Biology subjects

Hsiao, Y.-C.

Publications and source records attributed to Hsiao, Y.-C..

14 recordsLinked to original sources

bioRxiv2026

Conserved RGF1 peptide signaling regulates root meristem development through ROS in Arabidopsis and rice

The root meristem is essential for stem cell maintenance and root development in plants. In Arabidopsis, Root meristem Growth Factor (RGF) peptides and their receptors regulate root meristem size through reactive oxygen species (ROS)-dependent signalling. RGF1-mediated ROS redistribution post-translationally stabilises the root meristem master regulator PLETHORA2 (PLT2). Although genomic studies suggest that RGF-receptor modules are evolutionarily conserved across land plants, their functional characterisation has remained largely limited to Arabidopsis. Here, we show that Oryza sativa RGF1-1 (OsRGF1-1) functions as a rice homologue of Arabidopsis RGF1 (AtRGF1). CRISPR/Cas9-generated Osrgf1-1 mutants exhibited shorter seminal roots, reduced root meristem size, and decreased superoxide (O2*-) accumulation. EdU staining further confirmed that cell proliferation activity was reduced in the Osrgf1-1 mutants. The Osrgf1-1 mutants were sensitive to low concentrations of chemically synthesised mature OsRGF1-1 peptide. This low dose of OsRGF1-1 peptide restored seminal root growth and O2*- accumulation in the Osrgf1-1 mutants but had no detectable effect on the wild type. Functional analyses using Arabidopsis rgfr receptor mutants further demonstrated that OsRGF1-1 is perceived through conserved RGF receptor machinery. Together, our findings provide the first functional evidence that the RGF1-receptor-ROS signalling module is evolutionarily conserved between dicots and monocots in the regulation of root meristem development.

plant biology↗

bioRxiv2026

APOBEC3A is the predominant global editor of cytosines in human mRNAs and in single-strand RNA viruses

APOBEC cytidine deaminases can convert cytosines to uracils in DNA as well as in RNA. The knowledge of DNA deamination motifs preferred by individual APOBECs revealed APOBEC3A as a major source of hypermutation in cancer. However, the extent and relative contribution of specific APOBECs into RNA editing remains unclear as their preferred RNA-editing motifs have not been defined. Here, using a parallel DNA and RNA sequencing strategy, coupled with motif-centered statistical analyses, we sought to identify mRNA edits and diagnostic editing motifs in yeast and human cells overexpressing individual APOBEC enzymes. This approach revealed a prevailing global enrichment for the uCg trinucleotide motif with even greater preference to the motifs cytosines located in 3 base of a loop within a hairpin-loop secondary structure when APOBEC3A, but not any other tested APOBEC, was overexpressed. Further analysis revealed the APOBEC3A-like diagnostic motif enrichment in editing calls from human cancers and blood cells. The APOBEC3A-like editing motif also prevailed in the RNA genomes of SARS-CoV-2 pandemic isolates, as well as in infectious persistent rubella viruses, and in polioviruses emerging from live-attenuated vaccine strains. Together, our results indicate that APOBEC3A is the predominant global APOBEC RNA editor with a potential to impact cell physiology and viral evolution.

genetics↗

bioRxiv2025

Root meristem growth factor (RGF) peptide signaling as a molecular bridge between root development and non-lethal thermal stress adaptation

O_LIRoots adapt to temperature ranges that restrict growth but are not lethal. Although lethal heat shock and moderately high temperatures have been studied in detail, the effects of non-lethal high temperatures on root development remain largely unknown. We defined 31{degrees}C as a non-lethal thermal stress in Arabidopsis thaliana and examined its impact on root growth using phenotypic analyses and developmental-zone-specific transcriptomics. C_LIO_LICompared to growth at 22{degrees}C, at 31{degrees}C, primary root growth, meristem size, and superoxide (O2-) accumulation were reduced, and the distribution of the meristem master regulator PLETHORA2 (PLT2) became restricted. Transcriptome analysis revealed a strong downregulation of RGFs, RGFRs, and PLT2, rather than activation of heat shock-inducible genes. C_LIO_LIThese gene mutants were more sensitive to non-lethal thermal stress. In contrast, RGF treatment recovered heat-stress-induced defects. Beyond alleviating the stress in the primary root meristem, RGF treatments promoted lateral root elongation under prolonged non-lethal thermal stress, resulting in a more complex root system. C_LIO_LIThese results indicate that the RGF-RGF receptor-PLT2 pathway plays a central role in root adaptation to non-lethal heat stress rather than the canonical heat shock response pathway and suggest that manipulating RGF signaling could enhance root thermotolerance and crop resilience under elevated temperatures. C_LI

plant biology↗

bioRxiv2025

Motif-Centered Analyses Elucidate Mutagenic Mechanisms Operating in Normal Human Tissues

