Biology subjects

Hayashi, T.

Publications and source records attributed to Hayashi, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Haplotype Bias Detection Using Pedigree-Based Transmission Simulation: Traces of Selection That Occurred in Apple Breeding

With the increasing ability to integrate pedigree and genomic data, it is essential to evaluate their potential to uncover valuable genetic insights that can drive the advancement of crop breeding and conservation of genetic diversity. Pedigree analysis remains a fundamental approach for investigating the inheritance of phenotypic traits, exploring evolutionary history, and understanding hybridization processes in crop plants. Among these approaches, gene drop simulations using pedigree and allele origin data enable the construction of genetic maps and provide insights into complex genetic backgrounds. In this study, we developed a new method to identify useful genetic regions associated with single-nucleotide polymorphism (SNP) markers based on gene drop simulations, focusing on 185 Japanese domestic apple cultivars. By performing 10 million gene drop simulations, we generated null distributions for each founder haplotype, which revealed SNP markers with significant frequency biases, which is a potential signal for selection. Frequency biases were identified in eight founder haplotypes that were particularly consistent with genome-wide association studies peaks associated with key fruit traits such as malic acid and fructose content. Gene Ontology enrichment analysis suggested that these SNPs are not only associated with fruit traits but may also play a role in critical biological functions, including stress tolerance and reproductive processes, highlighting their broader relevance to crop resilience. Our integrative approach, which combines founder haplotype analysis with extensive gene drop simulations, effectively detects selection pressure, provides new insights into the genetic basis of apple breeding, and identifies SNP markers with strong potential to improve breeding programs.

genetics↗

bioRxiv2025

A super-enhancer actuated by heterodimerization of a specific YAP1 isoform, YAP1-2α, with TAZ endows cancer stemness and drug resistance

The pro-oncogenic transcriptional coactivator YAP1 comprises multiple splice isoforms, including YAP1-2, which retains an intact leucine zipper by skipping exon 6. Here, we show that YAP1-2 has a markedly greater capacity to form nuclear condensates via liquid-liquid phase separation (LLPS) than other YAP1 isoforms. Mechanistically, the YAP1-2/TEAD complex interacts with the TAZ/TEAD complex through the leucine zippers on YAP1 -2 and TAZ, forming a tetrameric complex that is further assembled multivalently by BRD4 to induce LLPS. The resulting YAP1-2 /TAZ/TEAD/BRD4 complexes activate TEAD-associated super-enhancers and strongly stimulate pro-oncogenic gene expression. Cancer cells with elevated YAP1-2 display enhanced malignant traits, including sphere formation, invasion, and chemoresistance. In high-grade serous ovarian cancers (HGSOCs), higher YAP1-2 mRNA levels are associated with nuclear YAP1 biomolecular condensates and more advanced clinical stages. Our study shows that YAP1-2 drives cancer cell aggressiveness, identifying the LLPS-induced YAP1-2/TAZ/TEAD super-enhancers as a promising target for the treatment of refractory cancers.

cancer biology↗

bioRxiv2024

Large MAF Transcription Factors Reawaken Evolutionarily Dormant Fast-Glycolytic Type IIb Myofibers in Human Skeletal Muscle

Small mammals rely on type IIb myofibers, expressing the fastest myosin IIb (encoded by MYH4), for rapid muscle contraction. In contrast, larger mammals, including humans, show reduced or absent MYH4 expression and type IIb myofibers, favoring slower-contracting myofibers. The evolutionary mechanisms underlying this shift remain unclear. Here, we identify large MAF transcription factors (MAFA, MAFB, MAF) as key regulators of MYH4 expression in large mammals, including human and bovine. Overexpression of large MAFs induces MYH4 expression and enhances glycolytic capacity in human myotubes, supported by RNA-seq and metabolic flux analyses. RNA-seq of human muscle biopsies reveals a positive correlation between MAFA, MAF, and MYH4 expression, with these genes elevated in power-trained individuals. These findings reveal a conserved mechanism across mammals, showing that large MAFs can induce type IIb myofibers even in humans, with potential applications for enhancing athletic performance and addressing age-related muscle weakness associated with the loss of fast-twitch myofibers.

