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Venetia Pliatsika1, Tess Cherlin1, Phillipe Loher1
1Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
Nucleic acids research
|October 16, 2023
概括
线粒体和核rRNA碎片数据库 (MINRbase) 可访问超过13万个来自核糖核糖核糖核酸的碎片 (rRF). 该资源揭示了rRF生产受个人属性和生物背景的调节.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 核糖体RNA衍生碎片 (rRFs) 越来越多地被认可为它们的生物作用.
- 了解rRFs的起源和监管对于各种研究领域至关重要.
- 现有的研究rRF的资源在范围和可访问性方面是有限的.
研究的目的:
- 介绍MINRbase,这是一个全面的数据库,用于探索人类核和线粒体rRNA衍生碎片 (rRFs).
- 为研究人员提供一个用户友好的平台,用于查询和分析rRF表达式配置文件.
- 促进关于rRF生物发生和调节的新发现.
主要方法:
- 从 11,632 个公共数据集 (GEUVADIS,TCGA) 中编制了 130,238 个表达的 rRF 资料.
- 开发一个交互式Web界面,用于基于序列,丰度和元数据的复杂查询.
- 集成详细的表达式摘要和可视化工具,用于准备出版的图表.
主要成果:
- MINRbase提供了从人类核 (18S,5.8S,28S,5S) 和线粒体 (12S,16S) 的rRNA和45S前rRNA间隔器的rRF.
- 分析显示,45S前rRNA内部间隔器是丰富的rRFs的重要来源.
- rRF生产表现出一个受个人属性 (性别,祖先) 和生物背景 (组织类型,疾病) 影响的规范模式.
结论:
- 对于rRF研究社区来说,MINRbase是一个有价值的知识库.
- 该数据库支持关于rRF起源的新发现,包括来自rRNA边界和间隔器的新发现.
- rRF表达受到宿主特异性因素和细胞状态的显著调节,突出了它们作为生物标志物的潜力.
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