Biology subjects

Song, J. H.

Publications and source records attributed to Song, J. H..

At least 19 recordsLinked to original sources

bioRxiv2026

Engineering the NAT-ULT module increases seed number per pod in soybean

Seed number per pod is a major soybean yield-component trait, yet experimentally validated causal modules remain poorly defined. Here, we identify and functionally validate a soybean NAT-ULT regulatory module controlling ovule and seed number per pod. Through a visual screen of a fast-neutron-irradiated Glycine max cv. Williams 82 population, we isolated MO27, which increased four-seeded pod frequency from approximately 2-4% in wild type to 27-30%, without major changes in plant architecture, total pod number, or seed morphology. Comparative genome hybridization mapped the phenotype to a 46.7-kb chromosome 2 deletion containing GmNAT1 and chromosome 6 deletions encompassing GmULT-B1 and GmULT-B3. Ovule-clearing analysis showed that increased seed number originated before fertilization through elevated formation of four-ovule ovaries. CRISPR/Cas9-mediated mutagenesis of GmNAT1, GmULT-B1, and GmULT-B3 increased four-seeded pod frequency without detectable penalties in 100-seed weight, total pod number, or plant height. Tomato SlULT triple mutants also increased floral organ and locule number, supporting conserved ULT-like function in reproductive organ patterning. RNA-seq interaction analysis revealed a chromosome 6-dominant transcriptional state, accompanied by selective non-additive reprogramming of hormone/ovule-number and cell-wall-remodeling modules. Integrated genetic and transcriptomic analyses support a hierarchical model in which NAT-ULT perturbation may enhance meristematic competence and remodel reproductive developmental programs, while additional fast-neutron-background-associated transcriptional changes may further modulate the phenotype. These findings define NAT-ULT as a molecular target for engineering soybean seed number per pod.

plant biology↗

bioRxiv2026

Sequence-to-function deep learning decodes human cis-regulatory evolution

Deciphering the regulatory consequences of sequence divergence across human evolution is essential to understanding the molecular basis of human-specific traits and disease. Although millions of derived alleles distinguish humans from great apes, only a small fraction are likely to influence human-specific traits. Previous studies have focused on regions of elevated sequence divergence, assuming that rapid evolution reflects functional adaptation, yet individual high-impact regulatory mutations evade such scans. Here, we apply sequence-to-function deep learning to predict chromatin accessibility across modern human, archaic hominin, and great ape personalized genomes, identifying lineage-specific cis-regulatory elements (linCREs) across diverse cellular contexts. Compared to conserved elements, linCREs are shorter, less pleiotropic, less conserved, and enriched in neurodevelopmental pathways. Many linCREs occur in regions with limited sequence divergence that acceleration-based approaches would overlook. We validate lineage-specific enhancer activity through luciferase reporter assays and demonstrate that a single motif-generating derived allele nominated by model interpretability tools drives a hominin-specific neurodevelopmental enhancer.

genomics↗

bioRxiv2026

Hypothalamic Cell Type Evolution across Vertebrates

The hypothalamus regulates vital functions and is highly conserved among vertebrates occupying diverse niches, but little is known about the evolution of its cell types. Using comparative single-cell transcriptomics across major vertebrate classes, we identified deeply conserved and clade-specific cell types. While homologous cell types express conserved transcription factors and neuropeptides, their regulatory linkages are often rewired across evolution. The paraventricular nucleus largely retains its neuropeptide expression and responds to dehydration with fine cellular resolution from amphibians to mammals, whereas lamina terminalis neurons are specific to terrestrial vertebrates and exhibit gene expression divergence in cell types activated by dehydration and heat. We propose that a conserved set of keystone cell types sustain essential functions across vertebrates, while flexible gene regulatory programs alongside numerous clade-specific cell types offer evolutionary fluidity.

