disorders caused by defects in the splicing machinery, frequently affect the craniofacial skeleton and limb, but the molecular mechanism underlying this tissue-specific sensitivity remains unclear. Splicing factors and small nuclear ribonucleoproteins (snRNPs) are core components of splicing machinery, and splicing factors are further controlled by post-translational modifications, among which arginine methylation is one of the most prevalent. We determined the splicing mechanisms in the cranial neural crest cells (CNCCs), a multipotent developmental population that gives rise to the majority of the craniofacial skeleton, and focused on an upstream regulator of splicing proteins, protein arginine methyltransferase 1 (PRMT1). PRMT1 is the highest expressing arginine methyltransferase in CNCCs and its role in craniofacial development is evident from our earlier investigation, where CNCC-specific Prmt1 deletion caused cleft palate and mandibular hypoplasia. PRMT1 catalyzes arginine methylation of splicing factors to modify protein localization, expression and activity. In the present study, we uncover roles of PRMT1 in the regulation of intron retention, a type of alternative splicing where introns are retained in the mature mRNA. CNCCs from mandibular primordium of Prmt1-deficient embryos demonstrated an increase in the percentage of intron-retaining mRNA of matrix genes, which triggered NMD, causing a reduction in matrix mRNA abundance. We further identified SFPQ as a substrate of PRMT1 that depends on PRMT1 for arginine methylation and protein expression in the developing craniofacial structures. Depletion of SFPQ in CNCCs phenocopied PRMT1 deletion whereby matrix, Wnt signaling components and neuronal gene transcripts contained higher IR and exhibited lower expression. We further recognized gene length as a common feature among SFPQ-regulated genes in CNCCs. Altogether, these findings demonstrate that the PRMT1-SFPQ pathway modulates matrix gene expression via IR-triggered NMD in CNCCs during craniofacial development.

developmental biology↗
bioRxiv2024

Neural crest and periderm-specific requirements of Irf6 during neural tube and craniofacial development

IRF6 is a key genetic determinant of syndromic and non-syndromic cleft lip and palate. The ability to interrogate post-embryonic requirements of Irf6 has been hindered, as global Irf6 ablation in the mouse causes neonatal lethality. Prior work analyzing Irf6 in mouse models defined its role in the embryonic surface epithelium and periderm where it is required to regulate cell proliferation and differentiation. Several reports have also described Irf6 gene expression in other cell types, such as muscle, and neuroectoderm. However, analysis of a functional role in non-epithelial cell lineages has been incomplete due to the severity and lethality of the Irf6 knockout model and the paucity of work with a conditional Irf6 allele. Here we describe the generation and characterization of a new Irf6 floxed mouse model and analysis of Irf6 ablation in periderm and neural crest lineages. This work found that loss of Irf6 in periderm recapitulates a mild Irf6 null phenotype, suggesting that Irf6-mediated signaling in periderm plays a crucial role in regulating embryonic development. Further, conditional ablation of Irf6 in neural crest cells resulted in an anterior neural tube defect of variable penetrance. The generation of this conditional Irf6 allele allows for new insights into craniofacial development and new exploration into the post-natal role of Irf6.

developmental biology↗
bioRxiv2024

A Novel Regulation on the Developmental Checkpoint Protein Sda that Controls Sporulation and Biofilm Formation in Bacillus subtilis

