Abstract
BackgroundIn addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. For example, genes with H3K27me3 chromatin marks are not only suppressed but also poised for activation. However, the responsiveness of genes to perturbations has never been studied systematically. To distinguish gene responses to specific factors from responsiveness in general, it is necessary to analyze gene expression profiles of cells responding to a large variety of disturbances, and such databases did not exist before.ResultsWe estimated the responsiveness of all genes in mouse ES cells using our recently published database on expression change after controlled induction of 53 transcription factors (TFs) and other genes. Responsive genes (N = 4746), which were readily upregulated or downregulated depending on the kind of perturbation, mostly have regulatory functions and a propensity to become tissue-specific upon differentiation. Tissue-specific expression was evaluated on the basis of published (GNF) and our new data for 15 organs and tissues. Non-responsive genes (N = 9562), which did not change their expression much following any perturbation, were enriched in housekeeping functions. We found that TF-responsiveness in ES cells is the best predictor known for tissue-specificity in gene expression. Among genes with CpG islands, high responsiveness is associated with H3K27me3 chromatin marks, and low responsiveness is associated with H3K36me3 chromatin, stronger tri-methylation of H3K4, binding of E2F1, and GABP binding motifs in promoters.ConclusionsWe thus propose the responsiveness of expression to perturbations as a new way to define the dynamic status of genes, which brings new insights into mechanisms of regulation of gene expression and tissue specificity.
Highlights
In addition to determining static states of gene expression, it is important to characterize their dynamic status
Gene expression is regulated by the interplay of various kinds of factors including transcription factors (TFs) that bind to DNAs in a sequence-specific manner, the chromatin structure [1,2,3,4], and the association of genes with the nuclear lamina/matrix [5,6]
We found that binding of several TFs (E2F1, ZFX, and MYCN) and the presence of TF binding motifs (NRF1, GABP, and YY1) in proximal regulatory regions are associated with low TF-responsiveness
Summary
In addition to determining static states of gene expression (high vs. low), it is important to characterize their dynamic status. In addition to identifying static states of gene expression (e.g., high vs low) it is types, tissues, and organs [8] It did not distinguish between responsiveness of genes and their tissuespecific expression. This paper examines the responsiveness of all genes in mouse ES cells estimated using our recently published database on gene expression changes after controlled induction of 53 transcription factors (TFs) and other genes [9]. Among genes with CpG islands, responsiveness is strongly associated with their epigenetic marks (e.g., histone modifications such as H3K27me and H3K36me3), as well as with binding of certain TFs in promoters These results suggest that TF-responsiveness can be used as a novel indicator of the dynamic status of genes
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