Rao Aliz R, Pellegrini Matteo
Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA.
BMC Syst Biol. 2011 Oct 12;5:160. doi: 10.1186/1752-0509-5-160.
When growing budding yeast under continuous, nutrient-limited conditions, over half of yeast genes exhibit periodic expression patterns. Periodicity can also be observed in respiration, in the timing of cell division, as well as in various metabolite levels. Knowing the transcription factors involved in the yeast metabolic cycle is helpful for determining the cascade of regulatory events that cause these patterns.
Transcription factor activities were estimated by linear regression using time series and genome-wide transcription factor binding data. Time-translation matrices were estimated using least squares and were used to model the interactions between the most significant transcription factors. The top transcription factors have functions involving respiration, cell cycle events, amino acid metabolism and glycolysis. Key regulators of transitions between phases of the yeast metabolic cycle appear to be Hap1, Hap4, Gcn4, Msn4, Swi6 and Adr1.
Analysis of the phases at which transcription factor activities peak supports previous findings suggesting that the various cellular functions occur during specific phases of the yeast metabolic cycle.
在持续的营养限制条件下培养出芽酵母时，超过一半的酵母基因呈现出周期性表达模式。在呼吸作用、细胞分裂时间以及各种代谢物水平中也能观察到周期性。了解参与酵母代谢周期的转录因子有助于确定导致这些模式的调控事件级联。
通过使用时间序列和全基因组转录因子结合数据的线性回归来估计转录因子活性。使用最小二乘法估计时间平移矩阵，并用于模拟最显著转录因子之间的相互作用。顶级转录因子具有涉及呼吸作用、细胞周期事件、氨基酸代谢和糖酵解的功能。酵母代谢周期各阶段之间转换的关键调节因子似乎是Hap1、Hap4、Gcn4、Msn4、Swi6和Adr1。
对转录因子活性达到峰值的阶段进行分析，支持了先前的研究结果，即各种细胞功能在酵母代谢周期的特定阶段发生。