cell biology↗

bioRxiv2024

Novel function of Hox13 in regulating outgrowth of the newt hindlimb bud through interaction with Fgf10 and Tbx4

5Hox genes regulate pattern formation along the axes of the limb. Previously, we showed that Hoxa13/Hoxd13 double mutant newts lacked all digits of the forelimbs during development and regeneration, showing that newt Hox13 is necessary for digit formation in development and regeneration. In addition, we found another unique phenotype. A part of the Hox13 crispant newts showed hindlimb defects, in which whole or almost whole hindlimbs were lost, suggesting a novel function of Hox13 in limb development. Using germline mutants, we showed that mutation in Hox13 led to hindlimb defects. The limb buds of Hox13 crispants formed, however, did not show outgrowth. Expression of Fgf10 and Tbx4, which are involved in limb outgrowth, decreased in the hindlimb buds of Hox13 crispants. In addition, hindlimb defects were observed in both Fgf10 and Tbx4 crispant newts. Finally, Fgf10 and Tbx4 interacted with Hox13 genetically. Our results revealed a novel function of Hox13 in regulating the outgrowth of the newt hindlimb bud through interaction with Fgf10 and Tbx4.

developmental biology↗

bioRxiv2024

Distinct optimization of motor control and learning: Self-paced motor learning achieves different motor patterns from overtrained

Self-paced movement, refined through extensive training and optimization, serves as an ideal model for investigating internal objectives within the sensorimotor system without external constraints. Previous studies have demonstrated that self-paced movement is consistent within individuals but variable across individuals, emphasizing a robust and unique optimization in self-paced motor control. While motor learning is also an optimization process, it remains unclear whether the internal objectives overlap between motor control and learning, or, more specifically, whether motor patterns identified in self-paced motor control are replicated in motor learning. Given that optimality principles typically address redundancy, human behavioral experiments were designed to equate movement distances for both motor control and learning in self-paced movements and to thus compare redundant motion parameters, movement velocity and duration. We dissected participants reaching movements at their preferred pace, controlling a visual cursor to a target on a display over specified movement distances, through a detailed analysis that that accommodates nonlinear interaction and significant inter-individual baseline differences of movement velocity and duration. In self-paced motor control, participants adjusted both velocity and duration in response to changes in target distances. However, when visuomotor shift perturbations were applied to the cursor in the longitudinal direction, triggering motor learning, participants adapted their movement distance solely by modulating velocity, while leaving duration unchanged. These results suggest that distinct optimization strategies are employed in motor control and learning to resolve movement redundancy. Significance statementNatural behaviors are thought to be well-optimized. Self-paced movements--an important form of such behaviors--showing significant stability within individuals but variability across individuals. This suggests that the sensorimotor system in the central nervous system operates through a unique and robust optimization process for self-paced motor control. Self-paced motor control is further refined through motor learning. However, it remains unclear whether motor control and learning share a common objective function. Our findings demonstrate that laboratory-based motor learning does not replicate the motor patterns observed in overtrained, self-paced movements performed under natural conditions. This suggests that distinct optimization mechanisms are at play in motor control and learning, indicating that these processes are not contiguous.

neuroscience↗

bioRxiv2024

Concentration-dependent formation of intersegment interactions in viral droplets of influenza A virus infected cells

The influenza A virus genome consists of eight RNA segments, each incorporated into a virion. It has been proposed that intersegment interactions bundle these segments, and viral inclusions, which contain viral ribonucleoproteins (vRNPs) and Rab11, facilitate this process. However, the locations and mechanisms of intersegment interaction formation remain unclear. To investigate this, we identified comprehensive intersegment interactions in infected cells using customized LIGR-seq. Our results revealed that intersegment interactions in infected cells overlapped with those in the virion and were partially formed through direct RNA-RNA interactions. Additionally, we found that the formation of these interactions was delayed in cells expressing a Rab11 dominant-negative. Furthermore, artificially increasing vRNP concentrations in the nucleus, where intersegment interactions typically do not occur, triggered the formation of these interactions, which again overlapped with those in the virion. These results suggest that intersegment interactions are formed in viral inclusions where progeny vRNPs accumulate.

