Biology subjects

Gao, Y.

Publications and source records attributed to Gao, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Molecular architecture of OXGR1 reveals evolutionary conserved mechanisms for metabolite surveillance

The ability of cells to sense and respond to metabolic signals is fundamental to life, yet the molecular mechanisms underlying metabolite surveillance remain incompletely understood. Here, we elucidate the structural basis of metabolite recognition by OXGR1, a GPCR that monitors key intermediates in the tricarboxylic acid cycle (TCA). Using cryo-electron microscopy, we determined four cryo-EM structures of OXGR1 bound to -ketoglutarate (AKG), itaconate (ITA), and structural related succinate (SUC) and maleate (MA). These structures reveal a positively charged binding pocket and an extensive hydrogen-bond network critical for OXGR1 recognizing dicarboxylic acids. In addition, we identify a distinct arrangement of hydrophobic residues that modulates ligand potency and selectivity. Mutational analysis and molecular dynamics simulations further demonstrate that non-canonical micro-switch motifs, including FRY and NLxxY, are essential for ligand recognition and receptor activation. Comparative structural and evolutionary analyses indicate that these mechanisms are conserved across species, underscoring the critical role of OXGR1 in maintaining metabolic homeostasis. Together, our findings provide a mechanistic framework for metabolite sensing via OXGR1 and suggest potential strategies for therapeutic modulation of metabolic and inflammatory diseases.

molecular biology↗

bioRxiv2025

Class A PBPs reinforce the septal cell wall following initial synthesis by SEDS-bPBP pairs during bacterial cytokinesis

Bacterial cytokinesis requires the coordinated action of septal peptidoglycan (PG) synthases to ensure efficient and accurate septum formation. Two major types of synthases contribute: SEDS-bPBP and bifunctional class A PBPs (aPBPs). How their activities are organized in space and time has remained unclear. Using Deinococcus radiodurans, which often contains both constricting and closed septa in the same cell, we show that septal PG synthesis proceeds through distinct steps at different regions. Primary synthesis at the leading edge by SEDS-bPBP pairs drives constriction, whereas aPBPs act later at the lagging edge and in closed septa to thicken the wall, enhance cross-linking, and reinforce septal integrity. At the single-molecule level, both synthase types move directionally to perform processive PG synthesis at distinct sites. We also observed spatiotemporal separation of SEDS-bPBP and aPBP synthases in Staphylococcus aureus, suggesting that secondary septal PG synthesis is a conserved mechanism securing successful cytokinesis.

microbiology↗

bioRxiv2025

Stress granule sequestration of OXPHOS gene transcripts exacerbates glycolytic restriction

Stress granules (SGs) are dynamic organelles formed under cellular stress and they are generally regarded as protective entities. Meanwhile, their role in pathogenesis is becoming increasingly recognized, but the underlying mechanisms remain elusive due to the diverse nature of both stress types and biological contexts. Here we investigate SG dynamics and temporal changes in bulk and SG-associated transcriptomes under different regimens that inhibit glycolysis. We subject cells to either single assaults of glucose depletion (GD) or 2-deoxy-D-glucose addition (2DG) or a combined treatment (GD+2DG). We find that SGs formed under these conditions exhibit distinct properties, including eIF2 phosphorylation dependency, mRNA composition, and capacity to disassembly. Our results show that SGs induced by GD+2DG uniquely trap oxidative phosphorylation (OXPHOS) gene transcripts, leading to mitochondrial dysfunction. We provide evidence suggesting that the persistency of SGs formed under GD+2DG treatment is interwoven with mitochondrial dysfunction resulting in heightened apoptosis, effects that can also be recreated under single assaults when combined with mitochondrial inhibition. Our findings suggest that SG formation induced by inhibiting a single metabolic pathway can widen its impact in intensifying cellular metabolic stress under specific conditions, providing mechanistic insights into the paradoxical dual nature of SGs in stress response and pathology.