Biofilm formation by Bacillus subtilis is triggered by an unusually simple environmental sensing mechanism. Certain serine codons, the four TCN codons (N for A, T, C, or G), in the gene for the biofilm repressor SinR caused lowered SinR translation and subsequent biofilm induction during transition from exponential to stationary growth. Global ribosome profiling showed that ribosomes pause when translating the four UCN (U for T on the mRNA) serine codons on mRNA, but not the two AGC/AGU serine codons. We proposed a serine codon hierarchy (AGC/AGT vs TCN) in that genes enriched in the TCN serine codons may experience reduced translation efficiency when serine is limited. In this study, we designed an algorithm to score all protein-coding genes in B. subtilis NCIB3610 based on the serine codon hierarchy. We generated a short list of 50 genes that could be subject to regulation by this novel mechanism. We further investigated one such gene from the list, sda, which encodes a developmental checkpoint protein regulating both sporulation and biofilm formation. We showed that synonymously switching the TCN serine codons to AGC in sda led to delayed biofilm formation and sporulation. This engineered strain also outgrew strains with other synonymously substituted sda alleles (TCN) in competition assays for biofilm formation and sporulation. Lastly, we showed that the AGC serine codon substitutions in sda elevated the Sda protein levels. This serine codon hierarchy-based novel signaling mechanism could be exploited by bacteria in adapting to stationary phase and regulating important biological processes. ImportanceGenome-wide ribosome profiling in Bacillus subtilis shows that under serine limitation, ribosomes pause on the four TCN (N for A, C, G, and T), but not AGC/AGT serine codons, during translation at a global scale. This serine codon hierarchy (AGC/T vs TCN) differentially influences translation efficiency of genes enriched in certain serine codons. In this study, we designed an algorism to score all 4000+ genes in the B. subtilis genome and generated a list of 50 genes that could be subject to this novel serine codon hierarchy-mediated regulation. We further investigated one such gene, sda, encoding a developmental check point protein. We show that sda and cell developments controlled by Sda are also regulated by this novel mechanism.

genetics↗
bioRxiv2024

Aquatic risk calibration of tire wear particle in interaction with leaching time, high temperature and UV radiation based on reproductive toxicity to zooplankton

The aquatic toxicity of tire wear particles (TWPs) depends on the leaching of various components. The leaching process is time-dependent and influenced by various environmental factors, leading to fluctuation in leachate toxicity. In this study, we quantified the temporal dynamics of leachate toxicity using the dose-response model. Meanwhile, to simulate weathering conditions, TWPs were exposed to ultraviolet (UV) irradiation and elevated temperature. The results indicated that the leachate toxicity over time fitted a biphasic pattern, with an initial increase followed by a decrease, peaking at the 11th day. The toxicity fluctuation cannot be characterized by any single component, but rather leachate should be considered as an integral whole aligning with a typical hormesis dose-response curve. High temperature of road surface increased leachate toxicity by 66%, due to elevated concentrations of 67 identified organic compounds. UV irradiation, however, mitigated this effect, acting as antagonism. These findings underline the seasonal and spatial heterogeneity in leachate toxicity. Additionally, high temperature induced the volatilization of organic compounds within TWPs, highlighting an independent exposure pathway. The methodology developed in this study will provide foundation and standard for future research on the aquatic ecotoxicity of TWPs. Environmental ImplicationThe toxicity of leachate from ubiquitous tire wear particles (TWPs) to aquatic organisms has been confirmed in field and experimental studies. However, existing researches indirectly used TWPs quantity as sole proxy for leachate toxicity, neglecting its fluctuations over leaching duration and in situ environmental factors, potentially confounding toxic effects. Herein, this study quantifies these dynamics of leachate toxicity based on measurable biological response, aiming to establish a standard scale for further quantitative assessment of TWPs ecological risk.

ecology↗
bioRxiv2024

Unlocking Herbal Potentials: Novel Shikimate Kinase Inhibitors in the Fight Against Antibiotic Resistance

Against a backdrop of stagnant antibiotic innovation, the escalating prevalence of antibiotic-resistant pathogens forecasts a challenging future [6]. Traditionally, antibiotics, predominantly derived from fungal sources, employ a limited set of mechanisms to inhibit bacterial growth [6, 16]. Shikimate Kinase has emerged as a promising antibacterial target due to its exclusivity to bacteria and the lethality of its inhibition [4, 13, 14, 15, 28, 29, 30]. Although synthetic inhibitors have been developed, the exploration of plant-derived alternatives remains untapped. Naturally derived plant-based compounds provide a more viable option because of the high cost of creating synthetic compounds. This study examines the Goldenrod plant, reputed in Native American Ethno-medicine for its antimicrobial properties [3, 12, 17]. Employing Liquid Chromatography - Mass Spectrometry (LC-MS) and Quantitative Structure Activity Relationship (QSAR) models, the study evaluates the plants compounds for their potential as antibacterial agents. Antibacterial activity against Bacillus Subtilis was assessed using the Kirby-Bauer Disk Diffusion assay, and genetic sequencing was performed on mutants that overcame the initial inhibition zone. By comparing the parent and mutant strains, the mode of inhibition by the plant antibiotic was determined by backtracking. The study identified Shikimate Kinase as the inhibitory target of the plant-derived compounds. Molecular docking revealed a binding affinity of -8.9 kcal/mol for the most effective compound, which is statistically significant compared to Shikimate Acid, the enzymes natural substrate. Through Pymol visualization, competitive inhibition was confirmed, with the compounds binding pocket exhibiting a druggability score of 0.84, approaching the threshold of clinical drugs. This research suggests new antibiotic classes targeting the Shikimate Kinase pathway, offering an alternative approach to tackling ESKAPE pathogens and enhancing health outcomes.