microbiology↗

bioRxiv2024

Charting Cortical-Layer Specific Area Boundaries Using Gibbs Ringing Attenuated T1w/T2w-FLAIR Myelin MRI

Cortical areas have traditionally been defined by their distinctive layer cyto- and/or myelo- architecture using postmortem histology. Recent studies have delineated many areas by measuring overall cortical myelin content and its spatial gradients using the T1w/T2w ratio MRI in living primates, including humans. While T1w/T2w studies of areal transitions might benefit from using the layer profile of this myelin-related contrast, a significant confound is Gibbs ringing artefact, which produces signal fluctuations resembling cortical layers. Here, we address these issues with a novel approach using cortical layer thickness-adjusted T1w/T2w-FLAIR imaging, which effectively cancels out Gibbs ringing artefacts while enhancing intra-cortical myelin contrast. Whole-brain MRI measures were mapped onto twelve equivolumetric layers, and layer-specific sharp myeloarchitectonic transitions were identified using spatial gradients resulting in a putative 182 area/subarea partition of the macaque cerebral cortex. The myelin maps exhibit notably high homology with those in humans, suggesting cortical myelin shares a similar developmental program across species. Comparison with histological Gallyas myelin stains explains over 80% of the variance in the laminar T1w/T2w-FLAIR profiles, substantiating the validity of the method. Altogether, our approach provides a novel, noninvasive means for precision mapping layer myeloarchitecture in the primate cerebral cortex, advancing the pioneering work of classical neuroanatomists.

neuroscience↗

bioRxiv2024

Shifts in neural tuning systematically alter sensorimotor learning ability

Sensorimotor learning can change the tuning of neurons in motor-related brain areas and rotate their preferred directions (PDs). These PD rotations are commonly interpreted as reflecting motor command changes; however, cortical neurons that display PD rotations also contribute to sensorimotor learning. Sensorimotor learning should, therefore, alter not only motor commands but also the tuning of neurons responsible for this learning, and thus impact subsequent learning ability. Here, we investigate this possibility with computational modeling and by directly measuring adaptive responses during sensorimotor learning in humans. Modeling shows that the PD rotations induced by sensorimotor learning, predict specific anisotropic changes in PD distributions that in turn predict a specific spatial pattern of changes in learning ability. Remarkably, experiments in humans then reveal large, systematic changes in learning ability in a spatial pattern that precisely reflects these model-predicted changes. We find that this pattern defies conventional wisdom and implements Newtons method, a learning rule where the step size is inversely proportional rather than proportional to the learning gradients amplitude, limiting overshooting in the adaptive response. Our findings indicate that PD rotation provides a mechanism whereby the motor system can simultaneously learn how to move and learn how to learn.

neuroscience↗

bioRxiv2024

Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.

microbiology↗

bioRxiv2024

Metabolic mode estimated by breathing reflects long-term motor memory

Respiration is a crucial metabolic process that converts macronutrients, carbohydrates and fats, and oxygen (O2) into energy and carbon dioxide (CO2) to support motor actions. In addition to the energy demands of movements, the brain is a significant energy consumer, accounting for approximately 20% of the bodys total energy expenditure and relying primarily on carbohydrates for neural activity and plasticity. However, it is not known whether O2-CO2 gas composition in breathing can serve as an indicator of neural activity and plasticity as they can for movement intensity. In the human reaching movement tasks, we evaluated time-constants of sensorimotor learning while recording O2-CO2 gas exchange. We computed the respiratory exchange ratio (RER), indicating which carbohydrate or fat is used preferentially, and found that the RER was unaffected by the execution and learning of reaching movements and that it was stable within individuals but varied across individuals. Interestingly, using computational modeling to identify short and long-time constants of sensorimotor learning, individual RER levels correlated with the magnitude of long-term, but not short-term memory. Furthermore, to experimentally manipulate the individual RER, we provided 200 kcal of glucose immediately before the task. Surprisingly, this simple intervention dramatically increased 24-hour retention by 21%. Together, the RER served as a remarkable proxy for long-term motor memory, and glucose intake shifted the physiological idling state for sensorimotor learning.

