转录因子结合位点的位置特定演变,以及F81模型的快速概率计算
Pavitra Selvakumar1,2, Rahul Siddharthan1,2
1The Institute of Mathematical Sciences, Chennai, India.
Royal Society open science
|January 25, 2024
概括
新的位置特定静止向量 (PSSV) 揭示了核酸适应性如何塑造转录因子结合位 (TFBS) 进化. 这种方法揭示了祖先核酸对DNA序列施加的进化压力.
科学领域:
- 进化生物学是进化的生物学.
- 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:
- 转录因子结合位 (TFBS) 是调节基因表达的关键DNA序列.
- 了解TFBS的进化动态对于破译基因调节至关重要.
- 现有的模型通常假设均的核酸进化,这可能不准确地代表功能性DNA位点,如TFBS.
研究的目的:
- 引入和验证一种新的方法,位置特定静止向量 (PSSV),用于分析TFBS演变.
- 在描述TFBS核酸分布时,将PSSV与传统的位置重量矩阵 (PWM) 进行比较.
- 研究祖先核酸对TFBS进化轨迹的影响.
主要方法:
- 用两个既定的进化模型推断人类转录因子的PSSV:Felsenstein 1981 (F81) 和Hasegawa-Kishino-Yano 1985 (HKY85).
- 将推断的PSSV与从PWM中得出的核酸分布进行了比较.
- 根据推断的祖先核酸状态计算条件PSSV,以评估进化压力.
主要成果:
- PSSVs成功地捕获TFBS内的核酸分布,类似于PWMs,但具有潜在降低的特异性.
- 分析显示,某些祖先核酸对TFBS中的邻近序列施加了显著的进化压力.
- 为F81模型开发了一个计算效率高的概率计算,使得大规模的TFBS进化研究成为可能.
结论:
- PSSV提供了一种关于TFBS序列组成和功能的新的,基于进化的观点.
- 推断出的进化压力凸显了TFBS中核酸身份,位置和功能约束之间的复杂相互作用.
- 开发的计算方法促进了进化序列分析在TFBS研究中的更广泛应用.
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