microbiology↗
bioRxiv2024

Gene Expression Reactomes Across Species Do Not Correlate with Gene Structural Similarity

Mammalian animal model species for preclinical drug testing share a large number of genes with similar names and/or protein primary structures, but gene expression patterns in different tissues and in response to different drugs have not been previously systematically characterized. Here, we experimentally measure the gene expression responses (reactomes) of each gene in the mouse and rat genomes in 10 different organs to 3 different drugs. Surprisingly, we observe that gene reactomes across species generally do not correlate with structural similarity. Thus, we propose an alternative functional cross-species gene mapping approach, based on organ-specific gene expression response to drug dosing.

molecular biology↗
bioRxiv2024

Whole-Genome Sequencing of a Janthinobacterium sp. Isolated from the Patagonian Desert

Janthinobacterium is a genus of Gram-negative environmental bacteria that survive extreme conditions by forming biofilms and producing pigments. Janthinobacterium sp. LS2A, an extremophile isolated from soil in the Chilean Patagonia, contains seven known biosynthetic gene clusters, including the purple pigment violacein, which may aid in its survival in harsh environments.

genomics↗
bioRxiv2024

Tcf12 controls dynamic calvarial bone growth and motor learning in mice

Heterozygous loss-of-function mutations of TCF12 and TWIST1 can each cause craniosynostosis and neurodevelopmental delay in humans. Twist1-Tcf12 interaction plays an important role in regulating suture development. Although the molecular and cellular mechanisms underlying craniosynostosis and neurocognitive dysfunctions in Twist1+/- mice have been studied, less information on the role of Tcf12 in these defects is available. To investigate the functional mechanism of Tcf12 in regulating skull and brain development, we analyzed the skull shape of Wnt1-Cre;Mesp1-Cre;Tcf12fl/fl mice and found that, despite mild coronal synostosis, their skull shape appears to be similar to that of controls. We also found evidence of impaired motor learning ability in Tcf12 mutant mice. Furthermore, loss of Tcf12 in neural crest lineage leads to upregulated Runx2 expression in the calvarial mesenchyme and posterior expansion of the frontal bone in Wnt1-Cre;Tcf12fl/fl mice. Mechanistically, we show that Lmx1b is a direct downstream target of Tcf12 for the regulation of osteogenic differentiation in the calvarial mesenchyme during embryonic development. Importantly, overexpression of Lmx1b inhibits osteogenic differentiation in the calvarial mesenchyme of Wnt1-Cre;Tcf12fl/fl mice, indicating Tcf12s regulation of Lmx1b expression is crucial for controlling osteogenesis during calvarial bone development. Our study suggests that Tcf12 expression in the brain is crucial for motor learning. Moreover, this study establishes a new molecular mechanism underlying regulation of calvarial bone formation. Author SummaryCraniosynostosis is characterized by premature fusion of cranial sutures and associated with abnormal skull growth, delayed brain development, and often impaired brain functions. Loss-of-function mutation of TCF12 can cause coronal synostosis and neurodevelopmental delay in humans. In developing mouse sutures, Tcf12 is essential for maintaining the boundary between sutural and osteogenic cells. However, roles of Tcf12 in skull formation and brain development have not been fully investigated. In this study, we show that loss of Tcf12 leads to brain abnormalities even in the absence of coronal synostosis and that frontal bone expansion results from upregulated osteogenic differentiation in the calvarial mesenchyme in mice. Furthermore, we identify Lmx1b as a downstream target of Tcf12 for the regulation of osteogenic differentiation in the calvarial mesenchyme during frontal bone development. Our findings highlight the role of Tcf12 in the development of calvarial bones and provide new insight into molecular mechanisms for regulation of calvarial bone formation.