cell biology↗

bioRxiv2025

Sequencing of distinct wing behaviors during Drosophila courtship

Some behaviors, like biting followed by chewing and then swallowing, unfold in stereotyped sequences, while others, such as limb movements during defensive maneuvers, can be flexibly combined as needed. During courtship, male Drosophilid flies produce a series of actions, including orientation, tapping, singing, licking, and copulation, that follow an ordered but temporally variable sequence [1,2]. At shorter timescales, however, individual actions remain highly dynamic. For example, courtship songs are composed of variable sequences of distinct syllables, with their patterning and amplitude actively shaped by female cues [3-5]. Leveraging recent advances in behavioral quantification [6], we discover a new courtship wing behavior that we term "waggling", which is present across multiple Drosophila species and characterized by rhythmic, anti-phase wing movements. We identify an intermediate level of stereotyped behavioral structure: a directional three-part motif where males and females first decelerate to near-complete stillness, followed by male-initiated waggling, which then transitions into courtship song. Wing kinematics during waggle bouts are predictive of wing choice in subsequent songs, suggesting waggling may serve as a preparatory behavior. We then focus on P1/pC1 neurons, known to promote courtship [5,7-11]. Optogenetic activation of specific P1/pC1 neuron subsets in solitary males, without any female cues, is sufficient to recapitulate the entire stillness-to-waggling-to-singing progression. These findings reveal a new layer of stereotyped structure within a flexible courtship display and demonstrate that P1/pC1 neurons can orchestrate multi-action behavioral programs through internal dynamics. HighlightsO_LIDrosophila males produce "waggling," an oscillatory, anti-phase movement of the two wings that is distinct from the unilateral wing vibration that generates courtship song. C_LIO_LIWaggling is part of a structured behavioral sequence: from stillness, to waggling, and then to singing during male-female courtship interactions. C_LIO_LIThis full behavioral sequence is internally driven and can be triggered in solitary males by optogenetic activation of specific subsets of P1/pC1 neurons. C_LIO_LIP1/pC1 neurons show functional diversity in locomotor control. C_LI

neuroscience↗

bioRxiv2025

Hypobaric hypoxia drives citrate cycle reprogramming to suppress tumor progression

High altitude residents present lower tumor incidence and mortality than plain residents, suggesting that hypobaric hypoxia displays protective effect against tumor development. The results of our studies showed that hypobaric hypoxia exposure significantly suppressed tumor progression in subcutaneous bearing and lung metastasis tumor models. With single-cell transcriptome analysis, we identified HIF-1 pathway was significantly downregulated in tumor tissues with high altitude hypoxia, leading to decreased glycolysis and angiogenesis and improved antitumor immune response. Mechanistically, systemic hypoxia rewired citric acid cycle, with enhanced CS and IDH2 expression and reduced OGDH and SUCLG2 expression, to induce -ketoglutarate accumulation and succinate decline in tumor microenvironment, further mediating HIF-1 pathway inhibition. Moreover, hypobaric hypoxia treatment significantly improved the antitumor effects of adjuvant therapies (including chemotherapy, anti-angiogenic therapy and immunotherapy). Our findings reveal the role and mechanism of hypobaric hypoxia for tumor regression and yield new insights into tumor therapy.

cancer biology↗

bioRxiv2025

Tumor necrosis factor receptor 2 inhibits HIV-1 infection by blocking the binding of gp120 to CD4

The HIV-1 envelope glycoprotein gp120 binds to CD4 molecule and then undergoes conformational changes to interact with the co-receptors CCR5 or CXCR4, resulting in cellular entrance. However, certain types of cells, such as macrophages and CD4+Foxp3+ regulatory T cells (Tregs), have shown to resist HIV-1 infection despite co-expressing CD4 and co-receptors. In this study, we found that TNF receptor type II (TNFR2) directly bound to gp120, with the binding site on gp120 in close proximity to that of CD4. Intriguingly, exogenous TNFR2 had the capacity to inhibit the binding of gp120 to CD4 T cells. Furthermore, the infection of CD4+CCR5+ cells by pseudoviruses containing the HIV-1 envelope was inhibited by TNFR2 protein. In contrast, TNFR1, similar in structure to TNFR2 and sharing the same ligand, failed to inhibit the infection of CD4+ T cells by HIV-1 pseudoviruses. This property of TNFR2 may be harnessed in the prevention or treatment of HIV-1 infection and thus warrant future investigation. SUMMARYThis study reveals that TNFR2 directly binds to HIV-1 gp120, inhibiting its interaction with CD4 and reducing HIV-1 infection in CD4+ T cells. The findings highlight TNFR2s potential role in protecting cells and offer insights for HIV-1 prevention or therapy.

immunology↗

bioRxiv2025

Population genomics of the endangered scaly-foot snail defines conservation units amid deep-sea mining threats in Indian Ocean vents

