Biology subjects

Son, K. H.

Publications and source records attributed to Son, K. H..

3 recordsLinked to original sources

bioRxiv2024

Gencube: Efficient retrieval, download, and unification of genomic data from leading biodiversity databases

MotivationWith the daily submission of numerous new genome assemblies, associated annotations, and experimental sequencing data to genome archives for various species, the volume of genomic data is growing at an unprecedented rate. Major genomic databases are establishing new hierarchical structures to manage this data influx. However, there is a significant need for tools that can efficiently access, download, and integrate genomic data from these diverse repositories, making it challenging for researchers to keep pace. ResultsWe have developed Gencube, a command-line tool with two primary functions. First, it facilitates the utility of genome assemblies, related annotations, gene set sequences, and cross-species data from various leading biodiversity databases. Second, it helps researchers intuitively explore experimental sequencing data that meets their needs and consolidates the metadata of the retrieved outputs. Availability and implementationGencube is a free and open-source tool, with its code available on GitHub: https://github.com/snu-cdrc/gencube.

bioinformatics↗

bioRxiv2023

Extracellular vesicle-mediated Transfer of miR-1 from Primary tumor Repress Metastasis Growth

Metastases originate from primary tumors that conquer distant organs. Growing evidence suggests that metastases are still under primary tumor dominance, even out of the primary territory. However, the mechanism by which primary tumors prime the fate of metastasis is unclear. Here, we investigated the influence of primary tumor-derived extracellular vesicles (pTDEs) on distant metastasis. Metastatic growth was remarkably suppressed when cells were treated with pTDEs in vitro and intravenously in a spontaneous metastatic mouse model. pTDEs from primary tumors with cancer stem cell (CSC) characteristics inhibit metastatic growth by inducing intracellular ROS/DNA double-stranded damage, thus inhibiting G2/M phase accumulation. We found that miR-1 was the most abundant in pTDEs and showed a stronger inhibitory effect when miR-1 was overloaded in pTDEs. Collectively, we demonstrated that the primary tumor could control distant metastatic cancer via primary tumor-derived EV-miR-1. Additionally, our approach suggests the development of anticancer drugs for metastasis based on pTDE-miR-1.

cancer biology↗

bioRxiv2022

Integrative mapping of the dog epigenome: reference annotation for comparative inter-tissue and cross-species studies

The domestic dog has become a valuable model in exploring multifaceted diseases and biology important for human health. Large-scale dog genome projects produced high-quality draft references but still lack comprehensive annotation of encoded functional elements. Through the integrative next generation sequencing of transcriptomes paired with histone marks and DNA methylome profiling of 11 adult tissue types, implemented in a cross-species approach, we generated a reference epigenome of a domesticated dog. Using genome orthologues and synthenies, we deciphered the dogs epigenetic code by defining distinct chromatin states, allowing for genome-wide, integratable data production. We then characterized somatic super-enhancer landscapes and showed that genes mapped on these regions are associated with a broad range of biological and disease traits and are traceable to their tissue-of-origin. Ultimately, we delineated conserved epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog for comparative biology and medical research.

genomics↗