Biology subjects

Ryu, K. H.

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

4 recordsLinked to original sources

bioRxiv2026

Cell-specific dedifferentiation in Arabidopsis thaliana

Single somatic plant cells are capable of dedifferentiation and reversion to totipotency. However, understanding of dedifferentiation remains incomplete, limiting efforts to reprogram plant cell identities with engineered properties. Here, we describe the transcriptional dynamics of 125,091 Arabidopsis thaliana whole seedling protoplasts along a time course of dedifferentiation and varied chemical perturbations using single-cell RNA sequencing. We observed widespread cell-type-specific transcriptional reprogramming concomitant with cell wall digestion, including a guard cell-specific somatic embryogenic-like program initiated by ectopic LEC2 expression. Contrasting cell states between chemical perturbations across real time revealed that phytohormones antagonize cell aging, promote retention of transcriptional diversity, and selectively suppress wound responses. By dissecting time-resolved transcriptional dynamics, we discovered that dedifferentiation is accompanied by the activation of stem-cell and meristematic marker genes and associated with prevalent chromatin remodeling. Despite discovery of a shared regulatory program underlying early dedifferentiation, temporal modeling of diverse somatic cell types uncovered extensive bias in dedifferentiation potential, including epithem-derived dedifferentiated cells, variable dedifferentiation rates, and diversity in early reprogramming outcomes as a major source of in vitro heterogeneity. Taken together, these data showcase how initial somatic cell identity, phytohormone signaling, chromatin remodeling, and reprogramming heterogeneity combine to coordinate the early transcriptional events defining cellular dedifferentiation.

plant biology↗

bioRxiv2025

scCoBench: Benchmarking single cell RNA-seq co-expression using promoter-reporter lines

Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for uncovering transcriptomic heterogeneity and reconstructing gene regulatory networks in complex tissues. However, the sparsity, high noise levels, and dropout events inherent to scRNA-seq data pose challenges for accurate inference of gene-gene relationships. In this study scCoBench, we systematically benchmark correlation metrics, pseudo bulk analysis, and imputation methods using promoter-reporter and native gene pairs as internal controls to evaluate the performance of ten widely used gene-gene co-expression measurements. Interestingly, we found that commonly used data scaling and normalization approaches lead to lower correlation between promoter reporter and native gene pairs in most of the co-expression methods. Moreover, we assess the impact of five popular imputation techniques, including scImpute, SAVER, Autoencoder (AE), Variational Autoencoder (VAE), and Generative Adversarial Network (GAN) on recovering biologically relevant co-expression patterns. Our results demonstrate that imputation models not only markedly enhance correlation between each promoter-reporter and native gene pair but also increase the number of cells co-expressing both genes. Imputation also improved transcription factor target gene correlations and revealed stronger associations among genes within the same protein complex. This work highlights the utility of promoter-reporter systems for benchmarking computational methods and underscores the potential of deep learning-based imputation to improve the biologically relevant signals of scRNA-seq data.

bioinformatics↗

bioRxiv2024

Diversification of gene expression across extremophytes and stress-sensitive species in the Brassicaceae

Plants are composed of diverse cell types that facilitate adaptations to the environment, yet cross-species comparisons of such response programs at single-cell resolution remain scarce. To explore this diversity, here we profiled >200,000 root cells from five Brassicaceae species, including stress-sensitive species (Arabidopsis thaliana, Sisymbrium irio), extremophytes (Eutrema salsugineum, Schrenkiella parvula), and the polyploid crop Camelina sativa under control, NaCl, and abscisic acid (ABA) treatments. We developed a computational pipeline to characterize the conservation and divergence of cell-type gene expression across the Brassicaceae, revealing that approximately half of previously defined Arabidopsis cell-type markers fail to maintain conserved expression in one or more non-Arabidopsis species. Therefore, we curated a refined set of pan-Brassicaceae markers and identified orthologs whose expression profiles have diverged across lineages. Using in situ hybridization, we mapped distinct cortex subpopulations to specific cortical layers across species, and found flavonoid biosynthesis programs preferentially localized to the inner cortex layer, linking cortex-layer specification to metabolic specialization. Cell-type contributions to stress responses differed among species and across treatments, with lineage-specific losses of responsiveness occurring less frequently but evolutionarily more favored than lineage-specific gains. In C. sativa, sub-genomes contributed equally to stress responses, and homeologs with divergent responses typically lacked other signatures of functional divergence. Together, this work establishes a foundational root single-cell atlas and an analytical framework for multi-species comparative transcriptomics, providing insights into how stress responses diversify across cell types, stress-sensitive to stress-adapted species, and in crop lineages.

plant biology↗

bioRxiv2020

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana

Similar to other complex organisms, plants consist of diverse and highly specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs and their associated regulatory mechanisms. Recently, single cell transcriptomic approaches have been applied on Arabidopsis thaliana root protoplasts allowing the accurate characterization of the transcriptional profiles of the cell-types composing seedling roots. As a first step in gaining a deeper understanding of the regulatory mechanisms controlling Arabidopsis gene expression, we report the use of single nucleus RNA sequencing (sNucRNA-seq) and single nucleus Assay for Transposase Accessible Chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single nuclei transcriptomes to previously published protoplast transcriptomes validated the use of nuclei as biological entities to establish cell-type specific transcriptomes from multicellular organs. Furthermore, our sNucRNA-seq results uncovered the transcriptome of additional cell subtypes not identified by scRNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters suggesting the differential remodeling of the chromatin between groups of cells according to their identity. To reveal the impact of chromatin remodeling on gene transcription, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes also display cell-type-specific pattern of chromatin accessibility. Our data suggest that the differential remodeling of the chromatin is a critical mechanism to regulate gene activity at the cell-type level.

plant biology↗