Hydrothermal vents in the Indian Ocean face imminent deep-sea mining, yet lack baseline high-resolution connectivity data for their endemic fauna. We present the first population genomic study of the endangered scaly-foot snail (Chrysomallon squamiferum), an iconic species distributed across three vent biogeographic provinces. Analysing 125 individuals from eight vent fields using 14 million single-nucleotide polymorphisms, we identify five genetic groups that warrant recognition as evolutionarily significant units. Demographic modelling reveals critical contributions from extinct or unsampled phantom populations to the contemporary genetic structure. Together with physical ocean modelling, we show that the deep currents drive asymmetric south-to-north gene flows, while transform faults act as dispersal barriers. We propose Longqi-Duanqiao fields on the Southwest Indian Ridge and Wocan field on the Carlsberg Ridge as two isolated populations prioritised for protection. Given its exceptional adaptations, wide distribution, and public recognition, the scaly-foot snail is well-positioned to serve as both a flagship and umbrella species to ensure the survival of a broader suite of vent biodiversity. As the International Seabed Authority finalises its Mining Code in 2025, our findings provide essential genomic evidence to mitigate the impacts of mining on genetic diversity and inform transboundary conservation strategies for this vulnerable ecosystem.

ecology↗

bioRxiv2025

Iterative delivery of mRNA by MEFI

Conventional therapeutic mRNA delivery systems are inherently single-use, limiting expression potency, duration, and penetration across biological barriers. To address this, we engineered the mRNA Exporting and Ferrying Implement (MEFI), a platform that enables iterative cell-to-cell transfer of cargo mRNA, allowing a single mRNA molecule to be utilized multiple times across various cells. MEFI encodes a fusion protein that assembles virus-like particles (VLPs) and encapsulates both itself and cargo mRNA into these VLPs, orchestrating reproduction of VLPs from targeted cells and continuous intercellular spreading. MEFI significantly amplified cargo protein expression in the transfected cell populations ([~]20-fold) and in organs ([~]500-fold in lung) from mice administered systemically. Notably, through intramuscular injection of naked plasmids, MEFI promoted robust ([~]20-fold) and durable ([~]2-month) cargo expression, interorgan mRNA transfer, and successful crossing of the blood-brain barrier. Moreover, modified MEFI demonstrated cell-type-specific targeting, mediating the elimination of antigen-expressing cells. Collectively, MEFI establishes a modular platform for enhancing mRNA delivery, leveraging the concept of iterative delivery of mRNA. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/667827v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@14522c2org.highwire.dtl.DTLVardef@1ecfa7dorg.highwire.dtl.DTLVardef@1314347org.highwire.dtl.DTLVardef@1380cc7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Single-Molecule FRET Reveals Two T4 Phage MR Complex Exonuclease States Regulated by the Mre11 Dimer Interface

The Mre11/Rad50 (MR) complex serves as an initial responder to double-stranded DNA breaks and is conserved across all domains of life. Rad50 possesses ATPase activity that provides energy for the nuclease activities of Mre11. To elucidate the variation in exonuclease activity across the T4 phage MR complex population, we conducted smFRET studies utilizing a dual-labeled Cy3 and Cy5 double-stranded DNA substrate. Our findings revealed that the wild-type (WT) MR complex population was predominantly divided into two distinct rates of exonuclease activity. The majority of the population (94%) exhibited rapid exonuclease activity, with an average rate exceeding 20 nucleotides per second, while the remaining fraction showed substantially slower exonuclease activity, averaging 0.50 nucleotides per second. Furthermore, we compared the activity of the WT population to a mutant complex harboring the Mre11 mutation L101D, which has previously been shown to disrupt the Mre11 dimer interface. The MR complex with the L101D mutation exhibited a much higher percentage of the population displaying slow exonuclease activity (78%), while the remaining population exhibited fast exonuclease activity at a rate similar to that of the WT population. Additional activity parameters were evaluated, such as pause times and transition amplitudes, under various enzyme concentrations, revealing further differences between the WT and L101D MR complexes. Our results provide new insights into the molecular mechanisms of MR complex exonuclease activity and suggest that the complex may adopt different conformations with distinct kinetic properties.

biochemistry↗

bioRxiv2025

The Amplified Burden of Depression in Drug-Resistant Epilepsy: Role of Limbic Network Dynamic Reconfiguration

