Stress induces remodelling of yeast interaction and co-expression networks
Stress induces remodelling of yeast interaction and co-expression networks
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DOI：
10.1039/c3mb25548d
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发表时间：
2013-01-01
影响因子：
--
通讯作者：
Pancaldi, Vera
中科院分区：
文献类型：
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作者：
Lehtinen, Sonja;Marsellach, Francesc Xavier;Pancaldi, Vera
网络分析为解释全基因组数据提供了一个强大的框架。虽然静态网络方法已被证明是卓有成效的，但人们对分析不同条件下的蜂窝网络所获得的见解越来越感兴趣。在这项工作中，我们研究了压力对分裂酵母细胞网络的影响。应激引起复杂和大规模的细胞反应，包括将资源从细胞生长和新陈代谢转移到保护和维持。以前的工作表明，这些变化可以在网络层面上得到认可。本文研究了两类细胞网络：基因共调控网络和加权蛋白质相互作用网络。我们表明，为了应对氧化应激，协同调节网络重新组织成一种更模块化的结构：当一组基因变得更紧密地协同调节时，这些模块之间的协同调节减少。这种转变意味着更长的平均最短路径长度、更高的传递性和减少这些网络中的模块重叠。我们还发现，在对氧化应激和氮饥饿的反应中，加权蛋白质相互作用网络在结构上也发生了类似的变化，证实并扩展了先前的发现。网络结构的这些变化可能代表网络健壮性的提高和/或更专业的功能模块的出现。此外，我们发现应激导致非编码RNA的紧密协同调节，降低剪接因子的功能重要性，以及参与染色质组织、细胞骨架组织、细胞分裂和蛋白质周转的基因的中心性改变。
Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks under different conditions. In this work, we study the effect of stress on cellular networks in fission yeast. Stress elicits a sophisticated and large scale cellular response, involving a shift of resources from cell growth and metabolism towards protection and maintenance. Previous work has suggested that these changes can be appreciated at the network level. In this paper, we study two types of cellular networks: gene co-regulation networks and weighted protein interaction networks. We show that in response to oxidative stress, the co-regulation networks re-organize towards a more modularised structure: while sets of genes become more tightly co-regulated, co-regulation between these modules is decreased. This shift translates into longer average shortest path length, increased transitivity, and decreased modular overlap in these networks. We also find a similar change in structure in the weighted protein interaction network in response to both oxidative stress and nitrogen starvation, confirming and extending previous findings. These changes in network structure could represent an increase in network robustness and/or the emergence of more specialised functional modules. Additionally, we find stress induces tighter co-regulation of non-coding RNAs, decreased functional importance of splicing factors, as well as changes in the centrality of genes involved in chromatin organization, cytoskeleton organization, cell division, and protein turnover.