Biology subjects

Li, C.

Publications and source records attributed to Li, C..

At least 343 records · Page 19Linked to original sources

bioRxiv2025

Transgenerational maintenance of H3K27me3 heterochromatin is balanced by chromodomain proteins in Caenorhabditis elegans

The ability to replicate and pass information to descendants is a fundamental requirement for life. In addition to the DNA-based genetic information, modifications of the DNA or DNA-associated proteins can create patterns of heritable gene regulation. Such epigenetic inheritance allows for adaptation without mutation, but its limits and regulation are incompletely understood. Here we developed a C. elegans system to study the transgenerational epigenetic inheritance of H3K27me3, a conserved histone posttranslational modification associated with gene repression. We find that induced alterations of the genome-wide H3K27me3 landscape and the associated fertility defects persist for many generations in genetically wildtype descendants under selective pressure. We uncover that the inheritance of the altered H3K27me3 landscape is regulated by two chromodomain proteins with antagonizing functions, and provide mechanistic insight into how this molecular memory is initiated and maintained. Our results demonstrate that epigenetic inheritance can act as a mutation-independent, heritable mechanism of adaptation. In BriefOzdemir et al. demonstrate that an altered genomic distribution of the histone modification H3K27me3 can be epigenetically inherited across many generations through the activity of HERI-1/SET-32/MES-4, which is antagonized by CEC-6/PRC2 in C. elegans. HighlightsO_LIAltered H3K27me3 landscapes can be inherited for at least 15 generations in C. elegans. C_LIO_LIThe chromodomain proteins CEC-6 and HERI-1 have opposite roles in antagonizing or promoting the maintenance of the altered H3K27me3 landscape. C_LIO_LIH3K23me3 and H3K36me3 replace H3K27me3 to promote the intergenerational and transgenerational inheritance of the altered epigenome. C_LI

genetics↗

bioRxiv2025

Thermal and mechanical modalities converge in the noxious range

SummaryThere are competing theories on how nociceptive input is encoded by sensory fibers. That sensory modalities are exclusively conveyed by distinct populations of fibers is supported by ablation studies, indicating that TRPV1+and MrgprD+afferents selectively encode for heat and mechanical input, respectively. However, interpreting ablation results can be clouded by compensatory plasticity. Furthermore, a population-level parametric analysis of afferent response profiles to natural stimuliin vivois still scarce. Using functional imagingin vivoin mice, we found that most TRPV1+neurons responded to noxious heat, but not cooling. While none of them responded to innocuous mechanical input, about half were also sensitive to noxious mechanical stimuli. In contrast, 80% of MrgprD+neurons responded to noxious mechanical stimuli. Yet, 70% were also sensitive to noxious thermal stimuli. Of innocuous mechanosensitive MrgprD+neurons, <15% responded to innocuous warming and none to innocuous cooling. Polymodality in the innocuous thermal and mechanical range also occurred in <10% of all primary afferents. Acute silencing of TRPV1+or MrgprD+afferents inhibited both thermal and mechanical nociception. In contrast, ablation did not reproduce a combined loss of sensitivity, which appeared to be due to compensatory central disinhibition. Our findings reveal that modality separation dominates in the innocuous regime, while polymodality predominates in the noxious range.

neuroscience↗

bioRxiv2025

AarMIXTAs: key factors of T-shaped non-glandular trichome development in Artemisia argyi

Trichomes are necessary for stress resistance and metabolite synthesis in plant. T-shaped non-glandular trichomes (TSTs) as the main component of moxa floss, which are the specific characteristics of A. argyi. Here, we observed that TSTs were at an extremely high density on the lower surfaces in A. argyi leaves. The key transcription factors (TFs) involved in regulation of TSTs development of A. argyi were identified through RNA sequencing of TSTs and non-TSTs. The core regulatory genes, AarMIXTAs showed allelic amplification and functional differentiation compared with A. annua, might contribute development of TSTs. The overexpression of AarMIXTA1.2 significantly increased the density of TSTs in transgenic Arabidopsis and may regulate trichome development by regulating the downstream genes, which played an important positively regulatory role in the development of TSTs. This study provides a good reference for the molecular mechanisms related to the development of TSTs and a theoretical basis for the high-yield moxa floss cultivation of A. argyi.