ObjectivesTo explore potential associations between drug resistance and limbic network (LN) dynamic functional interactions in temporal lobe epilepsy (TLE), whether these LN alterations are associated with and potentially mediate comorbid depression severity, and their potential neurochemical and transcriptomic underpinnings. MethodsThis cross-sectional study included 49 patients in the Responsive group, 33 patients in the Resistant group, and 50 healthy controls (HCs). Using resting-state fMRI, we derived LN dynamic integration coefficients and used non-negative matrix factorization (NMF) to identify coactivation patterns. Depressive symptoms (Self-Rating Depression Scale, SDS), LN integration, and NMF pattern expression were compared across groups (ANOVA) and correlated. Mediation analysis tested if LN integration mediated the relationship between drug resistance status and SDS scores. LN integration differences were spatially correlated with neurotransmitter receptor density and Allen Human Brain Atlas transcriptomic data. ResultsPatients in the Resistant group reported significantly higher SDS scores than patients in the Responsive group (p = 0.008). LN integration with the dorsal attention network (DAN) and fronto-parietal network (FPN) was significantly lower in the Resistant group compared to the Responsive group (p = 0.001; p < 0.001). NMF analysis identified key LN-DAN (p = 0.013) and LN-FPN (p < 0.001) coactivation patterns. In TLE patients, DAN-LN integration was negatively correlated with depressive symptoms (r = -0.28, p = 0.01), and lower integration levels significantly mediated the relationship between group status (Resistant vs. Responsive) and increased symptom severity (p < 0.001). These LN integration coefficient differences (Responsive group vs. Resistant group) were associated with 5-hydroxytryptamine 1B (5-HT1B; r = 0.29, p = 0.036) and dopamine D2 (D2; r = -0.29, p = 0.034) receptor densities, and linked to gene expression pathways including telomerase activity regulation (p < 0.001). InterpretationThis study identifies dynamic LN dysregulation, supported by distinct neurochemical and transcriptomic profiles, as a core bridging mechanism potentially contributing to comorbid depression linked to drug response status in TLE patients.

neuroscience↗

bioRxiv2025

A Paracrine-to-Autocrine Shunt of GREM1 Fuels Colorectal Cancer Metastasis via ACVR1C

Tumor cells typically rely on paracrine stromal signals to guide malignant behaviors, but whether they acquire signaling autonomy to support metastasis remains unclear. We elucidate this in colorectal cancer (CRC) by uncovering a paracrine-to-autocrine shunt of Gremlin1 (GREM1), a canonical stromal-secreted antagonist of bone morphogenetic proteins (BMPs). We demonstrate that while GREM1 remains restricted to stromal cells in earlier-stage (I-III) CRC, its ectopic expression in tumor epithelium increases markedly in stage IV. Mechanistically, we identify ACVR1C as a novel, high-affinity epithelial receptor for GREM1. Their interaction activates SMAD2/3 signaling, which upregulates SNAI1 and GREM1, establishing a feedback loop that amplifies epithelial-mesenchymal transition (EMT). Disrupting this loop impairs CRC metastasis in vivo. Clinically, epithelial GREM1 or ACVR1C expression predicts metastasis and poor survival. These findings define a paradigm in which tumor cells hijack stromal GREM1 to establish a GREM1-ACVR1C autocrine loop that sustains EMT and metastasis, marking a shift toward signaling autonomy and revealing a targetable vulnerability in advanced CRC.

cancer biology↗

bioRxiv2025

Buyang Huanwu Decoction Ameliorates Peripheral Nerve Injury by Promoting Cell Cycle through Activation of PI3K/AKT/mTOR/HIF-1α Pathway

BackgroundPeripheral nerve injury (PNI) can lead to partial or even total motor and sensory dysfunction, severely affecting the work and life of patients, but recovery of nerve function is often poor due to the complexity of the nerve repair and regeneration process. Cumulative evidence suggests the contribution of cell cycle regulation in repairing PNI injury, and p27KIP1 is a key molecule in regulating the cell cycle. ObjectiveThe aim of this study is to elucidate the repair mechanism of peripheral nerve injury (PNI) from the point of view of regulating cell cycle and to explore the therapeutic effect of Buyang Huanwu Decoction (BHD). To provide new strategies for the treatment of PNI and to explore valuable drugs initially. MethodsThe clamp injury model was chose as a PNI model and different doses of BHD extract were administered by gavage for 14 days. Limb motor function, sciatic nerve index and sciatic nerve pathology were assessed and p27Kip expression level was determined. The in vivo chemical composition of BHD extract was determined and drug targets were retrieved by TCMSP, STITCH and Swiss Target Prediction to predict the mechanism of BHD treatment for PNI using network pharmacology. Pathway-related proteins including P-PI3K, P-AKT, P-mTOR and HIF-1a were validated by western blotting assay. ResultsCompared with control rats, PNI rats had abnormal motor function, sciatic nerve damage and reduced p27Kip expression. Administration of BHD for 14 days significantly improved PNI in rats, which not only repaired sciatic nerve function, attenuated sciatic nerve pathology and inhibited p27Kip expression to regulate the cell cycle in PNI rats, but also activated the PI3K/AKT/mTOR/HIF-1a pathway. ConclusionThe above results suggest that PI3K/AKT/mTOR/HIF-1a mediated cell cycle regulation may be an important repair mechanism for PNI, and that BHD can improve PNI by accelerating the cell cycle to promote neural repair and regeneration.

