Biology subjects

Park, S. G.

Publications and source records attributed to Park, S. G..

8 recordsLinked to original sources

bioRxiv2026

Structure of the Type I-F3 CAST holo integration complex reveals licensing mechanisms during RNA-guided DNA integration

Precise genomic integration of large DNA cargo remains a central challenge in genome engineering. In this context, CRISPR-associated transposases (CASTs) offer a promising solution by coupling RNA-guided DNA recognition to transposon-mediated integration. Type I-F3 CASTs exhibit exceptional targeting fidelity, making them a leading focus for biotechnology and gene therapy applications. Yet, despite extensive characterization, the structural basis for RNA-guided DNA integration of type I-F3 CASTs has remained elusive. Here, using cryo-EM and functional assays, we report the structural licensing mechanism of the Vibrio cholerae CAST (VchCAST) holo integration complex (HIC). Our structures reveal that sequential conformational licensing events govern selective activation of the integration machinery at the on-target site. Different components, including Cascade-TniQ, TnsC, and TnsA/B, undergo conformational changes upon assembly into the HIC, and the catalytically competent state is stabilized only within the fully assembled complex. Finally, comparison with existing CAST integration complex structures reveals a set of conserved architectural features, suggesting a common molecular basis for RNA-guided transposition across CAST diversity.

biochemistry↗

bioRxiv2026

Programmable DNA integration with New-to-Nature tools using Computational Protein Design

Programmable integration of large DNA cargo ([≥] 2 kb), without inducing double-strand breaks, remains challenging for genome editing technologies. Current approaches have limitations in programmability, depend on co-delivery of multiple components, require multiple enzymatic steps, or have variable on-target editing outcomes. Here, we address this challenge using de novo protein design to create highly active, new-to-nature RNA-guided transposons. Our strategy exploits the modular architecture of CRISPR-associated transposons (CASTs), reconfiguring their conserved transposition machinery to interface with widely adopted Cas9. The resulting system, which we call NovoCAST, simplifies the CAST architecture from eight distinct proteins to four, establishing the simplest CAST described to date. NovoCAST exhibits sharply defined integration profiles, a 500-fold increase in activity relative to the parental PmcCAST, and general programmability. Using structural and biochemical analyses, we confirmed that the designed proteins fold and function as intended. Finally, we demonstrate robust programmable genomic integration in human cells highlighting its broad potential applications in research and therapeutics. Together, these results establish de novo protein design as a powerful strategy for engineering efficient genome-editing systems and for coupling CRISPR-mediated DNA recognition to heterologous functions through de novo designed protein interfaces.

biochemistry↗

bioRxiv2022

Immature Myeloid Cell Deposition in Old Bone Marrow Revealed by Single-Cell Transcriptome Analysis

Aging causes dysfunction of innate immunity, although hematopoietic stem cells of aged bone marrow (BM) show an increased differentiation potential to myeloid lineage cells. The alteration of cellular heterogeneity and intercellular communications between BM immune cells may provide important clues to understanding age-dependent immune dysfunction. Here, we provide a deep single-cell transcriptomic analysis of total immune cell populations of young and old BM. We identified the well-organized differentiation status of 11 myeloid/lymphoid lineage cell populations and age-dependent alterations in the proportions of cells. The neutrophil lineages showed the most prominent alteration by aging, and subclustering of neutrophils indicated that the specific immature neutrophils are increased in old BM. In addition, we identified age-dependent alterations in secretory phenotypes associated with a decline in innate immunity and immune cell differentiation. Among these secretory phenotypes, SPP1 could be suggested as a representative signal that triggers myeloid skewing and immature neutrophil deposition in aged BM. Collectively, these results provide a novel link between the altered immune cell proportions in BM and age-dependent dysregulation of innate immunity.

bioinformatics↗

bioRxiv2019

Raptor genomes reveal evolutionary signatures of predatory and nocturnal lifestyles