plant biology↗

bioRxiv2025

Exogenous melatonin mitigates drought stress by promoting the living cortical area of roots in cotton

The root cortex plays a critical role in water absorption, influencing root function and metabolic activity. However, the effects of melatonin on root cortical cells and its role in drought resistance remain unclear. This study examines the impact of exogenous melatonin on the root cortex of cotton under drought stress, focusing on its relationship with water uptake and drought resilience. Cotton plants were treated with 8% PEG6000 for drought stress and 100 {micro}M melatonin by foliar application. The results demonstrated that melatonin application significantly increased the living cortical area of roots under drought stress, with notable increases of 26.34% and 59.00% at distances of 1 cm and 13 cm from the root tip, respectively. Melatonin also enhanced root cortical thickness, promoted osmotic regulation, increased respiratory enzyme activity, and improved water and nutrient uptake. Furthermore, melatonin application promoted both root and shoot growth. Notably, the living cortical area positively correlated with osmotic substance accumulation, root respiration, and absorption capacity under drought conditions. In conclusion, exogenous melatonin alleviates drought-induced damage by enhancing the living cortical area, optimizing osmotic regulation, and improving root absorption, thus promoting cotton growth and drought resistance. These findings highlight melatonin as a promising regulator for enhancing drought resistance. HighlightExogenous melatonin increases root cortical integrity of cotton roots under drought stress, improves the absorption of water and nutrients, promotes the growth of cotton, and enhances its drought resistance.

physiology↗

bioRxiv2025

Dendritic Architecture Enables de Novo Computation of Salient Motion in the Superior Colliculus

Dendritic architecture plays a crucial role in shaping how neurons extract behaviorally relevant information from sensory inputs. Wide-field neurons in the superior colliculus integrate visual information from the retina to encode cues critical for visually guided orienting behaviors. However, the principles governing how these neurons filter their inputs to generate appropriate responses remain unclear. Using viral tracing, two-photon calcium imaging, and computational modeling, we show that wide-field neurons receive functionally diverse inputs from twelve retinal ganglion cell types, forming a layered, type-specific organization along their dendrites. This structured arrangement allows wide-field neurons to multiplex salient motion cues, selectively amplifying movement and suppressing static features. Computational models reveal that the spatial organization of dendrites and inputs enables the selective extraction of behaviorally relevant stimuli, including de novo computations. Our findings underscore the critical role of dendritic architecture in shaping sensory processing and neural circuit function.

neuroscience↗

bioRxiv2025

Predicting the Regenerative Potential of Retinal Ganglion Cells Based on Developmental Growth Trajectories

Retinal ganglion cells in the mammalian central nervous system fail to regenerate following injury, with the capacity to survive and regrow varying by cell type. This variability may be linked to differences in developmental programs that overlap with the genetic pathways that mediate regeneration. To explore this correlation, we compared the structural changes in mouse retinal ganglion cells during development with those occurring after axonal injury. The dendritic trees of over 1,000 ganglion cells were reconstructed at different developmental stages, revealing that each cell type follows a distinct timeline. ON-sustained (sON) cells reach maturity by P14, whereas ON-transient (tON) cells achieve their maximum dendritic size by P10. Modeling of the dendritic changes indicate that while sON and tON follow similar growth programs the onset of growth was later in sON. After optic nerve crush, the remodeling of dendritic architecture differed between the two cell-types. sON cells exhibited rapid dendritic shrinkage, while tON cells shrank more gradually with changes in branching features. Following injury, sON cells reverted to an earlier developmental state than tON cells. In addition, after co-deletion of PTEN and SOC3, neurons appeared to regress further back in developmental time. Our results provide evidence that a ganglion cells resilience to injury and regenerative potential is predicted by its maturation timeline. Understanding these intrinsic differences could inform targeted neuroprotective interventions.

neuroscience↗

bioRxiv2025

Functional connectivity in the social perception pathway at birth is linked with attention to faces at 4 months