Somatic mutations are inevitable in human genomes and can lead to tumorigenesis, yet baseline mutagenesis in non-cancerous normal cells remain poorly understood. Here, we analyzed the mutation profiles of 11,949 normal samples across 25 tissues obtained from whole-genome and whole-exome sequencing datasets. We applied stringent statistical hypothesis for detecting enrichment and enrichment-adjusted Minimal Estimate of Mutation Load (MEML) in trinucleotide motifs preferred by known mutagenic processes. We found several cancer-associated mutational motifs in cancer-free tissues. Samples enriched with C[->]T mutations in nCg motif associated with clock-like spontaneous meCpG deamination were detected across all tissues. We revealed another clock-like motif, T[->]C substitutions in aTn motif associated with exposure to small epoxides and other SN2 electrophiles, in several tissues. Donors with several non-cancerous diseases showed significantly higher, age-independent, and concordant accumulation of aTn and nCg motifs compared to healthy donors. Motifs associated with chemical exposures showed sporadic, tissue and disease-specific mutagenesis. APOBEC-induced C[->]T and C[->]G mutations in tCw motif were enriched in bladder, lung, small intestine, liver, and breast with preference for APOBEC3A-like mutagenesis in most. Together, our analyses elucidated several ongoing mutagenic processes in normal human tissues and provided a robust analytical framework for identifying mutagenic sources from somatic mutation catalogues.

genomics↗

bioRxiv2025

Formaldehyde Exposure Induces Systemic Epigenetic Alterations in Histone Methylation and Acetylation

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA-protein crosslinking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, critical for regulating gene expression, may contribute to FA-induced pathogenesis as lysine and arginine residues serve as targets for FA-protein adduct formation. This study aimed to elucidate the effects of FA on histone methylation and acetylation patterns. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (100 M) and high-dose (500 M) FA for 1 hour, and their histone extracts were analyzed using high-resolution liquid chromatography-tandem mass spectrometry-based proteomics, followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79 and changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40, as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimers disease. This study provides novel evidence of FA epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.

pharmacology and toxicology↗

bioRxiv2024

Sex-specific effects of gut microbiome on shaping bile acid metabolism

Gut microbiome is a group of microorganisms that plays important roles in contributing to health and diseases. These bacterial compositions have been demonstrated to impact bile acids (BAs) profiles, either by directly metabolizing primary BAs to secondary BAs or indirect ways through host metabolism by influencing BAs synthesis, transportation and conjugation in liver. It has been observed sexually dimorphic gut microbiome and bile acids composition, with variations in expression levels of bile acid metabolizing genes in the liver. However, associations betweensex-specific differences in gut microbiome and BAs profiles are not well understood. This study aimed to investigate whether gut microbiome could influence BAs profiles in host in a sex-specific manner. We transplanted cecum feces of male and female C57BL/6 mice to male mice and measured BAs concentrations in feces, serum and liver samples 7 days after fecal transplantation. We found different BAs profiles between mice with male and female gut microbiome, including altering levels and proportions of secondary BAs. We also observed varied expression levels of genes related to bile acid metabolism in the liver and distal ileum.Our results highlight sex-specific effects of gut microbiome on shaping bile acid metabolism through gut bacteria and regulation of host genes.

microbiology↗

bioRxiv2024

RGF1 controls PLT2 protein stability through ROS-dependent regulation of a cysteine residue in root meristem development