neuroscience↗

bioRxiv2024

A role for condensin-mediator interaction in mitotic chromosomal organization

Eukaryotic genomes are organized by condensin into 3D chromosomal architectures suitable for chromosomal segregation during mitosis. However, molecular mechanisms underlying the condensin-mediated chromosomal organization remain largely unclear. Here, we investigate the role of newly identified interaction between the Cnd1 condensin and Pmc4 mediator subunits in fission yeast, Schizosaccharomyces pombe. We develop a condensin mutation, cnd1-K658E, that impairs the condensin-mediator interaction and find that this mutation diminishes condensin-mediated chromatin domains during mitosis and causes chromosomal segregation defects. The condensin-mediator interaction is involved in recruiting condensin to highly transcribed genes and mitotically activated genes, the latter of which demarcate condensin-mediated domains. Furthermore, this study predicts that mediator-driven transcription of mitotically activated genes contributes to forming domain boundaries via phase separation. This study provides a novel insight into how genome-wide gene expression during mitosis is transformed into the functional chromosomal architecture suitable for chromosomal segregation. O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/600663v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@488ab5org.highwire.dtl.DTLVardef@8a7a73org.highwire.dtl.DTLVardef@16d416eorg.highwire.dtl.DTLVardef@1e2d3db_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG In BriefMitotic chromosomes are organized by condensin into an architecture suitable for their segregation, although molecular mechanisms underlying how condensin assembles the functional chromosomal architecture remain unclear. This study with the fission yeast model organism shows that the protein interaction between condensin and mediator is involved in chromosomal segregation by forming a mitotic chromosomal architecture. A similar mechanism involving the condensin-mediator interaction is likely conserved in human cells, implying the evolutionary conservation of this mechanism. HighlightsO_LIThe Cnd1 condensin subunit interacts with the Pmc4 mediator component in fission yeast. C_LIO_LIThe condensin-mediator interaction is required to recruit condensin to highly transcribed and mitotically activated genes. C_LIO_LIThe condensin-mediator interaction is required to form chromatin domains during mitosis. C_LIO_LIMediator participates in the boundary formation of mitotic chromatin domains. C_LI

genomics↗

bioRxiv2024

Mapping vascular network architecture in primate brain using ferumoxytol-weighted laminar MRI

Mapping the vascular organization of the brain is of great importance across various domains of basic neuroimaging research, diagnostic radiology, and neurology. However, the intricate task of precisely mapping vasculature across brain regions and cortical layers presents formidable challenges, resulting in a limited understanding of neurometabolic factors influencing the brains microvasculature. Addressing this gap, our study investigates whole-brain vascular volume using ferumoxytol-weighted laminar-resolution multi-echo gradient-echo imaging in macaque monkeys. We validate the results with published data for vascular densities and compare them with cytoarchitecture, neuron and synaptic densities. The ferumoxytol-induced change in transverse relaxation rate ({Delta}R2*), an indirect proxy measure of cerebral blood volume (CBV), was mapped onto twelve equivolumetric laminar cortical surfaces. Our findings reveal that CBV varies 3-fold across the brain, with the highest vascular volume observed in the inferior colliculus and lowest in the corpus callosum. In the cerebral cortex, CBV is notably high in early primary sensory areas and low in association areas responsible for higher cognitive functions. Classification of CBV into distinct groups unveils extensive replication of translaminar vascular network motifs, suggesting distinct computational energy supply requirements in areas with varying cytoarchitecture types. Regionally, baseline R2* and CBV exhibit positive correlations with neuron density and negative correlations with receptor densities. Adjusting image resolution based on the critical sampling frequency of penetrating cortical vessels allows us to delineate approximately 30% of the arterial-venous vessels. Collectively, these results mark significant methodological and conceptual advancements, contributing to the refinement of cerebrovascular MRI. Furthermore, our study establishes a linkage between neurometabolic factors and the vascular network architecture in the primate brain. HighlightsCortical layer vascular mapping using ferumoxytol-weighted R2* MRI Vascular volume is high in primary sensory areas and low in association areas Correlation between R2* and vascular volume with neuron and receptor densities Vascularization co-varies with densities of specific interneuron types