evolutionary biology↗

bioRxiv2026

Projectomic Organization of the Serotonin System of the Mouse Brain

The serotonin system innervates nearly the entire brain to support diverse functions, and its dysfunction is implicated in multiple psychiatric disorders. Although recent studies suggested that this anatomically diffuse system supports differentiated rather than uniform modulation, its overall organization is unclear. Here, using systematic whole-brain axon tracing and integrated analyses, we show that the serotonin projectome is organized by functional relatedness rather than physical proximity of its targets. Dorsal and median raphe serotonin neurons partition into five projectomic groups, each preferentially innervating the hippocampus, basal ganglia, cortex, medial interbrain, or brainstem/lateral thalamus, with within-group structure ranging from discrete subgroups to continuous variation. Spatial transcriptomic analyses reveal that each projectomic group corresponds to a distinct combination of transcriptomic clusters, with transcriptome and somatic position jointly predicting projectomic identity. Projection-specific serotonin depletion produces dissociable behavioral phenotypes. Together, projectomic identity emerges as a central axis linking axon collateralization, molecular diversity, and behavioral function.

neuroscience↗

bioRxiv2026

The chitin receptor-interacting protein LIK1 regulates extracellular ATP signaling via interaction with P2K1 in Arabidopsis thaliana

Previously, the chitin receptor-interacting protein kinase LIK1 (LysM receptor kinase 1/CERK1-interacting kinase) was shown to play an important role in regulating chitin signaling and plant defense. A limited proteolysis proteomics study revealed several LIK1-derived peptides that showed differential abundance between ATP-treated and mock-treated Arabidopsis samples, suggesting a possible involvement of LIK1 in extracellular ATP (eATP) signaling. To explore this possibility, LIK1 mutants were obtained and examined for their response to ATP. The results showed that mutations in LIK1 significantly reduced the expression of eATP-responsive genes. In addition, LIK1 was found to interact with the eATP receptor P2K1 and to be phosphorylated by it. The LIK1 protein was localized to the plasma membrane and its gene expression appeared to be ubiquitous. Collectively, these findings indicate that LIK1 not only contributes to chitin signaling but also participates in eATP signaling, highlighting its potential role as a shared component in multiple signaling pathways to regulate plant responses to diverse internal and external cues.

plant biology↗

bioRxiv2025

Small Molecule Degradation of the microRNA-21 Precursor Rescues Pathogenic Pathways in Cellular Models of Fibrosis

MicroRNAs (miRNAs) are short RNA molecules that bind to target mRNAs, resulting in translational repression and gene silencing. Overexpression of microRNA-21 (miR-21) is associated with various human diseases, including autosomal dominant polycystic kidney disease (ADPKD) and pulmonary fibrosis. In this study, a previously described heterobifunctional molecule, TGP-21-RiboTAC, that degrades the miR-21 precursor (pre-miR-21) in triple negative breast cancer cells was investigated in polycystic kidney cell lines and a lung fibroblast cell line. In the former, TGP-21-RiboTAC degraded pre-miR-21 and de-repressed of miR-21s downstream target, Programmed Cell Death 4 (PDCD4) and Peroxisome Proliferator-Activated Receptor alpha (PPAR), known drivers of ADPKD. The heterobifunctional molecule also inhibited cyst growth and rescued the metabolic alterations that occur in ADPKD. In the lung fibroblast cell line, MRC-5, TGP-21-RiboTAC also reduced pre- and mature miR-21 levels, rescued Transforming Growth Factor {beta} (TGF-{beta})-induced repression of SMAD Family Member 7 (SMAD7) and inhibited cell invasion. Collectively, these studies demonstrate the potential of targeted RNA degradation as therapeutic agents that retard the development of organ fibrosis.

biochemistry↗

bioRxiv2025

Human-specific tandem repeat in CACNA1C modulates responses to neuronal stimulation

