Muskhelishvili Georgi, Sobetzko Patrick, Geertz Marcel, Berger Michael
Jacobs University, School of Engineering and Sciences, Campus Ring 1, D-28759 Bremen, Germany.
Mol Biosyst. 2010 Apr;6(4):662-76. doi: 10.1039/b909192k. Epub 2010 Feb 8.
Recent advances of systemic approaches to gene expression and cellular metabolism provide unforeseen opportunities for relating and integrating extensive datasets describing the transcriptional regulation system as a whole. However, due to the multifaceted nature of the phenomenon, these datasets often contain logically distinct types of information determined by underlying approach and adopted methodology of data analysis. Consequently, to integrate the datasets comprising information on the states of chromatin structure, transcriptional regulatory network and cellular metabolism, a novel methodology enabling interconversion of logically distinct types of information is required. Here we provide a holistic conceptual framework for analysis of global transcriptional regulation as a system coordinated by structural coupling between the transcription machinery and DNA topology, acting as interdependent sensors and determinants of metabolic functions. In this operationally closed system any transition in physiological state represents an emergent property determined by shifts in structural coupling, whereas genetic regulation acts as a genuine device converting one logical type of information into the other.
系统方法在基因表达和细胞代谢方面的最新进展为关联和整合描述整个转录调控系统的大量数据集提供了意想不到的机会。然而，由于该现象具有多面性，这些数据集通常包含由基础方法和所采用的数据分析方法决定的逻辑上不同类型的信息。因此，为了整合包含染色质结构状态、转录调控网络和细胞代谢信息的数据集，需要一种能够实现逻辑上不同类型信息相互转换的新方法。在这里，我们提供了一个整体概念框架，用于将全局转录调控作为一个由转录机制与DNA拓扑结构之间的结构耦合协调的系统进行分析，转录机制与DNA拓扑结构作为相互依赖的代谢功能传感器和决定因素。在这个操作上封闭的系统中，生理状态的任何转变都是由结构耦合的变化所决定的一种涌现特性，而基因调控则作为一种真正的装置，将一种逻辑类型的信息转换为另一种逻辑类型的信息。
