Biology subjects

Tung, L.

Publications and source records attributed to Tung, L..

5 recordsLinked to original sources

bioRxiv2025

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

Newly transcribed introns are immediately identified by early splicing factors that recognize the intron 5 splice site (5SS) and branch site (BS). In the budding yeast, these critical splice-site sequences are generally constrained, whereas degeneracy is the rule in higher eukaryotes. Yet, [~]40% of the yeast introns do diverge, to a certain degree, from the canonical sequences. Exactly how these non-canonical introns are recognized and spliced remains unknown. Here we show that the conserved Prp40 WW domains promote non-canonical intron splicing by enhancing stable U1 snRNP and BBP recruitments. AlphaFold predicts a topologically conserved unstructured region between Prp40 WW and FF domains. Alignment of the AlphaFold Prp40 structure with published U1 snRNP structure positions WW domains adjacent to 5SS and Luc7, which is known to be critical for 5SS recognition. Indeed, deletion of this unstructured region negatively impacts on splicing of the non-canonical 5SS introns. Taken together, our results suggest that the conserved WW domains may have evolved to deal with the highly degenerate 5SS and BS sequences in higher eukaryotes, so as to accommodate increased splicing complexity. HighlightsO_LIThe evolutionarily conserved Prp40 WW domains promote splicing of introns harboring non-canonical 5 splice site or branch site. C_LIO_LIPrp40 WW domains enhance stable U1 snRNP and BBP recruitments to nascent transcripts containing non-canonical splice sites. C_LIO_LIA topologically conserved unstructured region between WW and FF domains helps to position Prp40 WW domains close to the 5 splice site. C_LIO_LIThe N-terminal WW domain sterically hinders conformational rearrangements required for efficient release of a BBP variant during spliceosome assembly. C_LIO_LIA reporter assay identified 13 non-canonical introns whose splicing, under various environmental conditions, depend on Prp40 WW domains. C_LI

biochemistry↗

bioRxiv2025

Genome-wide screen uncovers novel host factors for L-A virus maintenance and a mutualistic-symbiosis relationship in yeast

Viruses are often regarded as obligate intracellular parasites that exploit host resources for their own propagation. However, emerging evidence suggests that virus-host interactions can be more complex than simple antagonism. Here, we performed a genome-wide screen in Saccharomyces cerevisiae to identify host factors required for the maintenance of the L-A double-stranded RNA virus, a persistent and non-lytic resident of most laboratory yeast strains. Using two complementary mutant collections encompassing [~]6,000 yeast genes ([~]93% genome coverage), we identified 96 host genes essential for L-A maintenance, spanning diverse biological functions. Transcriptome profiling revealed that the presence of L-A virus alters the host stress-response gene expression program. Strikingly, competitive fitness assays under environmental stress conditions showed that L-A enhances host stress tolerance, revealing a previously unrecognized mutualistic relationship. Together, our findings redefine the L-A-yeast interaction as a form of stable mutualism and highlight the utility of functional genomics and systems-level approaches in uncovering hidden dimensions of virus-host coevolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/655038v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@4bfa69org.highwire.dtl.DTLVardef@25205forg.highwire.dtl.DTLVardef@1703f19org.highwire.dtl.DTLVardef@3e9375_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Computational Study of the Excitation of Human Induced Pluripotent Stem-Cell Derived Cardiomyocytes