The recent development of long-read sequencing has made it possible to catalog variable number tandem repeats (VNTRs) in the human genome. However, little is known about their functional consequences. Here, we characterized the effect of TRACT, a VNTR that is unique to humans and that has sequence variants linked to risk for bipolar disorder and schizophrenia. By adding or removing this VNTR in both mouse models and human neural organoids, we find that TRACT, which is intronic to the L-type voltage-gated calcium channel gene CACNA1C, increases intracellular calcium after neuronal stimulation and leads to widespread changes in activity-dependent transcription programs in neurons. TRACT-dependent changes are enriched for genes associated with synapse formation and plasticity, and partially recapitulate evolutionary changes in activity-dependent transcription between species. These findings demonstrate that a single, human-specific, non-coding element can strongly affect the neuronal response to stimulation, and motivate the study of VNTRs as a genetic source of phenotypic variation in both evolution and disease.

genetics↗

bioRxiv2025

Pretraining Improves Prediction of Genomic Datasets Across Species

Recent studies suggest that deep neural network models trained on thousands of human genomic datasets can accurately predict genomic features, including gene expression and chromatin accessibility. However, training these models is computation- and time-intensive, and datasets of comparable size do not exist for most other organisms. Here, we identify modifications to an existing state-of-the-art model that improve model accuracy while reducing training time and computational cost. Using this stream-lined model architecture, we investigate the ability of models pretrained on human genomic datasets to transfer performance to a variety of different tasks. Models pretrained on human data but fine-tuned on genomic datasets from diverse tissues and species achieved significantly higher prediction accuracy while significantly reducing training time compared to models trained from scratch, with Pearson correlation coefficients between experimental results and predictions as high as 0.8. Further, we found that including excessive training tasks decreased model performance and that this compromised performance could be partially but not completely rescued by fine-tuning. Thus, simplifying model architecture, applying pretrained models, and carefully considering the number of training tasks may be effective and economical techniques for building new models across data types, tissues, and species.

genomics↗

bioRxiv2025

Inverse expression of Ten3 and Lphn2 across the developing mouse brain reveals a global strategy for circuit assembly

Precise wiring of neural circuits requires molecular strategies that ensure accurate target selection across diverse brain regions. Here, we identify inverse expression between a ligand-receptor pair, Teneurin-3 (Ten3) and Latrophilin-2 (Lphn2), across the developing mouse brain. Ten3 and Lphn2 exhibit inverse expression gradients along a retinotopic axis orthogonal to the ephrin-A and EphA gradients; along the tonotopic axis across multiple brainstem auditory nuclei; and along the dorsomedial-ventrolateral axis in striatum and pallidum. Their inverse expression also creates discrete domains of cerebellar Purkinje cells and cerebellar nuclei. Using conditional tag mice, we show that inverse Ten3 and Lphn2 expression patterns predict connectivity, following a Ten3[->]Ten3, Lphn2[->]Lphn2 rule in all above circuits, and that Lphn2 is required in executing this rule in Purkinje cells[->]cerebellar nuclei projection. Our findings suggest a global strategy of coordinating gene expression of key wiring molecules with circuit connectivity across the developing brain.

neuroscience↗

bioRxiv2025

Activating RET Mutations Promotes Osteoblastic Bone Metastases in Medullary Thyroid Cancer

Development of bone metastases increases mortality in patients with medullary thyroid cancer (MTC), with [~]50% survival at 5 years after diagnosis, but the underlying mechanisms are unknown. We show that patient-derived MTC cells (RETC634W mutant TT cells and RETM918T mutant MZCRC1 cells) promote an osteoblastic phenotype due to reduced bone resorption. Mechanistically, activated RET increases the expression of osteoprotegerin (OPG), an inhibitor of bone resorption, leading to decreased osteoclast differentiation. Furthermore, RET knockdown or pharmacological RET inhibition attenuates tumor burden and osteoblastic lesions in MTC-bearing femurs. Circulating levels of OPG were increased in the plasma of MTC patients who developed bone metastases and this was associated with poor overall survival. Patients who were treated with multi-kinase inhibitors have lower circulating levels of OPG. These novel findings identify a link between the RET signaling pathway and abnormal osteoblastic bone formation and suggest OPG as a potential biomarker of MTC bone metastases. HighlightsO_LIPatient-derived MTC cells promote osteoblastic lesions in a mouse model. C_LIO_LIActivating the RET mutation promotes osteoprotegerin. C_LIO_LIBlocking RET kinase activity inhibits tumor growth and the osteoblastic lesion phenotype. C_LIO_LIHigh levels of circulating osteoprotegerin are associated with poor overall survival. C_LI