cell biology↗

bioRxiv2025

Neural Timescale of Adolescents Major Depressive Disorder

Adolescent major depressive disorder (MDD) is characterized by heterogeneous symptomatology and complex neurodevelopmental underpinnings. Here, we investigated whether cortical intrinsic neural timescales (INT)--a measure of temporal stability in neural activity--are altered in adolescents with MDD and whether these alterations relate to clinical symptoms, suicidality, early-life adversity, and underlying neurobiological mechanisms. Using resting-state fMRI in adolescents with MDD and healthy controls (HCs), we found widespread reductions in INT in frontal, parietal, and sensorimotor regions, with a notable prolongation in the left temporoparietal junction. Disrupted timescales significantly impaired network modularity and clustering, and SVR-based machine learning revealed that altered INT patterns predicted individual depression and anxiety severity. INT abnormalities were further associated with suicidal ideation and childhood trauma, particularly emotional and physical neglect. Biophysical modeling linked INT variations to local recurrent excitation and external input strength, differing between HCs and MDD. Spatial correlations with PET-derived neurotransmitter receptor maps demonstrated that INT alterations colocalize with serotonergic, dopaminergic, and cholinergic systems. Transcriptomic enrichment analysis revealed associations with genes involved in mitochondrial function, synaptic signaling, and metabolic regulation. Together, these findings identify neural timescale disruption as a core pathophysiological feature of adolescent MDD, bridging macroscale dynamics with microcircuit and molecular architecture. INT may serve as a promising biomarker and mechanistic target for precision psychiatry in youth depression.

neuroscience↗

bioRxiv2025

Cholesterol Metabolism in a Murine Model of Vertical Sleeve Gastrectomy

The most effective and durable treatment for obesity is metabolic bariatric surgery. Currently, vertical sleeve gastrectomy (VSG) has become the preferred surgical method to achieve sustained weight loss and reverse obesity-related disease, including dyslipidemias. Human studies indicate that 40% of VSG patients can discontinue statin treatment by 6 months, while alterations in plasma bile acids and synthesis have been observed after bariatric surgery. Although it is well known that cholesterol is the precursor for all bile acids, the link between changes in plasma cholesterol and bile acids remains unclear in the context of VSG. Here, we present a murine model of VSG that leads to a marked decrease in plasma cholesterol levels despite no difference in body weight compared to sham surgery. Our results demonstrate that gastric resection lowers systemic cholesterol burden by promoting the hepatobiliary elimination of cholesterol through the upregulation of bile acid synthesis. These observations imply that gastric resection impacts overall hepatic physiology and cholesterol homeostasis independent of weight loss.

physiology↗

bioRxiv2025

An artificially selected cytokinin-pathway transcription factor balances soybean yield and pathogen resistance

Soybean contributes to sustainable food and feed production, but some modern varieties favor yield at the cost of disease resistance. Using a bottom-up approach, we demonstrate that the RR2b transcription factor activates cytokinin signaling for plant growth and reproductive fitness but represses disease-resistance and root-nodulation pathways. RR2b was artificially selected during domestication and improvement, and its expression levels correlate with ATT repeat polymorphisms in its promoter. Most wild soybeans and landraces have either more or less ATT repeats: more lead to weak RR2b expression with lower yield and enhanced resistance to soybean bacterial blight, and fewer cause strong RR2b expression, higher yield but reduced disease resistance. Elite cultivars instead balance yield and defense via moderate RR2b expression and several ATT repeats. This confers contrasting RR2b functionality across haplotypes in response to contrasting selection pressures and offers insights into decoupling trade-offs between yield and disease resistance to enhance crop productivity.

genetics↗

bioRxiv2025

Copper-Containing ROS-Scavenging Nanozyme Paradoxically Drives Alpha-Synucleinopathy by Amplifying Nitrosative Stress

