论文标题
RNA分子,家庭和网络的统计物理方法
Statistical-physics approaches to RNA molecules, families and networks
论文作者
论文摘要
该贡献着重于引人入胜的RNA分子,其序列依赖性折叠是由碱基对相互作用驱动的,这些相互作用与自然进化之间的相互作用及其多重调节作用。我们四个人使用无序系统的统计物理学的工具和精神挖掘了这些主题,尤其是无序(能量/健身)景观的概念。在介绍了RNA分子和观点之后,它们不仅在进化和合成生物学中开放,而且在医学中开放,我们将为这些分子引入重要的能量和健身景观概念。在第三节中,我们将回顾一些模型和算法,以了解RNA序列至中等结构映射。第四节讨论了如何从解压缩数据得出的二级结构能量格局。 V节介绍了从不同生物体中采样的进化序列数据的RNA结构的推断。这将把焦点从第三节中描述的“序列到结构”映射转变为可以从DNA适体的实验室进化数据推断出的“序列到功能”景观。最后,在第六节中,我们将讨论富裕的理论图片将RNA分子相互作用的网络与健壮的系统性调节程序组织的组织联系起来。因此,我们将探索空间,分子数量和时间的多个尺度的现象,以显示RNA世界的生物复杂性如何通过统计物理学的统一概念来捕获。
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us have dug into these topics using the tools and the spirit of the statistical physics of disordered systems, and in particular the concept of a disordered (energy/fitness) landscape. After an introduction to RNA molecules and the perspectives they open not only in evolutionary and synthetic biology but also in medicine, we will introduce the important notions of energy and fitness landscapes for these molecules. In Section III we will review some models and algorithms for RNA sequence-to-secondary-structure mapping. Section IV discusses how the secondary-structure energy landscape can be derived from unzipping data. Section V deals with the inference of RNA structure from evolutionary sequence data sampled in different organisms. This will shift the focus from the `sequence-to-structure' mapping described in Section III to a `sequence-to-function' landscape that can be inferred from laboratory evolutionary data on DNA aptamers. Finally, in Section VI, we shall discuss the rich theoretical picture linking networks of interacting RNA molecules to the organization of robust, systemic regulatory programs. Along this path, we will therefore explore phenomena across multiple scales in space, number of molecules and time, showing how the biological complexity of the RNA world can be captured by the unifying concepts of statistical physics.