生物信息学模型在预测血管生成翻译控制方面的价值。
Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.
作者信息
Shaposhnikov Michal, Thakar Juilee, Berk Bradford C
机构信息
Department of Cellular and Molecular Pharmacology and Physiology (M.S., B.C.B.), University of Rochester School of Medicine and Dentistry, NY.
Department of Medicine, Aab Cardiovascular Research Institute (M.S., B.C.B.), University of Rochester School of Medicine and Dentistry, NY.
出版信息
Circ Res. 2025 May 9;136(10):1147-1165. doi: 10.1161/CIRCRESAHA.125.325438. Epub 2025 May 8.
Angiogenesis, the formation of new blood vessels, is a fundamental biological process with implications for both physiological functions and pathological conditions. While the transcriptional regulation of angiogenesis, mediated by factors such as HIF-1α (hypoxia-inducible factor 1-alpha) and VEGF (vascular endothelial growth factor), is well-characterized, the translational regulation of this process remains underexplored. Bioinformatics has emerged as an indispensable tool for advancing our understanding of translational regulation, offering predictive models that leverage large data sets to guide research and optimize experimental approaches. However, a significant gap persists between bioinformatics experts and other researchers, limiting the accessibility and utility of these tools in the broader scientific community. To address this divide, user-friendly bioinformatics platforms are being developed to democratize access to predictive analytics and empower researchers across disciplines. Translational control, compared with transcriptional control, offers a more energy-efficient mechanism that facilitates rapid cellular responses to environmental changes. Furthermore, transcriptional regulators themselves are often subject to translational control, emphasizing the interconnected nature of these regulatory layers. Investigating translational regulation requires advanced, accessible bioinformatics tools to analyze RNA structures, interacting micro-RNAs, long noncoding RNAs, and RBPs (RNA-binding proteins). Predictive platforms such as RNA structure, human internal ribosome entry site Atlas, and RBPSuite enable the study of RNA motifs and RNA-protein interactions, shedding light on these critical regulatory mechanisms. This review highlights the transformative role of bioinformatics using widely accessible user-friendly tools with a Web-browser interface to elucidate translational regulation in angiogenesis. The bioinformatics tools discussed extend beyond angiogenesis, with applications in diverse fields, including clinical care. By integrating predictive models and experimental insights, researchers can streamline hypothesis generation, reduce experimental costs, and find novel translational regulators. By bridging the bioinformatics knowledge gap, this review aims to empower researchers worldwide to adopt bioinformatics tools in their work, fostering innovation and accelerating scientific discovery.
血管生成,即新血管的形成,是一个基本的生物学过程,对生理功能和病理状况都有影响。虽然由缺氧诱导因子1α(HIF-1α)和血管内皮生长因子(VEGF)等因子介导的血管生成的转录调控已得到充分表征,但该过程的翻译调控仍未得到充分探索。生物信息学已成为增进我们对翻译调控理解的不可或缺的工具,提供利用大数据集来指导研究和优化实验方法的预测模型。然而,生物信息学专家与其他研究人员之间仍然存在很大差距,限制了这些工具在更广泛科学界的可及性和实用性。为了解决这一差距,正在开发用户友好的生物信息学平台,以使预测分析更普及,并使各学科的研究人员能够更好地利用这些工具。与转录调控相比,翻译控制提供了一种更节能的机制,有助于细胞对环境变化做出快速反应。此外,转录调节因子本身往往也受到翻译控制,这突出了这些调控层面的相互联系。研究翻译调控需要先进的、易于使用的生物信息学工具来分析RNA结构、相互作用的微小RNA、长链非编码RNA和RNA结合蛋白(RBP)。诸如RNA结构、人类内部核糖体进入位点图谱和RBPSuite等预测平台能够研究RNA基序和RNA-蛋白质相互作用,从而揭示这些关键的调控机制。本综述强调了生物信息学的变革性作用,利用具有网络浏览器界面的广泛可用的用户友好工具来阐明血管生成中的翻译调控。所讨论的生物信息学工具不仅适用于血管生成,还应用于包括临床护理在内的多个不同领域。通过整合预测模型和实验见解,研究人员可以简化假设生成、降低实验成本并发现新的翻译调节因子。通过弥合生物信息学知识差距,本综述旨在使全球研究人员能够在其工作中采用生物信息学工具,促进创新并加速科学发现。