Human induced pluripotent stem-cell derived cardiomyocytes (hiPSC-CMs) have proven to be a revolutionary advance for tissue engineering, disease modeling, and drug testing and discovery. Computational modeling enables a detailed electrophysiological analysis that is otherwise difficult or impossible to achieve under strictly experimental settings. Action potential characteristics of hiPSC-CMs measured in our lab at four different pacing rates were used it to modify the computational Kernik-Clancy hiPSC-CM model. The modified model was used to compare the excitation of single hiPSC-CMs with that of single human ventricular cardiomyocytes (hV-CMs) under varying conditions, including at stimulation at different strengths, rates and pulse durations. The physiological stimulation of both hiPSC-CMs and hV-CMs embedded within a tissue strand involves a biphasic waveform during which time excitatory currents (particularly INa, but also ICaT and ICaL for hiPSC-CMs and INaL and ICaL for hV-CMs) are activated during both phases of the waveform. INa in particular activated more slowly and with diminished amplitude under conditions of increasing pacing rate or increasing intracellular resistance. Lastly, histograms characterizing the relative amounts of excitatory currents in a population of hiPSC-CMs become broader with increasing levels of INa block, with ICaT and ICaL working in tandem to excite cells where INa has failed to activate. In general, hiPSC-CMs were found to be more excitable from rest compared with hV-CMs owing to their more depolarized resting potential and intrinsic automaticity despite a lower sodium channel density. Such a mismatch should be taken into consideration for applications using these cells, particularly for cardiac repair. Key PointsO_LICardiomyocytes (CMs) generated from human stem cells derived from blood or skin have great potential for cardiac repair, safety pharmacology and disease modeling, but understanding their excitability is crucial for their proper application. C_LIO_LIComputational modeling reveals greater excitability of these cells in terms of various metrics compared with that of human adult ventricular CMs at multiple pacing rates. C_LIO_LIThe excitation of CMs within a strand differs substantially from that usually used to study single isolated CMs and is dissected in terms of the underlying ionic currents. C_LIO_LIComputational modeling also predicts how a heterogeneous population of stem cell-derived CMs and their underlying ionic currents could respond to varying levels of reduced sodium current. C_LIO_LIOur study presents a cautionary note for applications using these cells, particularly for cardiac repair. C_LI

physiology↗

bioRxiv2020

Optogenetic currents in myofibroblasts acutely alter electrophysiology and conduction of co-cultured cardiomyocytes

Interactions between cardiac myofibroblasts and myocytes may slow conduction after cardiac injury, increasing the chance of life-threatening arrhythmia. While co-culture studies have shown that myofibroblasts can affect cardiomyocyte electrophysiology in vitro, the mechanism(s) remain debatable. In this study, primary neonatal rat cardiac myofibroblasts were transduced with the light-activated ion channel Channelrhodopsin-2, which allowed acute and selective modulation of myofibroblast currents in co-cultures with cardiomyocytes. Optical mapping revealed that myofibroblast-specific optogenetically induced inward currents decreased conduction velocity in the co-cultures by 27{+/-}6% (baseline = 17.7{+/-}5.3 cm/s), and shortened the cardiac action potential duration by 14{+/-}7% (baseline = 161{+/-}11 ms) when 0.017 mW/mm2 light was applied. When light irradiance was increased to 0.057 mW/mm2, the myofibroblast currents led to spontaneous beating in 6/7 co-cultures. Experiments showed that optogenetic perturbation did not lead to changes in myofibroblast strain and force generation, suggesting purely electrical effects in this model. In silico modeling of optogenetically modified myofibroblast-cardiomyocyte co-cultures largely reproduced these results and enabled a comprehensive study of relevant parameters. These results clearly demonstrate that myofibroblasts are sufficiently electrically connected to cardiomyocytes to effectively alter macroscopic electrophysiological properties in this model of cardiac tissue.

physiology↗

bioRxiv2018

NanoMEA: a versatile platform for high-throughput analysis of structure-function relationships in human stem cell-derived excitable cells and tissues

Somatic cells derived from human pluripotent stem cell (hPSC) sources hold significant potential as a means to improve current in vitro screening assays. However, their inconsistent ability to recapitulate the structural and functional characteristics of native cells has raised questions regarding their ability to accurately predict the functional behavior of human tissues when exposed to chemical or pathological insults. In addition, the lack of cytoskeletal organization within conventional culture platforms prevents analysis of how structural changes in human tissues affect functional performance. Using cation-permeable hydrogels, we describe the production of multiwell nanotopographically-patterned microelectrode arrays (nanoMEAs) for studying the effect of structural organization on hPSC-derived cardiomyocyte and neuronal function in vitro. We demonstrate that nanoscale topographic substrate cues promote the development of more ordered cardiac and neuronal monolayers while simultaneously enhancing cytoskeletal organization, protein expression patterns, and electrophysiological function in these cells. We then show that these phenotypic improvements act to alter the sensitivity of hPSC-derived cardiomyocytes to treatment with arrhythmogenic and conduction-blocking compounds that target structural features of the cardiomyocyte. Similarly, we demonstrate that neuron sensitivity to synaptic blockers is increased when cells are maintained on nanotopographically-patterned Nafion surfaces. The improved structural and functional capacity of hPSC-derived cardiomyocyte and neuronal populations maintained on nanoMEAs may have important implications for improving the predictive capabilities of cell-based electrophysiological assays used in preclinical screening applications.

bioengineering↗