BackgroundProcessing faces and speech is supported by the right-lateralized social visual perception pathway (social pathway) involving medial temporal/visual 5 area (MT/V5) and superior temporal sulcus (STS). Little is known about development of the social pathway and its links with later social outcomes. We examined intrinsic functional connectivity (iFC) in the right social pathway in neurotypical neonates, compared it with iFC in the left social and bilateral dorsal attention pathways, and interrogated prospective links between iFC and social attention in neurodiverse neonates. MethodsiFC in the social and dorsal pathways was measured in 517 full-term neonates from the developing Human Connectome Project (dHCP) and 73 full-term Yale neonates [Mage=41.5 weeks (SD=1.9)]. Social attention was assessed in 36 Yale neonates at Mage=4.2 months (SD=0.4) months. ResultsIn the dHCP sample, the iFC indices were positive in all the pathways (all p-values < 0.001) and did not vary by sex [all p>0.275], but the iFC in the right-lateralized social pathway was higher than in the remaining pathways [all p<0.001] and was positively associated with age at scan [r(517)=0.251, p<0.011]. In the prospective neurodiverse Yale sample, the iFC in the right social pathway was positively associated with social attention at 4 months [p=0.007], and greater social attention at 4 months predicted better social functioning in the second year [p=0.010]. ConclusionsThe early development of intrinsic functional connectivity in the right social perception pathway represents an area of interest for identifying neural mechanisms underlying emergence of atypical social attention associated with autism.

neuroscience↗

bioRxiv2025

A monophyletic origin of domesticated barley

The origin of domesticated barley has been debated extensively over the past century. Early botanical and comparative morphological research and recent genetic research supported a polyphyletic origin. A monophyletic origin was proposed after the discovery that a single genetic locus controls the presence of hull-less grains in all domesticated barley. Interpreting the origin of domesticated barley is further complicated by the archaeological record showing that the first domesticates had two rows of grain on the inflorescence, as does its wild progenitor. However, these two-rowed types effectively disappeared from the record for thousands of years, and they were replaced by derived six-rowed types that dominated barleys cultivation history and only reappeared in the record around one thousand years ago. Here, we used two independent datasets with large sample sizes and genome-wide genetic markers to re-evaluate barley cultivation history. We unequivocally demonstrate that modern domesticated barley has a monophyletic origin. Phylogenetic reconstruction and examination of current archaeological records suggests that the west Fertile Crescent was most likely where barley was first domesticated. Modern two-rowed types were likely derived from six-rowed domesticated types not earlier than 3,500 years ago in modern Turkiye and Iran. We conclude that the two distinct non-brittle rachis haplotypes, coinciding with distinct row types in cultivated barley, are likely the results of two chronological events along the same evolutionary line. Our results provide a reconcilable framework for explaining genetic and phytogeographic patterns and pave the way for a consensus on the origin of barley domestication.

evolutionary biology↗

bioRxiv2025

Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

Wheat is important for global food security and understanding the molecular mechanisms driving spike and spikelet development can inform the development of more productive varieties. In this study, we integrated single-molecule fluorescence in situ hybridization (smFISH) and single-cell RNA sequencing (scRNA-seq) to generate an atlas of cell clusters and expression domains during the early stages of wheat spike development. We characterized spatiotemporal expression of 99 genes by smFISH in 48,225 cells at the early transition, late double ridge, and floret primordia stages. These cells were grouped into 21 different expression domains, including four in the basal region of the developing spikelets and three different meristematic regions, which were consistent across spikelets and sections. Using induced mutants, we revealed functional roles associated with the specific expression patterns of LFY in intercalary meristems, SPL14 in inflorescence meristems, and FZP in glume axillae. Complementary scRNA-seq profiling of 26,009 cells from W2.5 and W3.5 stages identified 23 distinct cell clusters. We used the scRNA-seq information to impute the expression of 74,464 genes into the spatially anchored smFISH-labelled cells and generated a public website to visualize them. We used experimental and imputed expression profiles, together with co-expression studies and correlation matrices, to annotate the scRNA-seq clusters. From co-expression analyses, we uncovered genes associated with boundary genes TCP24 and FZP, as well as the meristematic genes AGL6 and ULT1. The smFISH and scRNA-seq studies provided complementary tools for dissecting gene networks that regulate spike development and identifying new co-expressed genes for functional characterization.

