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Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks.

Albergante L, Blow JJ, Newman TJ - Elife (2014)

Bottom Line: The gene regulatory network (GRN) is the central decision-making module of the cell.BQS explains many of the small- and large-scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response.BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, University of Dundee, Dundee, United Kingdom l.albergante@dundee.ac.uk.

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The E. coli GRN.The E. coli GRN derived from Salgado et al. (2012) using two evidence codes. Genes that are reported to regulate transcriptionally at least one other gene, that is transcription factors (TFs), are represented as red circles; the other genes are represented by blue circles. Arrows indicate a transcriptional interaction from the TF to the target gene. The arrows are colour-coded according to the number of genes regulated by the source TF. Note the logarithmic scale in the colour coding.DOI:http://dx.doi.org/10.7554/eLife.02863.003
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fig1: The E. coli GRN.The E. coli GRN derived from Salgado et al. (2012) using two evidence codes. Genes that are reported to regulate transcriptionally at least one other gene, that is transcription factors (TFs), are represented as red circles; the other genes are represented by blue circles. Arrows indicate a transcriptional interaction from the TF to the target gene. The arrows are colour-coded according to the number of genes regulated by the source TF. Note the logarithmic scale in the colour coding.DOI:http://dx.doi.org/10.7554/eLife.02863.003

Mentions: Transcriptional regulation plays a central role in the behaviour of cells in response to environmental cues and is aberrant in many diseases (Lee and Young, 2013). Moreover, networks representing transcriptional interactions have been derived for diverse organisms. These networks, termed ‘gene regulatory networks’ (GRNs), comprise directed links between pairs of genes. For a given pair of linked genes, one encodes a transcription factor (TF) that regulates the expression of the other (Buchanan et al., 2010). Figure 1 shows the GRN of Escherichia coli, with TFs coloured red and the arrows colour-coded according to the number of genes regulated by the source TF. Systematic network analysis of GRNs is possible because comprehensive and high quality GRN datasets are available for different organisms (Lee et al., 2002; Harbison et al., 2004; Luscombe et al., 2004; MacIsaac et al., 2006; Galan-Vasquez et al., 2011; Sanz et al., 2011; Garber et al., 2012; Gerstein et al., 2012; Salgado et al., 2012).10.7554/eLife.02863.003Figure 1.The E. coli GRN.


Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks.

Albergante L, Blow JJ, Newman TJ - Elife (2014)

The E. coli GRN.The E. coli GRN derived from Salgado et al. (2012) using two evidence codes. Genes that are reported to regulate transcriptionally at least one other gene, that is transcription factors (TFs), are represented as red circles; the other genes are represented by blue circles. Arrows indicate a transcriptional interaction from the TF to the target gene. The arrows are colour-coded according to the number of genes regulated by the source TF. Note the logarithmic scale in the colour coding.DOI:http://dx.doi.org/10.7554/eLife.02863.003
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4151086&req=5

fig1: The E. coli GRN.The E. coli GRN derived from Salgado et al. (2012) using two evidence codes. Genes that are reported to regulate transcriptionally at least one other gene, that is transcription factors (TFs), are represented as red circles; the other genes are represented by blue circles. Arrows indicate a transcriptional interaction from the TF to the target gene. The arrows are colour-coded according to the number of genes regulated by the source TF. Note the logarithmic scale in the colour coding.DOI:http://dx.doi.org/10.7554/eLife.02863.003
Mentions: Transcriptional regulation plays a central role in the behaviour of cells in response to environmental cues and is aberrant in many diseases (Lee and Young, 2013). Moreover, networks representing transcriptional interactions have been derived for diverse organisms. These networks, termed ‘gene regulatory networks’ (GRNs), comprise directed links between pairs of genes. For a given pair of linked genes, one encodes a transcription factor (TF) that regulates the expression of the other (Buchanan et al., 2010). Figure 1 shows the GRN of Escherichia coli, with TFs coloured red and the arrows colour-coded according to the number of genes regulated by the source TF. Systematic network analysis of GRNs is possible because comprehensive and high quality GRN datasets are available for different organisms (Lee et al., 2002; Harbison et al., 2004; Luscombe et al., 2004; MacIsaac et al., 2006; Galan-Vasquez et al., 2011; Sanz et al., 2011; Garber et al., 2012; Gerstein et al., 2012; Salgado et al., 2012).10.7554/eLife.02863.003Figure 1.The E. coli GRN.

Bottom Line: The gene regulatory network (GRN) is the central decision-making module of the cell.BQS explains many of the small- and large-scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response.BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation.

View Article: PubMed Central - PubMed

Affiliation: College of Life Sciences, University of Dundee, Dundee, United Kingdom l.albergante@dundee.ac.uk.

Show MeSH
Related in: MedlinePlus