neuroscience↗

bioRxiv2024

Intraplacental injection of human iPSC-derived PDX1+ pancreatic progenitors prolongs Pdx1-deficient mice survival

Interspecies chimeras comprising human tissues have potential for use in disease modeling and regenerative medicine. Here, we successfully transplanted human induced pluripotent stem cell (iPSC)-derived PDX1+ pancreatic progenitor cells into Pdx1-deficient mouse embryos via intraplacental injection. The engrafted human cells predominantly localized to the duodenum, produced insulin, and extended the lifespan of Pdx1-/- mice by up to 10 days after birth. Transcriptomic analyses confirmed human pancreatic gene expression in human cells engrafted into the mouse duodenum. Our findings demonstrated the feasibility of generating interspecies chimeras with functional human pancreatic cells through in utero transplantation of lineage-committed progenitors. This approach circumvents developmental barriers while minimizing ethical concerns associated with PSCs. However, the incomplete rescue of the Pdx1-/- phenotype highlights the need for further research to enhance human cell engraftment and tissue integration. Overall, this study provides a foundation for developing human-animal chimera models for studying human development and regenerative therapies.

cell biology↗

bioRxiv2024

Different molecular recognition by three domains of the full-length GRB2 to SOS1 proline-rich motifs and EGFR phosphorylated sites

The adaptor protein human GRB2 plays crucial roles in mediating signal transduction from cell membrane receptors to RAS and its downstream proteins by recruiting SOS1. Recent studies have revealed that GRB2 also serves as a scaffold for liquid-liquid phase separation (LLPS) with SOS1 and transmembrane receptors, which is thought to regulate the magnitude of cell signalling pathways. In this study, we employed solution NMR spectroscopy to investigate the interactions of the full-length GRB2 with proline-rich motifs (PRMs) derived from ten potential GRB2-binding sites in SOS1, as well as a peptide from a phosphorylation site of EGFR. Our findings indicate that the binding affinity of the two SH3 domains of GRB2 for PRMs differs by a factor of ten to twenty, with the N-terminal SH3 domain (NSH3) exhibiting a markedly higher affinity. The interactions of PRMs with the SH3 domains affected not only the regions surrounding the PRM binding sites on the SH3 domains but also the linker area connecting the three domains and parts of the SH2 domain. Analysis of the interaction between the phosphorylated EGFR binding site and the SH2 domain revealed chemical shift perturbations in regions distal from the known binding site of SH2. Moreover, we observed that the inter-domain interactions of the two SH3 domains with the SH2 domain of GRB2 are asymmetric. These findings suggest that the local binding of PRMs and phosphorylated EGFR to GRB2 impacts the overall structure of the GRB2 molecule, including domain orientation and dimerisation, which may contribute to LLPS formation.

biophysics↗

bioRxiv2024

Computational Mechanisms of Neuroimaging Biomarkers Uncovered by Multicenter Resting-State fMRI Connectivity Variation Profile