cancer biology↗

bioRxiv2025

Human-chimpanzee tetraploid system defines mechanisms of species-specific neural gene regulation

A major challenge in human evolutionary biology is to pinpoint genetic differences that underlie human-specific traits, such as increased neuron number and differences in cognitive behaviors. We used human-chimpanzee tetraploid cells to distinguish gene expression changes due to cis-acting sequence variants that change local gene regulation, from trans expression changes due to species differences in the cellular environment. In neural progenitor cells, examination of both cis and trans changes -- combined with CRISPR inhibition and transcription factor motif analyses -- identified cis-acting, species-specific gene regulatory changes, including to TNIK, FOSL2, and MAZ, with widespread trans effects on neurogenesis-related gene programs. In excitatory neurons, we identified POU3F2 as a key cis-regulated gene with trans effects on synaptic gene expression and neuronal firing. This study identifies cis-acting genomic changes that cause cascading trans gene regulatory effects to contribute to human neural specializations, and provides a general framework for discovering genetic differences underlying human traits.

evolutionary biology↗

bioRxiv2025

Autism-Associated Genes and Neighboring lncRNAs Converge on Key Gene Regulatory Networks

Autism spectrum disorder (ASD) is highly heritable, and mutations in hundreds of genes have been implicated as individually rare causes of ASD1-3. Understanding how disruptions to these functionally diverse genes lead to the core features of ASD remains a major challenge4. Moreover, ASD is three- to four-fold more common in males than females5, and autistic females tend to carry more autosomal risk alleles for ASD compared to autistic males6,7, but the biological basis of this "female protective effect" (FPE) is unknown8,9. Here we show that individual perturbations of 18 ASD genes in human neural progenitor cells converge on shared effects on gene expression, including widespread downregulation of other ASD genes. De novo reconstruction of a gene regulatory network (GRN) enabled the identification of central transcriptional regulators, including the prominent ASD gene CHD8 as well as novel candidates such as REST, that drive this transcriptomic convergence. Furthermore, the X-linked transcription factor ZFX, which is expressed from both the active and the inactive X chromosomes in females10, emerged as a key activator of many ASD genes: we propose that the higher ZFX expression level observed in female brain can buffer damaging mutations in diverse ASD genes, contributing to the FPE. Together, these results reveal how key GRNs can become broadly and similarly dysregulated upon disruption of individual ASD genes and provide molecular insight into the female protective effect in ASD.

genetics↗

bioRxiv2024

Concerted modulation of spontaneous behavior and time-integrated whole-brain neuronal activity by serotonin receptors

Serotonin neurons from the raphe nuclei project across the entire brain and modulate diverse physiology and behavior by acting on over a dozen receptors. Here, we took a step towards dissecting this complex process by examining the effects of agonists and antagonists of four widely expressed serotonin receptors (2A, 2C, 1A, and 1B) on spontaneous mouse behavior, which we related to time-integrated whole-brain neuronal activity as assessed by the expression of Fos, a canonical immediate-early gene product. Low-dimensional representations of behavioral and Fos map data revealed the dominant factors of variation in each domain, captured predictable differences across drug groups, and enabled predictions of behavioral changes following perturbations in Fos maps and vice versa. Our study provides a rich resource describing the effects of manipulating serotonin receptors on animal behavior and whole-brain integrated neuronal activity. It also establishes an experimental and analysis paradigm for interrogating the relationship between behavior and neuronal activity across different time scales.

