Biology subjects

Chen, J.-N.

Publications and source records attributed to Chen, J.-N..

4 recordsLinked to original sources

bioRxiv2026

A Continuum of Atrial Peristalsis Initiates the Bicuspid to Quadricuspid Valve Transition

How chamber-specific hemodynamic shear forces coordinate the spatial and temporal patterning of cardiac valves remains poorly understood. The zebrafish atrioventricular (AV) valve transitions from 2-cusp to 4-cusp at 14 days post-fertilization (dpf) through commissural remodeling, differential cell proliferation, and chondrogenic matrix secretion. Orthogonal valvular axes are present at 25 hpf (hours), preceding endocardial cushion formation. AV canal remodeling aligns the shear stress with leaflet formation at 48 hpf and 14 dpf. At 28 hpf, the ventricle develops functional syncytium, while the atrial peristalsis remains and is necessary for the Klf2a-Snai1b signaling in Notch-negative and ccm1-positive endocardial cells. Without atrial contraction, the 2-to 4-cusp transition (86.7%) fails to occur. In the absence of ventricular contraction and relaxation, the formation of the first pair of leaflets (100%) does not initiate. As a corollary, we demonstrate that KLF4/SNAI1 expression at the commissure is conserved in the mammalian AV 2- to 4-cushion transition.

developmental biology↗

bioRxiv2025

A De Novo Design Strategy to Convert FAcD from Dimer to Active Monomer

Enzymes largely exist in various oligomeric states, but monomeric enzymes are more conducive to industrial applications. Converting an oligomeric enzyme into an active monomer is a significant challenge. In this study, we present a de novo design strategy to convert fluoroacetate dehalogenase (FAcD) from its native dimeric form to an active monomer. Using the AI-based method ProteinMPNN, we identified critical protein-protein interaction (PPI) sites at the dimer interface. ArDCA, another AI tool, was employed to pinpoint catalytic hotspots. Six mutants, Mu1-Mu6, were designed. Molecular dynamics (MD) simulations, coupled with mass spectrometry, confirmed that these mutants form stable monomers. The pre-reaction state (PRS) model predicted that three of these mutants exhibited catalytic activity. In particular, Mu5 with 11 mutations from the wild-type, was predicted to have high catalytic activity, and was subsequently confirmed by kinetics experiment, with a kcat of 672.2 min-1 and a T5030 > 100 {degrees}C, comparable to the wild-type enzyme (kcat = 676.3 min-1, T5030 = 84 {degrees}C). Notably, the Y149M mutation increased catalytic activity nearly forty-fold, demonstrating the effectiveness of our design strategy.

bioengineering↗

bioRxiv2023

Rtf1-dependent transcriptional pausing regulates cardiogenesis

Transcriptional pause-release critically regulates cellular RNA biogenesis, yet how dysregulation of this process impacts embryonic development is not fully understood. Rtf1 is a multifunctional transcription regulatory protein involved in modulating promoter-proximal pausing of RNA polymerase II. Using zebrafish and mouse as model systems, we show that Rtf1 activity is essential for the differentiation of the myocardial lineage from mesoderm. Ablation of rtf1 impairs the formation of nkx2.5+/tbx5a+ cardiac progenitor cells, resulting in the development of embryos without cardiomyocytes. Structure-function analysis demonstrates that Rtf1s cardiogenic activity requires its Plus3 domain, which confers interaction with the pausing/elongation factor Spt5. In Rtf1-deficient embryos, the occupancy of RNA Pol II at transcription start sites was reduced relative to downstream occupancy, suggesting a reduction in transcriptional pausing. Intriguingly, attenuating pause release by pharmacological inhibition or morpholino targeting of CDK9 improved RNA polymerase II occupancy at the transcription start sites of key cardiac genes and restored cardiomyocytes in Rtf1-deficient embryos. Thus, our findings demonstrate the crucial role that Rtf1-mediated transcriptional pausing plays in controlling the precise spatio-temporal transcription programs that govern early heart development.

developmental biology↗

bioRxiv2017

The Calcineurin-FoxO-MuRF1 Signaling Pathway Regulates Myofibril Integrity in Cardiomyocytes

Altered Ca2+ handling is often present in diseased hearts undergoing structural remodeling and functional deterioration. The influences of Ca2+ signaling on cardiac function have been examined extensively, but whether Ca2+ directly regulates sarcomere structure has remained elusive. Using a mutant zebrafish model lacking NCX1 activity in the heart, we explored the impacts of impaired Ca2+ homeostasis on myofibril integrity. Gene expression profiling analysis revealed that the E3 ubiquitin ligase MuRF1 is upregulated in ncx1-deficient hearts. Intriguingly, knocking down MuRF1 activity or inhibiting proteasome activity preserved myofibril integrity in ncx1 deficient hearts, revealing a MuRF1-mediated proteasome degradation mechanism that is activated in response to abnormal Ca2+ homeostasis. Furthermore, we detected an accumulation of the MuRF1 regulator FoxO in the nuclei of ncx1-deficient cardiomyocytes. Overexpression of FoxO in wild type cardiomyocytes induced MuRF1 expression and caused myofibril disarray, whereas inhibiting Calcineurin activity attenuated FoxO-mediated MuRF1 expression and protected sarcomeres from degradation in ncx1-deficient hearts. Together, our findings reveal a novel mechanism by which Ca2+ overload disrupts the myofibril integrity in heart muscle cells by activating a Calcineurin-FoxO-MuRF1-proteosome signaling pathway.

cell biology↗