The protein concentration gradients of the master regulators of the root meristem, named the PLETHORA proteins, modulate the root meristem size. Root meristem growth factor 1 (RGF1) peptide extends the PLETHORA2 (PLT2) protein gradients by altering reactive oxygen species (ROS) distributions. However, the underlying mechanism through which the ROS alterations regulate PLT2 remains unknown. Here, we demonstrate that the 212th cysteine of the PLT2 protein plays a pivotal role in modulating PLT2 stability through the ROS altered by RGF1. The substitution of the 212th cysteine of PLT2 with serine (PLT2C212S) enhanced the PLT2 protein stability upon RGF1 and resulted in robust resistance to ROS relative to the native PLT2. Accordingly, PLT2C212S modulated expressions of certain specific root development-related genes to a greater extent than native PLT2. In summary, these findings show that the PLT2 concentration gradient formation through ROS, modulated by RGF1, is dependent on a mechanism involving the 212th cysteine of PLT2.

plant biology↗

bioRxiv2023

Trans-Lesion Synthesis and Mismatch Repair Pathway Crosstalk Defines Chemoresistance and Hypermutation Mechanisms in Glioblastoma

Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides a new aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define novel molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.

cancer biology↗

bioRxiv2023

Brassinosteroid recruits FERONIA to safeguard cell expansion in Arabidopsis

Plant cell expansion is driven by turgor pressure and regulated by hormones. How plant cells avoid cell wall rupture during hormone-induced cell expansion remains a mystery. Here we show that brassinosteroid (BR), while stimulating cell elongation, promotes the plasma membrane (PM) accumulation of the receptor kinase FERONIA (FER), which monitors cell wall damage and in turn attenuates BR-induced cell elongation to prevent cell rupture. The GSK3-like kinase BIN2 phosphorylates FER, resulting in reduced FER accumulation and translocation from endoplasmic reticulum to PM. By inactivating BIN2, BR signaling promotes dephosphorylation and increases PM accumulation of FER, thereby enhancing the surveillance of cell wall integrity. Our study reveals a vital signaling circuit that coordinates hormone signaling with mechanical sensing to prevent cell bursting during hormone-induced cell expansion. One-Sentence SummaryBrassinosteroid recruits a cell wall integrity monitor to prevent growth-induced cell wall damage.

plant biology↗

bioRxiv2023

Utilization of Eco-friendly Imidazolium-Based Ionic Liquids for Gluten Extraction: Investigating the Influence of Side Chains and Anions

Gluten is a well-known food allergen globally, capable of triggering immune responses in both celiac and non-celiac gluten-sensitive individuals. Gluten comprises two major proteins: glutenin and gliadin. Gliadin, in particular, possesses a unique hydrophobic amino acid sequence. The Food and Drug Administration asserts that the toxicity of gliadin cannot be eliminated through fermentation and hydrolysis processes. A common approach to addressing gluten allergies is to adopt a gluten-free diet. However, the hydrophobic nature of gluten makes its detection challenging. Analysts often resort to using organic solvents or employing multiple procedures to denature gluten for extraction. Its worth noting that while organic solvents can rapidly extract gluten from a sample, they may also alter antibodies, leading to erroneous bio-test results. Ionic liquid (IL) is a highly adaptable green chemical compound consisting of organic salts. We modified imidazolium, a cationic structure, with various carbon side chain lengths (C=0, 1, 3, 5, 7, 9, and 12), and combined it with organic and inorganic anions (e.g., OMs-, Cl-, F-, NO{not}3-, HSO4-, and H2PO4-). We used different IL-to-water ratios to assess gluten solubility. We measured the solubility of gliadin in various imidazolium ILs and conducted kinetic studies on the dissolution of gliadin in 1% [C5DMIM][OMs]aq. Additionally, circular dichroism (CD) spectroscopy and enzyme-linked immunosorbent assay (ELISA) were employed to evaluate the structural changes in gliadin and its interaction with antibodies after treatment with 1% [C5DMIM][OMs]aq. An XTT assay was conducted to assess the cytotoxicity of [C5DMIM][OMs]aq on N2a cells. Our research findings indicate that 1% [C5DMIM][OMs]aq demonstrated excellent gluten solubility, dissolving more than 3000 ppm of gluten within 5 minutes. Importantly, [C5DMIM][OMs]aq did not disrupt the gluten structure, did not impede antibody binding to gluten, and exhibited no cell toxicity. This report highlights [C5DMIM][OMs] as a promising extraction solution for gluten detection.