Resting-state functional connectivity (rsFC) is increasingly used to develop biomarkers for psychiatric disorders. Despite progress, development of the reliable and practical FC biomarker remains an unmet goal, particularly one that is clinically predictive at the individual level with generalizability, robustness, and accuracy. In this study, we propose a new approach to profile each connectivity from diverse perspective, encompassing not only disorder-related differences but also disorder-unrelated variations attributed to individual difference, within-subject across-runs, imaging protocol, and scanner factors. By leveraging over 1500 runs of 10-minute resting-state data from 84 traveling-subjects across 29 sites and 900 participants of the case-control study with three psychiatric disorders, the disorder-related and disorder-unrelated FC variations were estimated for each individual FC. Using the FC profile information, we evaluated the effects of the disorder-related and disorder-unrelated variations on the output of the multi-connectivity biomarker trained with ensemble sparse classifiers and generalizable to the multicenter data. Our analysis revealed hierarchical variations in individual functional connectivity, ranging from within-subject across-run variations, individual differences, disease effects, inter-scanner discrepancies, and protocol differences, which were drastically inverted by the sparse machine-learning algorithm. We found this inversion mainly attributed to suppression of both individual difference and within-subject across-runs variations relative to the disorder-related difference by weighted-averaging of the selected FCs and ensemble computing. This comprehensive approach will provide an analytical tool to delineate future directions for developing reliable individual-level biomarkers.

neuroscience↗

bioRxiv2024

Effect of phage variation on Shiga toxin 2 (Stx2) production and the virulence of Stx-producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) causes serious gastrointestinal illness, including hemorrhagic colitis and hemolytic uremic syndrome. Although all known Stxs (Stx1 and Stx2) are encoded by bacteriophages (Stx phages), the production of Stx2 is known to be a major risk factor for severe STEC infections. The production of Stx2, but not Stx1, is tightly coupled with the induction of Stx phages, and Stx2 production levels vary between STEC strains, even within the same serotype. Here, we analyzed the genomic diversity of all Stx phages in 71 strains representing the entire O145:H28 lineage, one of the major STECs. Our analysis revealed the highly dynamic nature of the Stx phages in O145:H28, including the independent acquisition of similar Stx phages by different sublineages and the frequent changes in Stx phages in the same sublineages due to the gain and loss of Stx phages. Analyses of Stx2 production levels in O145:H28 strains and K-12 lysogens of Stx2 phages of specific groups and types, which were defined by their early region sequences and CI repressors, respectively, revealed that short-tailed Stx2a phages (S-Stx2a phages) confer significantly greater Stx2 production to host strains than long-tailed Stx2a phages (L-Stx2a phages). However, L-Stx2a phages that encode a specific type of CI repressor promoted Stx2 production, comparable to the level of production among S-Stx2a phages, as well as promoted virulence to host strains, exceeding the level among other L-Stx2a phages. We also showed a clear link between the phage induction efficiency, which was primarily determined by the early region of each phage, and the level of Stx2 production by host strains. These results provide important insights into the diversification and dynamism of Stx phages and the relationship between the variations in Stx2 phages and the amount of Stx2 production by their host strains. Author summaryShiga toxin (Stx)-producing Escherichia coli (STEC) is an important human intestinal pathogen that causes severe illnesses. These bacteria produce Stx1, Stx2 or both toxins, but the production of Stx2 is an important measure of the virulence of STEC strains. While both types of Stx are encoded by bacteriophages (Stx phages), Stx2 production is tightly coupled with phage induction, and variations in Stx2 phages have been associated with variations in Stx2 production levels by their host O157:H7 STEC strains. However, in non-O157 STEC strains, the variation in Stx phages and its association with host strain production of Stx2 have not yet been fully analyzed. This systematic study of Stx phages in O145:H28 STEC reveals not only the marked genomic diversity and dynamism of Stx phages in this STEC lineage but also that short-tailed Stx2 phages and a specific group of long-tailed Stx2 phages induce high levels of Stx2 production by host strains, and this increased production is linked to the efficient induction of phages.