neuroscience↗

bioRxiv2024

Differential growth enhancement followed by notable microbiota modulation in growing-finishing pigs by Bacillus subtilis strains ps4060, ps4100, and a 50:50 strain mixture

A 50:50 blend of two Bacillus subtilis strains positively impacted the productivity of finishing pigs. Given this observed effect, we hypothesized that each strain has distinct effects on weight gain and their influence on gut microbiota. In a 16-week test, 160 pigs were divided into four groups: basal diet, B. subtilis ps4100, B. subtilis ps4060, and 50:50 mixture supplemented. Subsequently, we compared body weight and fecal microbiota. Among the supplements, ps4100, ps4060, and the 50:50 mix yielded respective average daily weight gains (ADG) of 3.6%, 4.6%, and 3.9% by the 6th week. The weight difference was maintained through the 16th week. At the 11th week, the difference in -diversity among the fecal microbiota was marginal, and 17 of 229 genera showed differential abundance between the control and either of the treatment groups. A total of 12 of the 17 genera, including Lactobacillus, showed differential abundance between the ps4100 and ps4060-fed groups, and only Eubacterium consistently decreased in abundance in both the ps4100 and ps4060 groups. In comparison, microbial diversity was significantly different at the 16th week (p < 0.05), with 96 out of 229 genera exhibiting differential abundance. A total of 42 of the 96 genera exhibited similar patterns in both the ps4100 and ps4060 groups compared to the control group. Additionally, 236 of 687 microbial enzymes with differential abundance deduced from 16S rRNA reads showed similar differential abundance in both groups compared to the control group. We concluded that the overall microbial balance, rather than the dominance or significant decrease of a few specific genera, likely caused the enhanced ADG until the 11th week. Substantial changes in microbiota manifested at the 16th week did not cause dramatically increased ADG but were a consequence of weight gain and could positively affect animal physiology and health afterward.

microbiology↗

bioRxiv2024

Embryonically Active Piriform Cortex Neurons Promote Intracortical Recurrent Connectivity during Development

Neuronal activity plays a critical role in the maturation of circuits that propagate sensory information into the brain. How widely does early activity regulate circuit maturation across the developing brain? Here, we used Targeted Recombination in Active Populations (TRAP) to perform a brain-wide survey for prenatally active neurons in mice and identified the piriform cortex as an abundantly TRAPed region. Whole-cell recordings in neonatal slices revealed preferential interconnectivity within embryonically TRAPed piriform neurons and their enhanced synaptic connectivity with other piriform neurons. In vivo Neuropixels recordings in neonates demonstrated that embryonically TRAPed piriform neurons exhibit broad functional connectivity within piriform and lead spontaneous synchronized population activity during a transient neonatal period, when recurrent connectivity is strengthening. Selectively activating or silencing of these neurons in neonates enhanced or suppressed recurrent synaptic strength, respectively. Thus, embryonically TRAPed piriform neurons represent an interconnected hub-like population whose activity promotes recurrent connectivity in early development.

neuroscience↗

bioRxiv2021

Activation of retinoic acid receptor reduces metastatic prostate cancer bone lesions through blocking endothelial-to-osteoblast transition

Metastatic prostate cancer (PCa) in bone induces bone-forming lesions that contribute to progression and therapy resistance. Currently strategies targeting PCa-induced bone formation are lacking. We previously showed that PCa-induced bone originates from endothelial cells (EC) that have undergone endothelial-to-osteoblast (EC-to-OSB) transition in response to tumor-secreted BMP4. Here, we show that activation of retinoic acid receptor (RAR) inhibits EC-to-OSB transition and reduces PCa-induced bone formation. We found that palovarotene, a RAR{gamma} agonist being tested for heterotopic ossification in fibrodysplasia ossificans progressiva, inhibited EC-to-OSB transition and osteoblast mineralization in vitro, and decreased tumor-induced bone formation and tumor growth in several osteogenic PCa models. RAR/{beta}/{gamma} isoform knockdown in 2H11 ECs blocked EC-to-OSB transition and osteoblast mineralization. Pan-RAR agonist ATRA inhibited MycCaP-BMP4-induced bone formation and tumor growth under castration. Furthermore, palovarotene or ATRA reduced plasma Tenascin C, a factor secreted by EC-OSB cells, which may be used to monitor treatment response. Mechanistically, BMP4-activated pSmad1 forms a complex with RAR in the nucleus of 2H11 cells. RAR activation by palovarotene or ATRA causes pSmad1 degradation by recruiting E3-ubiquitin ligase Smurf1 into the nuclear pSmad1/RAR{gamma} complex. Our findings suggest that palovarotene can be repurposed to target PCa-induced bone formation to improve clinical outcomes for bone metastasis.