plant biology↗

bioRxiv2025

Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders

Most causal variants for neuropsychiatric disorders (NPD) remain unknown. A major hurdle is that disease variants may act in specific contexts, such as during neuronal activation, which is difficult to study in vivo at the population level. We profiled single-nucleus neuron-activation multiomics in human induced pluripotent stem cell (iPSC)-derived neurons from 100 donors, revealing the NPD-relevant transcriptomic/epigenomic landscape of neuronal activation. We identified abundant genetic variants associated with activity-dependent gene expression (eQTL) and chromatin accessibility (caQTL), the latter explaining larger proportions of NPD heritability. Integrating multiomic data with genome-wide association studies (GWAS) further revealed NPD risk variants and genes with effects detected only upon stimulation, such as activity-dependent cholesterol metabolism. Our work highlights the power of cell stimulation to reveal context-specific "hidden" genetic effects.

neuroscience↗

bioRxiv2025

Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.

neuroscience↗

bioRxiv2025

Single-Cell RNA Sequencing Reveals Hemocyte Heterogeneity, Differentiation Trajectories, and Viral Tropism in Shrimp (Macrobrachium rosenbergii) Infected with Decapod Iridescent Virus 1

Decapod Iridescent Virus 1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture. Hemocytes, the primary immune cells in shrimp, play crucial roles in host defense, yet their transcriptional heterogeneity and differentiation dynamics under viral infection remain poorly understood. Here, we characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection at single-cell resolution. We identified 12 distinct hemocyte clusters with unique molecular signatures. DIV1 infection induced significant shifts in hemocyte composition, with clusters 0, 5, 6, and 8 expanding, while clusters 9 and 10 exhibited resistance. Clusters 0, 5, and 8 were highly susceptible, showing elevated viral gene expression. Pseudo-time analysis revealed that DIV1 accelerates hemocyte differentiation, driving prohemocytes and semi-granulocytes toward terminally differentiated granulocytes and hyalinocytes, particularly the immune-active HC4 subpopulation. Functional enrichment analysis showed that susceptible hemocytes were associated with viral processes, oxidative stress, and phagocytosis, while resistant clusters exhibited distinct immune signatures. Furthermore, knockdown experiments confirmed the antiviral roles of PPO2, RAB11B, LAMP1, and Dorsal, as their silencing led to increased viral loads, higher MCP protein levels, and reduced shrimp survival. Taken together, our study provides the first single-cell resolution atlas of shrimp hemocytes under DIV1 infection, revealing their transcriptional heterogeneity, differentiation trajectories, and immune responses. These findings offer novel insights into shrimp antiviral immunity and lay the foundation for disease-resistant breeding and immunostimulatory strategies in aquaculture. ImportancesDecapod Iridescent Virus 1 (DIV1) is a highly pathogenic virus threatening crustacean aquaculture, causing severe economic losses. Hemocytes, the primary immune cells in shrimp, play crucial roles in antiviral defense, yet their diversity, differentiation, and responses to viral infection remain poorly understood. In this study, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively characterize hemocyte subpopulations in Macrobrachium rosenbergii before and after DIV1 infection. We identified 12 transcriptionally distinct hemocyte clusters and revealed significant changes in hemocyte composition following infection. Notably, we discovered that specific clusters (0, 5 and 8) were highly susceptible to DIV1, while others (9 and 10) exhibited resistance. Additionally, we reconstructed hemocyte differentiation trajectories and found that DIV1 infection drives hematopoiesis, accelerating the transition of progenitor cells into terminally differentiated immune-active hemocytes. Functional analysis highlighted key antiviral effectors, including PPO2, RAB11B, LAMP1, and Dorsal, which were significantly upregulated in response to infection. These findings provide novel insights into shrimp antiviral immunity and viral pathogenesis, offering potential targets for disease-resistant breeding and immunostimulatory interventions.

immunology↗

bioRxiv2025

From Archaea to the atmosphere: remotely sensing Arctic methane

Global atmospheric methane concentrations are rapidly rising and becoming isotopically more depleted, implying an unresolved microbial contribution. Rising Arctic temperatures are variably altering soil methane cycling, causing consequential uncertainty in the atmospheric methane budget. We demonstrated in an Arctic wetland that below-ground microbiota and methane-cycling features parallelled above-ground plant communities. To upscale emissions, we applied machine learning to remote sensing data to identify habitats, which were assigned average emissions. To upscale dynamically, we incorporated climate data, remotely-sensed water table variation, and habitat classes into a temporally-resolved biogeochemical model, to predict methane flux and isotope dynamics. This accurately estimated more depleted 13C-methane than previously used for Arctic habitats in global source partitioning. Remote-sensing of these rapidly changing inaccessible landscapes can thus help constrain the role of the Arctic in ongoing changes in global methane emissions.

