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结构:在结构性探测数据中检测异位基特RNA二次结构

Qingru Xu^1,2, Xiaoqiong Bao¹, Zhuobin Lin³

¹State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China.

BMC bioinformatics

|March 1, 2024

概括

一个名为AStruct的新工具可以检测基因变异中的等位基因特异性RNA二次结构 (ASRS). 该工具识别了与基因调节和疾病相关的功能性SNP,改善了我们对遗传变异的理解.

科学领域:

基因组学就是基因组学.
计算生物学计算生物学
在RNA生物学,RNA生物学.

背景情况:

识别功能性遗传变异对于理解基因调节和疾病至关重要.
高通量测序使得基因表达和甲基化等等位基因特异性事件的全基因组研究成为可能.
RNA的二次结构对于RNA的修饰,翻译和拼接至关重要,但对其等位基因特异性分析的工具有限.

研究的目的:

从RT-stop探测数据中开发一种用于检测等位基特定RNA二次结构 (ASRS) 的计算工具.
识别与ASRS相关的遗传变异,并评估它们的功能意义.

主要方法:

开发了一种计算工具"AStruct",该工具利用等位基变异,基配对和RT-stop信息.
验证了AStruct在模拟和公共icSHAPE数据集上的表现.
分析了AStruct识别的SNP的特征.

主要成果:

AStruct准确地检测出异位基因特异性RNA二次结构 (ASRS).
拥有较高AStruct分数的SNP在编码区域中得到了丰富,并被确定为功能性.
这些功能性SNP是保存的,可能会破坏m6A修饰或蛋白质结合部位,并且与疾病有关.

结论:

AStruct是一种新的工具,用于使用RT-stop数据检测异构性SNP中的动态和功能ASRS.
通过考虑动态细胞条件,AStruct的性能优于基于序列的工具.
该工具是用 JAVA 实现的,并公开提供.

关键词:

对等位基特异性的事件.功能变体的功能变体 RNA的二级结构是RNA的二级结构.结构性探测数据的数据.

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