developmental biology↗
bioRxiv2023

Discovery of a novel MarR-type transcriptional regulator that controls cell death in Bacillus subtilis biofilms

Pulcherriminic acid (PA) is a cyclic-L-leu-L-leu di-peptide produced by Bacillus subtilis during biofilm formation. When secreted, PA strongly chelates extracellular iron and forms a reddish- brown pigment, pulcherrimin. Production of pulcherriminic acid and formation of pulcherrimin modulate iron homeostasis in B. subtilis. Pulcherriminic acid also functions as an antioxidant to protect cells from increasing oxidative stress during biofilm formation. We previously showed that PA is involved in gene regulation, differentially regulating hundreds of genes in B. subtilis. One of the strongly upregulated genes by PA is yhjH, encoding a putative MarR-type transcription repressor. In this study, we characterized the regulation of the yhjH gene by PA, by PchR, a known transcription repressor for PA biosynthesis, and by YhjH itself. We also found that high expression of yhjH triggers rapid cell lysis in B. subtilis. Results from RNA-seq suggest that YhjH differentially regulates about 180 genes, among which there is a significant number of prophage genes. Lastly, we propose that YhjH be re-named as PcdR, for "pulcherriminic acid cell death regulator".

microbiology↗
bioRxiv2023

High Frequency Longitudinal RNAseq Reveals Temporally Varying Genes and Recovery Trajectories in Rats

When living organisms are exposed to potentially toxic chemicals, they respond via changes in gene expression. Traditional differentially expressed gene analysis based on before/after blood samples does not reveal the responses temporal dynamics, and often produces false positives and negatives. Here, we performed longitudinal daily RNA sequencing on rats dosed with tetracycline, isoniazid, carbon tetrachloride, or valproate. We identified 4,302 temporally variable genes (TVGs) with statistically strong change in expression following dosing. Projecting TVG expressions into a 3-dimensional principal component (PC) space reveals consistent trajectories for recovery following dosing, and enables separation of healthy from recovering states with 91% to 99% area under the receiver operator curve. Finally, we observed that Fast Recovery vs. Slow Recovery rats exhibited distinct temporal expression patterns in the TVGs, suggesting that individual variations could be potentially captured via longitudinal RNAseq analysis.

molecular biology↗
bioRxiv2023

A Plant Flavonol Rescues a Pathogenic Mutation Associated with Kinesin in Neurons

KIF1A, a microtubule-based motor protein responsible for axonal transport, is linked to a group of neurological disorders known as KIF1A-associated neurological disorder (KAND). Current therapeutic options for KAND are limited. Here, we introduced the clinically relevant KIF1A(R11Q) variant into the C. elegans homolog UNC-104, resulting in uncoordinated animal behaviors. Through genetic suppressor screens, we identified intragenic mutations in UNC-104s motor domain that rescued synaptic vesicle localization and coordinated movement. We showed that two suppressor mutations partially recovered motor activity in vitro by counteracting the structural defect caused by R11Q at KIF1As nucleotide-binding pocket. We found that supplementation with fisetin, a plant flavonol, improved KIF1A(R11Q) worms movement and morphology. Notably, our biochemical and single-molecule assays revealed that fisetin directly restored the ATPase activity and processive movement of human KIF1A(R11Q) without affecting wild-type KIF1A. These findings suggest fisetin as a potential intervention for enhancing KIF1A(R11Q) activity and alleviating associated defects in KAND.

cell biology↗
bioRxiv2023

Multigenerational effects of tire wear particle leachate through trophic transfer from producer to primary consumer

Tire wear particle (TWP) and their leachate have been known toxic for aquatic organism due to additives released from the rubber matrix. However, it is not clear whether the ecotoxicity of TWP leachate could be transferred through algae-zooplankton food chain especially after multi generations. In this work, the effect of different concentrations TWP leachate on growth of microalgae, Chlorella pyrenoidesa, was studied. Subsequently, those algae were fed to zooplankton rotifer, Brachionus calyciflorus, which continuously lasted for ten generations to explore multigenerational accumulation of TWP leachate ecotoxicity through food-chain transfer. The results showed that the TWP leachate displayed growth inhibition for algae with evident concentration effect. For rotifer fed with those contaminated microalgae, though the first two generations showed hormesis, the ecotoxicity exhibited after 2 generations, characterized by reduction of lifespan and offspring number. The ecological effects of TWP leachate were transferred from algae to rotifer. In addition, the ecotoxicity gradually aggravated along with generation passage and exposure concentration of algae. What was even more, population passage of rotifer collapsed totally with no offspring after 5-generations feed by algae exposed to high concentration TWP leachate. Based on those, it is summarized that the ecological effects of TWP leachate indeed can be transferred from low to high trophic level in food chain, and accumulate across generations passage. The indirect non-contact exposure through food chain should be considered at the risk assessment of TWP. Single generation exposure will underestimate their ecological risk from long term.