BackgroundBirds of prey (raptors) are dominant apex predators in terrestrial communities, with hawks (Accipitriformes) and falcons (Falconiformes) hunting by day, and owls (Strigiformes) hunting by night.\n\nResultsHere, we report new genomes and transcriptomes for 20 species of birds, including 16 species of birds of prey, and high-quality reference genomes for the Eurasian eagle-owl (Bubo bubo), oriental scops-owl (Otus sunia), eastern buzzard (Buteo japonicus), and common kestrel (Falco tinnunculus). Our extensive genomic analysis and comparisons with non-raptor genomes identified common molecular signatures that underpin anatomical structure and sensory, muscle, circulatory, and respiratory systems related to a predatory lifestyle. Compared with diurnal birds, owls exhibit striking adaptations to the nocturnal environment, including functional trade-offs in the sensory systems (e.g., loss of color vision genes and selection for enhancement of nocturnal vision and other sensory systems) that are probably convergent with other nocturnal avian orders. Additionally, we found that a suite of genes associated with vision and circadian rhythm were differentially expressed between nocturnal and diurnal raptors, indicating adaptive expression change during the transition to nocturnality.\n\nConclusionsOverall, raptor genomes showed genomic signatures associated with the origin and maintenance of several specialized physiological and morphological features essential to be apex predators.

genomics↗

bioRxiv2018

The draft genome of an octocoral, Dendronephthya gigantea

BackgroundCoral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities composed of octocorallian species, appear more resilient. The genomes of several species of cnidarians have been published, including stony corals, sea anemones, and hydra, but as of yet no octocoral species. To fill this phylogenetic gap within the cnidarian, we sequenced the octocoral, Dendronephthya gigantea, a non-symbiotic soft coral, commonly known as the carnation coral.\n\nFindingsThe D. gigantea genome size is approximately 276 Mb. A high-quality genome assembly was constructed using 29.85Gb (108x coverage) of PacBio long reads and 35.54Gb (128x coverage) of Illumina short paired-end reads resulting in the largest N50 value reported among cnidarian of 1.4 Mb. About 12 % of the genome consisted of repetitive elements. We found 28,879 protein-coding genes. This gene set contained about 94% metazoan single-copy orthologs, indicating the gene models were predicted with high quality compared to other cnidarians. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence occurred approximately 544 million years ago. Moreover, there is a clear difference in Hox gene composition: unlike in hexacorals, Antp superclass member Evx gene was absent in D. gigantea.\n\nConclusionsWe present the first genome assembly of a non-symbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including comparisons of stony and soft corals and symbiotic and non-symbiotic corals. In addition, the genome of this species may provide clues about differential genetic coping mechanisms between soft and stony coral regarding the global warming.

genomics↗

bioRxiv2018

The jellyfish genome sheds light on the early evolution of active predation

BackgroundUnique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column. One of the first animals to become free-swimming, jellyfish employ pulsed jet propulsion and venomous tentacles to capture prey.\n\nResultsTo understand these key innovations, we sequenced the genome of the giant Nomuras jellyfish (Nemopilema nomurai), the transcriptomes of its bell and tentacles, and transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains; possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes, and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation).\n\nConclusionsTaken together, the jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits that have combined to make these animals one of the worlds earliest and most successful multi-cellular predators.

genomics↗

bioRxiv2018

The whale shark genome reveals how genomic and physiological properties scale with body size

The endangered whale shark (Rhincodon typus) is the largest fish on Earth and is a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 81 animals and yeast. We examined scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic features also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: GC content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to large introns highly enriched in repetitive elements such as CR1-like LINEs, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale sharks genome had an expansion of gene families related to fatty acid metabolism and neurogenesis, with the slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan, and showed that the whale shark is a promising model for studies of neural architecture and lifespan.

genomics↗

bioRxiv2018

Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy

Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here we perform a genome-wide prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.

cancer biology↗