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Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans
Database: The Journal of Biological Databases and Curation ( IF 5.8 ) Pub Date : 2021-04-23 , DOI: 10.1093/database/baab025
Tzu-Hsien Yang, Chung-Yu Wang, Hsiu-Chun Tsai, Cheng-Tse Liu

It is now known that cap-independent translation initiation facilitated by internal ribosome entry sites (IRESs) is vital in selective cellular protein synthesis under stress and different physiological conditions. However, three problems make it hard to understand transcriptome-wide cellular IRES-mediated translation initiation mechanisms: (i) complex interplay between IRESs and other translation initiation–related information, (ii) reliability issue of in silico cellular IRES investigation and (iii) labor-intensive in vivo IRES identification. In this research, we constructed the Human IRES Atlas database for a comprehensive understanding of cellular IRESs in humans. First, currently available and suitable IRES prediction tools (IRESfinder, PatSearch and IRESpy) were used to obtain transcriptome-wide human IRESs. Then, we collected eight genres of translation initiation–related features to help study the potential molecular mechanisms of each of the putative IRESs. Three functional tests (conservation, structural RNA–protein scores and conditional translation efficiency) were devised to evaluate the functionality of the identified putative IRESs. Moreover, an easy-to-use interface and an IRES–translation initiation interaction map for each gene transcript were implemented to help understand the interactions between IRESs and translation initiation–related features. Researchers can easily search/browse an IRES of interest using the web interface and deduce testable mechanism hypotheses of human IRES-driven translation initiation based on the integrated results. In summary, Human IRES Atlas integrates putative IRES elements and translation initiation–related experiments for better usage of these data and deduction of mechanism hypotheses. Database URL: http://cobishss0.im.nuk.edu.tw/Human_IRES_Atlas/

中文翻译:

Human IRES Atlas:一个用于研究 IRES 驱动的人类翻译调控的综合平台

现在已知,由内部核糖体进入位点 (IRES) 促进的不依赖帽的翻译起始对于压力和不同生理条件下的选择性细胞蛋白质合成至关重要。然而,三个问题使得难以理解转录组范围的细胞 IRES 介导的翻译起始机制:(i)IRES 与其他翻译起始相关信息之间的复杂相互作用,(ii)计算机 IRES 研究的可靠性问题和(iii)劳动密集型体内IRES鉴定。在这项研究中,我们构建了人类 IRES Atlas 数据库,以全面了解人类的细胞 IRES。首先,使用当前可用且合适的 IRES 预测工具(IRESfinder、PatSearch 和 IRESpy)来获得转录组范围的人类 IRES。然后,我们收集了八种与翻译起始相关的特征,以帮助研究每种推定的 IRES 的潜在分子机制。设计了三种功能测试(保守性、结构 RNA-蛋白质评分和条件翻译效率)来评估已识别的推定 IRES 的功能。此外,实现了每个基因转录本的易于使用的界面和 IRES 翻译起始相互作用图,以帮助理解 IRES 和翻译起始相关特征之间的相互作用。研究人员可以使用 Web 界面轻松搜索/浏览感兴趣的 IRES,并根据综合结果推断人类 IRES 驱动的翻译启动的可测试机制假设。总之,人类 IRES Atlas 整合了推定的 IRES 元素和翻译起始相关实验,以更好地使用这些数据和推断机制假设。数据库网址:http://cobishss0.im.nuk.edu.tw/Human_IRES_Atlas/
更新日期:2021-04-23
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