microbiology↗

bioRxiv2024

Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation

Primordial follicle activation (PFA) is a pivotal event in female reproductive biology, coordinating the transition from quiescent to growing follicles. This study employed comprehensive single-cell RNA sequencing to gain insights into the detailed regulatory mechanisms governing the synchronized dormancy and activation between granulosa cells (GCs) and oocytes with the progression of the PFA process. Wntless (Wls) conditional knockout (cKO) mice served as a unique model, suppressing the transition from pre-GCs to GCs, and disrupting somatic cell-derived WNT signaling in the ovary. Our data revealed immediate transcriptomic changes in GCs post-PFA in Wls cKO mice, leading to a divergent trajectory, while oocytes exhibited modest transcriptomic alterations. Subpopulation analysis identified the molecular pathways affected by WNT signaling on GC maturation, along with specific gene signatures linked to dormant and activated oocytes. Despite minimal evidence of continuous up-regulation of dormancy-related genes in oocytes, the loss of WNT signaling in (pre-)GCs impacted gene expression in oocytes even before PFA, subsequently influencing them globally. The infertility observed in Wls cKO mice was attributed to compromised GC-oocyte molecular crosstalk and the microenvironment for oocytes. Our study highlights the pivotal role of the WNT-signaling pathway and its molecular signature, emphasizing the importance of intercellular crosstalk between (pre-)GCs and oocytes in orchestrating folliculogenesis. Author summaryIn mammalian ovaries, primordial follicles protect dormant oocytes from wasteful consumption. We explored the complex molecular dynamics of the critical process of primordial follicle activation (PFA) that underlies female reproductive health, with a focus on the role of WNT signaling. By utilizing a unique mouse model with disrupted WNT signaling, our study reveals novel insights into the regulatory dynamics of granulosa cells (GCs) and oocytes during PFA. Single-cell transcriptome profiling uncovered distinct cell populations and highlighted the impact of WNT signaling on ovarian cell types. This study reveals distinct transcriptomic changes in GCs post-PFA, which affects their differentiation trajectories and highlights the critical role of WNT signaling in establishing GC function. We further examined the consequences of disrupted microenvironments on oocytes and GC-oocyte interactions, which elucidated altered oocyte subclusters and potential links to infertility. These findings provide a foundation for understanding the connections between WNT signaling and ovarian function. Our comprehensive analysis contributes valuable knowledge to reproductive biology, emphasizing the clinical relevance of WNT signaling in female fertility.

bioinformatics↗

bioRxiv2023

Dual-specificity phosphatases 13 and 27 as key switches in muscle stem cell transition from proliferation to differentiation

Muscle regeneration depends on muscle stem cell (MuSC) activity. Myogenic regulatory factors, including myoblast determination protein 1 (MyoD), regulate the fate transition of MuSCs. However, the direct target of MYOD in the process is not completely clear. Using previously established MyoD knock-in (MyoD-KI) mice, we revealed that MyoD targets dual-specificity phosphatase (Dusp) 13 and Dusp27. In Dusp13:Dusp27 double knock-out (DKO) mice, the ability for muscle regeneration after injury was reduced. Moreover, single-cell RNA sequencing of MyoD-high expressing MuSCs from MyoD-KI mice revealed that Dusp13 and Dusp27 are expressed only in specific populations within MyoD-high MuSCs, which also express Myogenin. Overexpressing Dusp13 in MuSCs causes premature muscle differentiation. Thus, we propose a model where DUSP13 and DUSP27 contribute to the fate transition of MuSCs from proliferation to differentiation during myogenesis. Significance StatementMYOD protein is not expressed in quiescent muscle stem cells but accumulates rapidly following muscle injury, leading to the proliferation of myogenic progenitors for differentiation. However, the direct targets of MYOD, aside from myogenin, which play roles in myogenic differentiation remain incompletely understood. Using previously established MyoD knock-in mice and single-cell RNA sequencing, we discovered that Dusp13 and Dusp27 are potential target genes of MYOD that promote myogenesis during muscle regeneration in adult mice.

cell biology↗