Reactive oxygen and nitrogen species (RONS) are implicated in neurodegeneration, but their specific pathogenic roles remain unclear. Here, we developed a pair of iridium-based nanozymes with opposing functionalities to dissect these pathways. We show that a copper-tuned iridium nanozyme (Ir{square}Cu), despite being a superior ROS scavenger, paradoxically and dramatically exacerbated -synuclein (Syn) pathology in vivo. This pathology was causally linked to its ability to amplify RNS, as pharmacological inhibition of nitric oxide synthase (NOS) with L-NAME completely abrogated the pathology and reversed a human Parkinsons disease (PD)-like transcriptomic signature. In contrast, a copper-free, broad-spectrum RONS-scavenging iridium (Ir) nanozyme demonstrated substantial therapeutic efficacy across diverse brain-first, body-first, and Alzheimers disease with Lewy body co-pathology models. Our findings uncover the importance of the RNS pathway in driving -synucleinopathies and establish a critical design principle for nanomedicine, mandating caution in the use of redox-active copper for neuroprotective applications.

pathology↗

bioRxiv2025

Exploring the Effects of Teas with Different Fermentation Levels and Black Coffee on the Body via the Urine Proteome

Tea and black coffee, two of the most widely consumed beverages worldwide, play important roles in supporting overall health. Urinary proteins do not originate directly from the beverages. Instead, changes in the urine proteome reflect the changes in the body influenced by beverage consumption, rather than their metabolites. Can the effects of teas with different fermentation levels and black coffee on the body be explored via the urine proteome? In this study, urine samples were collected from rats before and after seven consecutive days of consuming green tea, oolong tea, black tea, Pu-erh tea, or black coffee. Both before-and-after comparisons and between-group comparisons were performed, and the samples were analyzed using liquid chromatography coupled with tandem mass spectrometry. The results showed that the urine proteome reflected the changes in rats after one week of consuming teas with different fermentation levels or black coffee. Biological processes and pathways enriched from differential proteins included fat cell differentiation, lipid metabolism, glucose metabolism, fatty acid transport, and immune response. Furthermore, the effects of teas with different fermentation levels and black coffee on the body exhibited a high degree of specificity. Additionally, several differential proteins identified in this study have been reported as biomarkers for diseases such as cancer and cardiovascular diseases. This suggests that beverage consumption, including tea and black coffee, should be considered in clinical application of urine biomarkers of diseases and related studies. And the use of biomarker panels may be necessary to improve accuracy. In conclusion, the urine proteome provides a comprehensive and systematic reflection of the overall effects of all components in tea and black coffee on the body, and can distinguish changes in the body after consuming teas with different fermentation levels and black coffee.

biochemistry↗

bioRxiv2025

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

The emergence of genomic language models (gLMs) has revolutionized the analysis of genomic sequences, enabling robust capture of biologically meaningful patterns from DNA sequences for an improved understanding of human genome-wide regulatory programs, variant pathogenicity and therapeutic discovery. Given that DNA serves as the foundational blueprint within the central dogma, the ultimate evaluation of a gLM is its ability to generalize across this entire biological cascade. However, existing evaluations lack this holistic and consistent framework, leaving researchers uncertain about which model best translates sequence understanding into downstream biological prediction. Here we present Genomic Touchstone, a comprehensive benchmark designed to evaluate gLMs across 36 diverse tasks and 88 datasets structured along the central dogmas modalities of DNA, RNA, and protein, encompassing 5.34 billion base pairs of genomic sequences. We evaluate 34 representative models encompassing transformers and convolutional neural networks, as well as emerging efficient architectures such as Hyena and Mamba. Our analysis yield four key insights. First, gLMs achieve comparable or superior performance on RNA and protein tasks compared to models pretrained on these molecules. Second, transformer-based models continue to lead in overall performance, yet efficient sequence models show promising task-specific capabilities and deserve further exploration. Third, the scaling behavior of gLMs remains incompletely understood. While longer input sequences and more diverse pretraining data consistently improve performance, increases in model size do not always translate into better results. Fourth, pretraining strategies, including the choice of training objectives and the composition of pretraining corpora, exert substantial influence on downstream generalization across different genomic contexts. Genomic Touchstone establishes a unified evaluation framework tailored to human genomics. By spanning multiple molecular modalities and biological tasks, it offers a valuable foundation for guiding future gLM design and understanding model generalizability in complex biological contexts.

bioinformatics↗