biochemistry↗

bioRxiv2022

Loss of the intracellular enzyme QPCTL limits chemokine function and reshapes myeloid infiltration to augment tumor immunity

Tumor-associated macrophages are composed of distinct populations arising from monocytes or tissue macrophages, with a poorly understood link to disease pathogenesis. Here, we demonstrate that mouse monocyte migration was supported by glutaminyl-peptide cyclotransferase-like (QPCTL), an enzyme that mediates N-terminal modification of several subtrates, including the monocyte-chemoattractants CCL2 and CCL7, protecting them from proteolytic inactivation. Knockout of Qpctl disrupted monocyte homeostasis, attenuated tumor growth and reshaped myeloid cell infiltration, with loss of monocyte-derived populations with immunosuppressive and pro-angiogenic profiles. Antibody blockade of the receptor CSF1R, which more broadly eliminates tissue macrophages, reversed tumor growth inhibition in Qpctl-/- mice, and prevented lymphocyte infiltration. Modulation of QPCTL synergized with anti-PD-L1 to expand CD8+ T cells and limit tumor growth. QPCTL inhibition constitutes an effective approach for myeloid cell-targeted cancer immunotherapy.

immunology↗

bioRxiv2020

ezGeno: An Automatic Model Selection Package for Genomic Data Analysis

To facilitate the process of tailor-making a deep neural network for exploring the dynamics of genomic DNA, we have developed a hands-on package called ezGeno that automates the search process of various parameters and network structure. ezGeno considers three different sets of search spaces, namely, the number of filters, dilation factors, and the connectivity between different layers. ezGeno can be applied to any kind of 1D genomic input such as genomic sequences, histone modifications, DNase feature data and so on. Combinations of multiple abovementioned 1D features are also applicable. Specifically, for the task of predicting TF binding using genomic sequences as the input, ezGeno can consistently return the best performing set of parameters and network structure, as well as highlight the important segments within the original sequences. For the task of predicting tissue-specific enhancer activity using both sequence and DNase feature data as the input, ezGeno also regularly outperforms the hand-designed models. In this study, we demonstrate that ezGeno is superior in efficiency and accuracy when compared to AutoKeras, a general open-source AutoML package. The average AUC of ezGeno is also consistently higher than the result of using a one-layer DeepBind model. With the flexibility of ezGeno, we expect that this package can provide future researchers not only support of model design in their analysis of genomic studies but also more insights into the regulatory landscape. AvailabilityThe ezGeno package can be freely accessed at https://github.com/ailabstw/ezGeno. ContactDr. Chien-Yu Chen, chienyuchen@ntu.edu.tw

bioinformatics↗

bioRxiv2020

Population-based Carrier Screening and Prenatal Diagnosis of Fragile X Syndrome in East Asian Populations

Identification of carriers of fragile X syndrome (FXS) with the subsequent prenatal diagnosis, and knowledge of FXS-associated genetic profiles are essential for intervention in specific populations. We report the results of carrier screening of 39,458 East Asian adult women and prenatal diagnosis from 87 FXS carriers. The prevalence of FXS carriers and incidence of full mutation fetuses in carrier pregnancies were found to be 1/556 and 11.0%, respectively. The prevalence of FXS carriers and full mutation fetuses was estimated to be 1/581 and 1/3124 in East Asian populations, respectively. We confirmed the validity of the current threshold of CGG repeats for FMR1 categorization; the integral risks of full mutation expansion were approximately 6.0%, 43.8%, and 100% for premutation alleles with 55-74, 75-89, and [≥]90 CGG repeats, respectively. The protective effect of AGG interruption in East Asian populations was validated, which is important in protecting premutation alleles with 75-89 CGG repeats from full mutation expansion. Lastly, family history was shown not an effective indicator for FXS carrier screening in East Asian populations and population-based screening was more cost-effective. This study provides an insight into the largest carrier screening and prenatal diagnosis for FXS in East Asian populations to date. The FXS-associated genetic profiles of East Asian populations are delineated and population-based carrier screening is shown to be promising for FXS intervention.

genetics↗

bioRxiv2019

Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Using high-throughput single-cell B-cell receptor sequencing (scBCR-seq) we obtained accurately paired full-length heavy- and light-chain variable domains from thousands of individual B cells in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells that were subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages that were not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.

immunology↗