Biology subjects

Chen, T.-C.

Publications and source records attributed to Chen, T.-C..

5 recordsLinked to original sources

bioRxiv2023

The HOMEODOMAIN-Like protein HDL mediates chromatin organization and rewires leaf epidermal patterning

The Arabidopsis leaf epidermis is comprised of trichomes, pavement cells, and stomata, originating from versatile precursor cells capable of dividing or differentiating to create unique epidermal patterns. The mechanism governing these transitions and the maintenance of cell heterogeneity remains unclear. In this study, we identified a novel homeodomain-like superfamily protein, HDL, localized in chromocenters and playing a role in chromatin organization. HDL interacts with histone deacetylase 6 (HDA6) and methyltransferases, indicating its function in modulating chromatin accessibility. In hdl mutants, we observed moderately increased chromatin accessibility in the promoter region of protein-coding genes, along with reduced stomatal density and elevated trichome numbers on leaf surfaces. Corresponding to these phenotypes, stomatal-related gene expression decreased, while a transcriptional reporter for GLABRA2, a trichome initiation gene, exhibited higher and more variable expression levels. These findings highlight how HDL-mediated chromatin organization influences epidermal cell fate by modulating gene expression and enhancing cell heterogeneity within the leaf epidermis. One Sentence SummaryA homeodomain-like protein functions with histone modifiers to regulate chromatin and influence cell fate decisions.

plant biology↗

bioRxiv2023

Virus-derived circular RNAs populate hepatitis C virus-infected cells

It is known that pre-mRNAs in eukaryotic cells can be processed to circular RNAs by a back- splicing mechanism. Circular RNAs have great stability and can sequester proteins or small RNAs to exert functions on cellular pathways. Because viruses often exploit host pathways, we explored whether the RNA genome of the cytoplasmic hepatitis C virus is processed to yield virus-derived circRNAs (vcircRNAs). Computational analyses of RNA-seq experiments predicted that the viral RNA genome is fragmented to generate hundreds of vcircRNAs. More than a dozen of them were experimentally verified by rolling-circle amplification. VcircRNAs that contained the viral internal ribosome entry site were found to be translated into novel proteins that displayed pro-viral functions. Furthermore, a highly abundant, non-translated vcircRNA was shown to enhance viral RNA abundance. These findings argue that novel vcircRNA molecules modulate viral amplification in cells infected by a cytoplasmic RNA virus. Significance StatementProcessing of an RNA viral genome into hundreds of circular RNAs provides novel pro-viral functions and can promote translation of novel viral peptides.

microbiology↗

bioRxiv2023

Refined novel techniques for long term cryo-storage using vitrification and laser warming

Vitrification and ultra-rapid laser warming technique is an important approach for cryopreservation of animal embryos and oocytes, as well as other cells with medicinal, genetic, and agricultural value. We believe that the long term cryo-storage after vitrification and for the following laser warming has only been achieved to date using our customized device which was first attempted to be developed in our study. In the present study, we focused on developing alignment and bonding techniques for special cryo-jig which were assembling jig tool and jig holder in one piece. This newly produced customized cryo-jig was demonstrated to have significantly high laser striking accuracy of 95% and a successful rewarming rate of 62%. This study was experimentally demonstrate an refined novel device for improvement of laser striking accuracy after long term cryo-storage using vitrification and laser warming technique. In addition, the customized device described herein was successfully applied to a biological sample with over a thousand coral larvae in long term cryo-storage (The first cryo-repository for coral larvae; the results related to coral cryobanking and repositry described in this preprint will be published separately in details). We anticipate that our core findings will provide further examples of cryobanking applications that use vitrification and nano-laser warming to help a wide range of cells and tissues from diverse species.

bioengineering↗

bioRxiv2020

Host-derived Circular RNAs Display Proviral Activities in Hepatitis C Virus - Infected Cells

Viruses subvert macromolecular pathways in infected host cells to aid in viral gene amplification or to counteract innate immune responses. Roles for host-encoded RNAs, including microRNAs, have been found to provide pro- and anti-viral functions. Recently, circular RNAs (circRNAs), that are generated by a nuclear back-splicing mechanism of pre-mRNAs, have been implicated to have roles in DNA virus-infected cells. This study examines the circular RNA landscape in uninfected and hepatitis C virus (HCV)-infected liver cells. Results showed that the abundances of distinct classes of circRNAs were up-regulated or down-regulated in infected cells. Identified circRNAs displayed pro-viral effects. One particular up-regulated circRNA, circPSD3, displayed a very pronounced effect on viral RNA abundances in both hepatitis C virus- and Dengue virus-infected cells. Surprisingly, circPSD3 also inhibited the cellular nonsense-mediated decay (NMD) pathway in liver cells. Thus, enhanced abundance of circPSD3 in virus-infected cells aids in viral replication and likely contributes to the known inhibition of NMD in HCV-infected cells. Findings from the global analyses of the circular RNA landscape argue pro-, and likely, anti-viral functions are executed by circRNAs that modulate both viral gene expression as well as host pathways. Because of their long half-lives, circRNAs likely play hitherto unknown, important roles in viral pathogenesis. Author SummaryUsually, cells are infected by one or a few virus particles that carry genomes with limited expression capacity. Thus, the expression of viral genomes has to compete with a sea of cellular components that aid in viral translation, replication and virion production. Depending on their lifestyle, viruses have evolved to avoid or to subvert cellular pathways, especially those that display anti-viral functions. Host-derived circular RNA molecules have recently been discovered in the cytoplasm of cells, although, as-of yet, few functions have been assigned to them. Here, we describe alterations in the circular RNA landscape in hepatitis C virus-infected liver cells. Up-regulated and down-regulated circular RNAs were identified, and three of the upregulated RNAs were shown to promote HCV infection. One of them, circPSD3, inhibited the cellular nonsense-mediated RNA decay that is a powerful antiviral response in infected cells. Because circular RNAs are more stable than linear RNAs, they may have important functions during viral infection, dictating the outcomes of innate immune responses and viral pathogenesis.

microbiology↗

bioRxiv2019

Selection of a Malignant Subpopulation from a Colorectal Cancer Cell Line

Colorectal cancer (CRC) is a leading cause of death from cancer worldwide. Thus, there is an emerging need for new experimental models that allow identification and validation of biomarkers for CRC-specific progression. In this study, we propose a repeated sphere-forming assay as a strategy to select a malignant subpopulation from a CRC line, HCT116. We validated our assay by confirming that three canonical stemness markers, Nanog, Oct4, and Lgr5, were up-regulated in the sphere state at every generation of the selection assay. The resulting line, after eight rounds of selection, exhibited an increased sphere-forming capacity in vitro and tumorgenicity in vivo. Furthermore, dipeptidase 1 (DPEP1) was identified as the major differentially expressed gene in the selected clone, and depletion of DPEP1 suppressed the elevated sphere-forming capacity in vitro and tumorgenicity in vivo. Overall, we have established an experimental strategy for the isolation of a malignant subpopulation from a CRC cell line. Results from our model also suggested that DPEP1 can serve as a promising prognostic biomarker for CRC.

cancer biology↗