cancer biology↗

bioRxiv2021

Prostate tumor-induced stromal reprogramming generates Tenascin C that promotes prostate cancer metastasis through YAP/TAZ inhibition

Metastatic prostate cancer (PCa) in bone induces bone-forming lesions that enhance PCa progression. How tumor-induced bone formation enhances PCa progression is not known. We have previously shown that PCa-induced bone originates from endothelial cells (EC) that have undergone endothelial-to-osteoblast (EC-to-OSB) transition by tumor-secreted BMP4. Here, we show that EC-to-OSB transition leads to changes in the tumor microenvironment that increases the metastatic potential of PCa cells. We found that conditioned medium (CM) from EC-OSB hybrid cells increases the migration, invasion and survival of PC3-mm2 and C4-2B4 PCa cells. Quantitative mass spectrometry (iTRAQ) identified Tenascin C (TNC) as one of the major proteins secreted from EC-OSB hybrid cells. TNC expression in tumor-induced osteoblasts was confirmed by immunohistochemistry of MDA-PCa118b xenograft and human bone metastasis specimens. Mechanistically, BMP4 increases TNC expression in EC-OSB cells through the Smad1-Notch/Hey1 pathway. How TNC promotes PCa metastasis was next interrogated by in vitro and in vivo studies. In vitro studies showed that a TNC neutralizing antibody inhibits EC-OSB-CM-mediated PCa cell migration and survival. TNC knockdown decreased, while addition of recombinant TNC or TNC overexpression increased migration and anchorage-independent growth of PC3 or C4-2b cells. When injected orthotopically, PC3-mm2-shTNC clones decreased metastasis to bone, while C4-2b-TNC overexpressing cells increased metastasis to lymph nodes. TNC enhances PCa cell migration through 5{beta}1 integrin-mediated YAP/TAZ inhibition. These studies elucidate that tumor-induced stromal reprogramming generates TNC that enhances PCa metastasis and suggest that TNC may be a target for PCa therapy.

cancer biology↗

bioRxiv2021

Genetic studies of human-chimpanzee divergence using stem cell fusions

Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or auto-tetraploid iPSCs. Analysis of gene expression patterns in inter-specific allo-tetraploid iPSCs shows that human-chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves, and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allo-tetraploid cells. We successfully generated derivative cells with nested deletions or inter-specific recombination on the X chromosome. These studies identify a long distance cis-regulatory domain of the Fragile X-associated gene (FMR1), confirm an important role for the X chromosome in trans-regulation of other expression differences, and illustrate the potential of this system for more detailed mapping of the molecular basis of human and chimpanzee evolution. Significance StatementComparative studies of humans and chimpanzees have revealed many anatomical, physiological, behavioral, and molecular differences. However, it has been challenging to map these differences to particular chromosome regions. Here, we develop a genetic approach in fused stem cell lines that makes it possible to map human-chimpanzee molecular and cellular differences to specific regions of the genome. We illustrate this approach by mapping chromosome regions responsible for species-specific gene expression differences in fused tetraploid cells. This approach is general, and could be used in the future to map the genomic changes that control many other humanchimpanzee differences in various cell types or organoids in vitro.

evolutionary biology↗