Biology subjects

Shi, D.-L.

Publications and source records attributed to Shi, D.-L..

4 recordsLinked to original sources

bioRxiv2024

N1-methylpseudouridine mRNA modification enhances efficiency and specificity of gene overexpression by preventing Prkra-mediated global translation repression

In vitro transcribed messenger RNA (IVT mRNA) has emerged as a pivotal tool in mRNA-based therapies and has been extensively employed in gene function studies and genetic tool applications. However, the IVT process generates double-stranded RNA (dsRNA) by-products that are recognized by dsRNA sensors, triggering innate immune responses. In this study, we comprehensively analyzed the detrimental effects of dsRNA by-products on early zebrafish embryos, revealing that these by-products induce cell necrosis and delay maternal-zygotic transition by reducing global translation efficiency via Prkra, a recently identified dsRNA sensor in pluripotent cells. Importantly, we demonstrate that N1-methylpseudouridine (m1{varphi}) modification of IVT mRNAs effectively mitigates these adverse effects, as m1{varphi}-modified dsRNAs exhibit significantly lower binding affinity to the Prkra dimer. Our findings underscore a previously overlooked challenge in the use of IVT mRNA in early embryos and offer a robust solution to enhance the fidelity of mRNA applications. Furthermore, we elucidate that m1{varphi} modification minimizes the dsRNA-induced stress response in pluripotent cells through a distinct mechanism.

developmental biology↗

bioRxiv2024

Sirt5 preserves cardiac function in ischemia-reperfusion injury by inhibiting ANT2 lactylation

Myocardial ischemia-reperfusion (IR) injury is the most common type of heart disease. IR-disrupted mitochondrial homeostasis affects heart energy metabolism and function, but the mechanism remains poorly understood. Here we report a cardioprotective role of the mitochondrial protein Sirt5 in a mouse model of cardiac IR injury. The down-regulation of Sirt5 in IR-injured heart is associated with an increased protein lactylation and impaired mitochondrial function. Overexpression of Sirt5 alleviates, whereas conditional knockout of Sirt5 aggravates, mitochondrial damage and cardiac injury. Mechanistically, Sirt5 interacts with the inner mitochondrial membrane protein adenine nucleotide translocase 2 (ANT2), inhibiting its lysine lactylation to promote its association with the outer mitochondrial membrane protein voltage-dependent anion-selective channel 1 (VDAC1). Lactylation-resistant ANT2 efficiently complexes with VDAC1 and improves cardiac function after injury. Therefore, we uncover a Sirt5-regulated interaction of ANT2 and VDAC1 in maintaining mitochondrial homeostasis, highlighting the potential of targeting ANT2 lactylation as a therapeutic strategy in the treatment of cardiac injury. TeaserSirt5 promotes the interaction of mitochondrial proteins to protect mitochondrial homeostasis and improve heart function in ischemia-reperfusion injury.

pathology↗

bioRxiv2024

Prkra is the double-stranded RNA sensor to mediate an embryonic integrated stress response

Double-stranded RNAs (dsRNAs), known as conserved pathogen-associated molecular patterns, are recognized by interferon-induced protein kinase R (PKR) to trigger an integrated stress response, characterized by the inhibition of global translation. However, the interferon system is inactive in pluripotent cells, thus the mechanism underlying dsRNA sensing and translational control is unclear. In this study, we utilized early zebrafish embryos as a model of pluripotent cells and discovered a PKR-independent blockage of translation initiation induced by dsRNA stimulation. Prkra dimer was identified as the genuine dsRNA sensor. Upon binding to dsRNAs, the dimerized dsRNA binding domain 3 becomes activated to sequester the eIF2 complexes from the translation machinery, leading to a hindrance in global protein synthesis. This distinctive embryonic stress response restricts RNA virus SVCV replication in zebrafish embryos but is also conserved in early mouse embryos and embryonic stem cells. Therefore, the Prkra-mediated dsRNA sensing and translation blocking mechanism potentially represents a common strategy for reestablishing physiological homeostasis in response to environmental stresses.

immunology↗

bioRxiv2017

Vegetally Localized Vrtn Functions As A Novel Repressor To Modulate bmp2b Transcription During Dorsoventral Patterning In Zebrafish

The vegetal pole cytoplasm represents a critical source of maternal signals for patterning the primary dorsoventral axis of the early embryo. Vegetally localized dorsal determinants are essential for the formation of the Spemann organizer, which expresses both bone morphogenetic proteins and their antagonists. The extracellular regulation of BMP signalling activity has been well characterized, however, transcriptional regulation of bmp genes along the dorsoventral axis remains largely unknown. Here, we report a novel mode of maternal regulation of BMP signalling in the lateral and ventral regions by analyzing the unexpected dorsalizing effect following vegetal yolk ablation experiment. We identified Vrtn as a novel vegetally localized maternal factor displaying dorsalizing activity. It functions as a novel transcriptional repressor to regulate bmp2b expression in the marginal region. Mechanistically, Vrtn binds bmp2b upstream sequence and inhibits its transcription independently of maternal Wnt/{beta}-catenin signalling. By creating vrtn loss-of-function mutation and analyzing maternal-zygotic mutant embryos, we further showed that Vrtn is required for the formation of dorsoventral axis. Our work thus unveils a novel maternal mechanism regulating BMP gradient during dorsoventral specification.

developmental biology↗