microbiology↗

bioRxiv2025

Phosphoproteomics Uncovers Tumor Heterogeneity and Therapeutic Opportunities in Early-Stage Hepatocellular Carcinoma

Mechanisms driving progression and metastasis in early-stage hepatocellular carcinoma (HCC) remain poorly clarified. Although phosphoproteomics has been applied to broader HCC cohorts, the heterogeneity of phosphorylation signaling in early-stage HCC remains unexplored. Here, we conducted integrated phosphoproteomic and proteomic analysis on early-stage HCC tumors and paired non-tumor tissues. By comparing tumor and non-tumor tissues, we identified markedly reduced phosphorylation of EGFR-mediated canonical ERK/MAPK signaling, alongside elevated atypical MAPK signaling in HCC. To further explore the signaling heterogeneity within tumors, we applied nonnegative matrix factorization (NMF) and consensus-clustering, and identified three distinct phosphoproteomic subtypes with unique phosphorylation signatures and clinical characteristics. Interrogating the most malignant subtype, we found markedly high abundance of phosphorylation of mRNA splicing regulators, and an enrichment of epithelial-mesenchymal transition (EMT) pathways in the proteome, with phosphorylation of the splicing factor SRSF3 emerging as a critical feature. Mechanistically, we show that SRSF3 hyperphosphorylation, driven by SRPK1/CLKs and potential PP1 phosphatase suppression, promotes metastasis and proliferation. Critically, SRPK1/CLKs inhibitors effectively suppressed SRSF3 hyperphosphorylation-mediated migration and invasion of HCC cells. Our study uncovers a new dimension of signaling-driven tumor heterogeneity in early-stage HCC and identifies the SRPK1/CLKs-SRSF3 hyperphosphorylation axis as a key metastatic driver, suggesting a potential therapeutic target for early intervention in HCC.

cancer biology↗

bioRxiv2025

Lactate dehydrogenase is the Achilles' heel of Lyme disease bacterium Borreliella burgdorferi

As a zoonotic pathogen, the Lyme disease bacterium Borreliella burgdorferi has evolved unique metabolic pathways, some of which are specific and essential for its survival and thus present as ideal targets for developing new therapeutics. B. burgdorferi dispenses with the use of thiamin as a cofactor and relies on lactate dehydrogenase (BbLDH) to convert pyruvate to lactate for balancing NADH/NAD+ ratios. This report first demonstrates that BbLDH is a canonical LDH with some unique biochemical and structural features. A loss-of-function study then reveals that BbLDH is essential for B. burgdorferi survival and infectivity, highlighting its therapeutic potential. Drug screening identifies four previously unknown LDH inhibitors with minimal cytotoxicity, two of which inhibit B. burgdorferi growth. This study provides mechanistic insights into the function of BbLDH in the pathophysiology of B. burgdorferi and lays the groundwork for developing genus-specific metabolic inhibitors against B. burgdorferi and potentially other tick-borne pathogens as well.

microbiology↗

bioRxiv2025

Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D

Extrachromosomal DNAs (ecDNAs) are large, acentric, circular DNA molecules that occur pervasively across many human cancers. EcDNA can drive tumor formation and evolution, contribute to drug resistance, and associate with poor patient survival outcomes. Beyond mediating high copy numbers, the circular topology and dynamic conformational changes of ecDNA disrupt topological domains and rewire regulatory networks, thereby conferring an important role in the transcriptional regulation of oncogenes. Here, we develop ec3D, a computational method for reconstructing the three-dimensional structures of ecDNA and analyzing significant interactions from high-throughput chromatin capture (Hi-C) data. Given a candidate ecDNA sequence and the corresponding whole-genome Hi-C as input, ec3D reconstructs the spatial structure of ecDNA by maximizing the Poisson likelihood of observed interactions. Ec3Ds performance was validated using both simulated ecDNA structures with varying conformations and Hi-C data from previously-characterized cancer cell lines. Our reconstructions reveal that ecDNAs occupy spherical configurations and mediate unique long-range interactions involved in gene regulation. Through algorithmic innovations, ec3D can resolve complex ecDNA structures with duplicated genomic segments, identify multi-way interactions, and distinguish between interactions arising from direct spatial proximity and secondary interactions resulting from alternative folding patterns or intermolecular (trans) contacts of ecDNA molecules. Our findings provide insights into how the spatial organization of ecDNA may influence gene regulation and contribute to increased oncogene expression. Code availabilityhttps://github.com/AmpliconSuite/ec3D