ecology↗
bioRxiv2023

Vacuolar H+-ATPase Determines Daughter Cell Fates through Asymmetric Segregation of the Nucleosome Remodeling and Deacetylase Complex

Asymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates through epigenetic mechanisms. However, the process of partitioning different epigenetic information into daughter cells remains unclear. Here, we demonstrate that the nucleosome remodeling and deacetylase (NuRD) complex is asymmetrically segregated into the surviving daughter cell rather than the apoptotic one during ACDs in Caenorhabditis elegans. The absence of NuRD triggers apoptosis via the EGL-1-CED-9-CED-4-CED-3 pathway, while an ectopic gain of NuRD enables apoptotic daughter cells to survive. We identify the vacuolar H+-adenosine triphosphatase (V-ATPase) complex as a crucial regulator of NuRDs asymmetric segregation. V-ATPase interacts with NuRD and is asymmetrically segregated into the surviving daughter cell. Inhibition of V-ATPase disrupts cytosolic pH asymmetry and NuRD asymmetry. We suggest that asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates.

cell biology↗
bioRxiv2023

All-optical interrogation of brain-wide activity in freely swimming larval zebrafish

We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in freely swimming larval zebrafish. The system consists of three main components: a 3D tracking module, a dual color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior. HighlightsO_LIWe develop an all-optical technique that enables simultaneous whole brain imaging and optogenetic manipulation of selective brain regions in freely behaving larval zebrafish. C_LIO_LIA combination of a genetically encoded calcium indicator and a long Stokes-shift red fluorescence protein, together with the adaptive filter algorithm, enables us to reliably distinguish calcium activity from motion-induced signal contamination. C_LIO_LIRapid 3D image reconstruction and registration enables real-time targeted optogenetic stimulation of distinct brain regions in a freely swimming larval zebrafish. C_LI

neuroscience↗
bioRxiv2023

Identification of cytokine predominant immunosuppressive class and prognostic risk signatures in glioma

PurposeThe advent of immune checkpoint blockade (ICB) therapies this year has changed the way glioblastoma (GBM) is treated. Meanwhile, some patients with strong PD-L1 expression remain immune checkpoint resistant. To better understand the molecular processes that influence the immune environment, there is an urgent need to characterize the immunosuppressive tumor microenvironment and identify biomarkers to predict patient survival outcomes. Patients and methodsOur study analyzed RNA-sequencing data from 178 GBM samples. Their unique gene expression patterns in the tumor microenvironment were analyzed by an unsupervised clustering algorithm. Through these expression patterns, a panel of T-cell exhaustion signatures, immunosuppressive cells, and clinical features correlates with immunotherapy response. The presence or absence of immune status and prognostic signatures was then validated with the test dataset. Results38.2% of GBM patients showed increased expression of anti-inflammatory cytokines, significant enrichment of T cell exhaustion signals, higher proportion of immunosuppressive cells (macrophages and CD4 regulatory T cells) and nine inhibitory checkpoints (CTLA4, PDCD1, LAG3, BTLA, TIGIT, HAVCR2, IDO1, SIGLEC7, and VISTA). The immunodepleted class (IDC) was used to classify these immunocompromised individuals. Despite the high density of tumor-infiltrating lymphocytes shown by IDC, such patients have a poor prognosis. Although PD-L1 was highly expressed in IDC, it suggested that there might be ICB resistance. There are many IDC predictive signatures to discover. ConclusionPD-1 is strongly expressed in a novel immunosuppressive class of GBM, but this cluster may be resistant to ICB therapy. A comprehensive description of this drug-resistant tumor microenvironment could provide new insights into drug resistance mechanisms and improved immunotherapy techniques.

immunology↗