Abstract
BackgroundOscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. Timing of gene expression is controlled by internal molecular clock keeping steady periodic expression. In this study, we shift attention towards a broad range of periodically expressed genes involved in multiple cellular functions which may or may not be under direct control of the intrinsic circadian clock. Are all molecular functions represented in expressed genes at all times? Alternatively, are different molecular functions performed at different times? Is there a pattern of succession for molecular processes and functions throughout their daily activity period?ResultsTo answer these questions, we re-analyzed a number of mouse circadian gene expression data available from public sources. These data represent the normal function of metabolically active peripheral tissues (white adipose tissue, brown adipose tissue, liver). We applied novel methods for the estimation of confidence in phase assignment to identify groups of synchronous genes peaking at the same time regardless of the amplitude or the absolute intensity of expression. Each synchronous group has been annotated to identify Gene Ontology (GO) terms and molecular pathways. Our analysis identified molecular functions specific to a particular time of the day in different tissues.ConclusionImproved methodology for datamining allowed for the discovery of functions and biological pathways in groups of genes with synchronized peak expression time. In particular, such functions as oxidative phase of energy metabolism, DNA repair, mRNA processing, lipid biosynthesis and others are separated in time. This timewise compartmentalization is important for understanding the cellular circuitry and can be used to optimize the time of intervention with drug or genome medication.
Highlights
Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes
The report shows a succession of molecular functions among genes expressed at different times
Data processing The data were normalized using a quantile algorithm similar to the one described by Bolstad et al [13]: xnorm 1⁄4 F−21ðGðxÞÞ where F is the distribution function of the Selection of oscillating expression profiles In this study we did not try to assess how many genes are expressed in oscillating pattern
Summary
Oscillations of different origin, period and amplitude play an important role in the regulation of cellular processes. Most widely studied is the circadian or approximately daily variation in gene expression activity. We shift attention towards a broad range of periodically expressed genes involved in multiple cellular functions which may or may not be under direct control of the intrinsic circadian clock. Is there a pattern of succession for molecular processes and functions throughout their daily activity period?. The question of how many genes oscillate in a circadian (i.e. approximately daily) period has been the subject of many debates [1,2,3,4] and the answers vary with tissue type, experimental conditions, technology, and statistics used to infer oscillating genes. The authors did not connect these observations with circadian molecular clock, but used the same diurnal time scale in their experiments
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