cancer biology↗

bioRxiv2025

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

Genes involved in the regulation of chromatin structure are frequently disrupted in cancer, contributing to an aberrant transcriptome and phenotypic plasticity. Yet, therapeutics targeting mutant forms of chromatin-modifying enzymes have yielded only modest clinical utility, underscoring the difficulty of targeting the epigenomic underpinnings of aberrant gene regulatory networks. Here, we sought to identify novel epigenetic vulnerabilities in diffuse large B-cell lymphoma (DLBCL). Through phenotypic screens and biochemical analysis, we demonstrated that inhibition of the H3K9 demethylases KDM4A and KDM4C elicits potent, subtype-agnostic cytotoxicity by antagonizing transcriptional networks associated with B-cell identity and epigenetically rewiring heterochromatin. KDM4 demethylases associated with the KRAB zinc finger ZNF587, and their enzymatic inhibition led to DNA replication stress and DNA damage-induced cGAS-STING activation. Broad surveys of transcriptional data from patients also revealed KDM4 family dysregulation in several other cancer types. To explore this potential therapeutic avenue, we performed high-throughput small molecule screens with H3K9me3 nucleosome substrates and identified novel KDM4 demethylase inhibitors. AI-guided protein-ligand binding predictions suggested diverse modes of action for various small molecule hits. Our findings underscore the relevance of targeting fundamental transcriptional and epigenetic mechanisms for anti-cancer therapy. HIGHLIGHTSO_LIPhenotypic screens identified JIB-04 as a potent anti-cancer agent for multiple subtypes of diffuse large B-cell lymphoma C_LIO_LIJIB-04 binds and inhibits KDM4 demethylases resulting in epigenomic rewiring of heterochromatin C_LIO_LIKDM4 demethylases cooperate with KRAB zinc fingers to limit DNA replication stress, and KDM4 inhibition instigates DNA-damage and cGAS-STING activation in several human cancers C_LIO_LIHigh-throughput small molecule screens with semi-synthetic nucleosome substrates and AI-guided molecular docking simulations identify novel KDM4 inhibitors C_LI

genomics↗

bioRxiv2025

A kinetics-based model of hematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells

Residing at the top of the hematopoietic hierarchy, long-term hematopoietic stem cells (HSCs) are capable of self-renewal and sustained blood cell regeneration. Over the past decades, single-cell and clonal analyses have revealed substantial functional and molecular heterogeneity within this compartment, challenging the notion that self-renewal is inherently tied to balanced, multi-lineage blood production. However, a cohesive model that explains the relationships among these diverse HSC states remains elusive. Here, we combined single-cell transplantations of over 1,000 highly purified murine long-term HSCs with in-depth phenotyping of their clonal progeny to achieve a detailed, time-resolved understanding of heterogeneous reconstitution outcomes. We identified reconstitution kinetics as an overall unifying metric of HSC functional potency, with the most potent HSCs displaying the greatest delay in hematopoietic reconstitution. Importantly, a progressive acceleration in reconstitution kinetics was also associated with a gradual shift in mature cell production from platelet and erythro-myeloid bias to balanced, and eventually lymphoid bias. Serial single-cell transplantations of HSCs revealed a unidirectional acceleration in reconstitution kinetics accompanied by a gradual decline in functional potency of daughter HSCs, aligning diverse phenotypes along a linear hierarchical trajectory. Mathematical modeling, together with experimental modulation of lineage-biased blood production, demonstrated that apparent lineage biases actually arise from cell-extrinsic feedback regulation and clonal competition between slow- and fast-engrafting clones to occupy the limited compartment sizes of mature lineages. Our study reconciles multiple layers of HSC heterogeneity into a unifying framework, prompting a reevaluation of the meaning of lineage biases in both normal and diseased hematopoiesis, with broad implications for other regenerating tissues during development, homeostasis, and repair.

cell biology↗