Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity

Alexei A. Sharov, Akira Nishiyama, Yulan Piao, Lina S. Correa-Cerro, Tomokazu Amano, Marshall Thomas, Samir Mehta, Minoru Ko

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Background: In 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.Results: We 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.Conclusions: We 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.

Original languageEnglish
Article number102
JournalBMC Genomics
Volume12
DOIs
Publication statusPublished - 2011 Feb 9
Externally publishedYes

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Histone Code
Organ Specificity
Transcription Factors
Genes
Chromatin
Databases
Gene Expression
Housekeeping
CpG Islands
Gene Expression Regulation
Transcriptome
Methylation
Down-Regulation

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. / Sharov, Alexei A.; Nishiyama, Akira; Piao, Yulan; Correa-Cerro, Lina S.; Amano, Tomokazu; Thomas, Marshall; Mehta, Samir; Ko, Minoru.

In: BMC Genomics, Vol. 12, 102, 09.02.2011.

Research output: Contribution to journalArticle

Sharov, Alexei A. ; Nishiyama, Akira ; Piao, Yulan ; Correa-Cerro, Lina S. ; Amano, Tomokazu ; Thomas, Marshall ; Mehta, Samir ; Ko, Minoru. / Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. In: BMC Genomics. 2011 ; Vol. 12.
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