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Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP - Mol. Syst. Biol. (2008)

Bottom Line: Based on these results, we define and characterize two modules composed of muscle- and epidermal-specifying transcription factors that function together within a single cell lineage to robustly specify multiple cell types.The expression of these two modules, although positively regulated by a common factor, is reliably segregated among daughter cells.The coupling of asynchronous and topologically distinct modules may be a general principle of module assembly that functions to potentiate genetic switches.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage-specific transcriptional regulatory network. These data are supported by selected reporter gene analyses and comprehensive yeast one-hybrid and promoter sequence analyses. Based on these results, we define and characterize two modules composed of muscle- and epidermal-specifying transcription factors that function together within a single cell lineage to robustly specify multiple cell types. The expression of these two modules, although positively regulated by a common factor, is reliably segregated among daughter cells. Our analyses indicate that these modules repress each other, and we propose that this cross-inhibition coupled with their relative time of induction function to enhance the initial asymmetry in their expression patterns, thus leading to the observed invariant gene expression patterns and cell lineage. The coupling of asynchronous and topologically distinct modules may be a general principle of module assembly that functions to potentiate genetic switches.

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A perturbation–expression matrix for a set of lineage-specific TFs. The graph indicates the fold increase or decrease (RNAi relative to untreated) and statistical significance (Z-score) for the effect of each TF RNAi (columns) on each TF expression level (rows). The time point with the largest fold-change was selected. Where the fold change is less than 1.3 fold, a small gray circle is shown. The rows and columns are organized by spatial expression pattern of each TF with the same color scheme as in Figure 1. Muscle and epidermal submatrices are outlined by gray and yellow dashed lines, respectively. Positive yeast one-hybrid results are indicated by gray squares and represent the interaction between the TF protein (column) and 1.5 kb of noncoding DNA sequence 5′ of a particular TF gene (row). All yeast one-hybrid combinations were tested with the exception of those involving the promoter of lin-26, which is a member of an operon. tbx-8 and tbx-9 are chromosomal neighbors transcribed in opposing directions, and consequently share a putative promoter region. Positive results for TBX-8 and TBX-9 have been combined (See Supplementary Figure 2 for complete data set).
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f2: A perturbation–expression matrix for a set of lineage-specific TFs. The graph indicates the fold increase or decrease (RNAi relative to untreated) and statistical significance (Z-score) for the effect of each TF RNAi (columns) on each TF expression level (rows). The time point with the largest fold-change was selected. Where the fold change is less than 1.3 fold, a small gray circle is shown. The rows and columns are organized by spatial expression pattern of each TF with the same color scheme as in Figure 1. Muscle and epidermal submatrices are outlined by gray and yellow dashed lines, respectively. Positive yeast one-hybrid results are indicated by gray squares and represent the interaction between the TF protein (column) and 1.5 kb of noncoding DNA sequence 5′ of a particular TF gene (row). All yeast one-hybrid combinations were tested with the exception of those involving the promoter of lin-26, which is a member of an operon. tbx-8 and tbx-9 are chromosomal neighbors transcribed in opposing directions, and consequently share a putative promoter region. Positive results for TBX-8 and TBX-9 have been combined (See Supplementary Figure 2 for complete data set).

Mentions: Analysis of the Drosophila segment polarity and dorsoventral gene regulatory networks has revealed substantial regulatory interactions among and between TFs and signaling molecules (Lawrence and Struhl, 1996; Stathopoulos et al, 2002). To identify potential regulatory effects among the set of all pal-1-regulated TFs, we examined the expression of each TF mRNA following RNAi of each other TF. The results are presented graphically in Figure 2. We found that the RNAi treatment was effective at decreasing transcript abundance of the target mRNA as indicated by the green circles along the diagonal of Figure 2. The left-most column of Figure 2 shows the effect of pal-1 RNAi on expression of each of the TFs, demonstrating that the TFs in the experiment do in fact mostly behave like PAL-1 targets, as their expression decreased following pal-1 RNAi. However, unc-120 expression appears to increase following pal-1 RNAi. This result is at odds with multiple microarray and reporter gene experiments and may indicate either a transient response to pal-1 inhibition that is subsequently resolved (Baugh et al, 2005a; Fukushige et al, 2006), or could be due to the mex-3 mutant background used for these studies. The other exception is elt-1, which despite the microarray data, we have validated as a pal-1 target by analysis of reporter constructs (see below). In addition, the known dependence of elt-3 and lin-26 expression upon elt-1 function (Gilleard et al, 1999b; Landmann et al, 2004) and the positive regulation of vab-7 by tbx-8,9 (Pocock et al, 2004b) are readily apparent in the data (Figure 2).


Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression.

Yanai I, Baugh LR, Smith JJ, Roehrig C, Shen-Orr SS, Claggett JM, Hill AA, Slonim DK, Hunter CP - Mol. Syst. Biol. (2008)

A perturbation–expression matrix for a set of lineage-specific TFs. The graph indicates the fold increase or decrease (RNAi relative to untreated) and statistical significance (Z-score) for the effect of each TF RNAi (columns) on each TF expression level (rows). The time point with the largest fold-change was selected. Where the fold change is less than 1.3 fold, a small gray circle is shown. The rows and columns are organized by spatial expression pattern of each TF with the same color scheme as in Figure 1. Muscle and epidermal submatrices are outlined by gray and yellow dashed lines, respectively. Positive yeast one-hybrid results are indicated by gray squares and represent the interaction between the TF protein (column) and 1.5 kb of noncoding DNA sequence 5′ of a particular TF gene (row). All yeast one-hybrid combinations were tested with the exception of those involving the promoter of lin-26, which is a member of an operon. tbx-8 and tbx-9 are chromosomal neighbors transcribed in opposing directions, and consequently share a putative promoter region. Positive results for TBX-8 and TBX-9 have been combined (See Supplementary Figure 2 for complete data set).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2267734&req=5

f2: A perturbation–expression matrix for a set of lineage-specific TFs. The graph indicates the fold increase or decrease (RNAi relative to untreated) and statistical significance (Z-score) for the effect of each TF RNAi (columns) on each TF expression level (rows). The time point with the largest fold-change was selected. Where the fold change is less than 1.3 fold, a small gray circle is shown. The rows and columns are organized by spatial expression pattern of each TF with the same color scheme as in Figure 1. Muscle and epidermal submatrices are outlined by gray and yellow dashed lines, respectively. Positive yeast one-hybrid results are indicated by gray squares and represent the interaction between the TF protein (column) and 1.5 kb of noncoding DNA sequence 5′ of a particular TF gene (row). All yeast one-hybrid combinations were tested with the exception of those involving the promoter of lin-26, which is a member of an operon. tbx-8 and tbx-9 are chromosomal neighbors transcribed in opposing directions, and consequently share a putative promoter region. Positive results for TBX-8 and TBX-9 have been combined (See Supplementary Figure 2 for complete data set).
Mentions: Analysis of the Drosophila segment polarity and dorsoventral gene regulatory networks has revealed substantial regulatory interactions among and between TFs and signaling molecules (Lawrence and Struhl, 1996; Stathopoulos et al, 2002). To identify potential regulatory effects among the set of all pal-1-regulated TFs, we examined the expression of each TF mRNA following RNAi of each other TF. The results are presented graphically in Figure 2. We found that the RNAi treatment was effective at decreasing transcript abundance of the target mRNA as indicated by the green circles along the diagonal of Figure 2. The left-most column of Figure 2 shows the effect of pal-1 RNAi on expression of each of the TFs, demonstrating that the TFs in the experiment do in fact mostly behave like PAL-1 targets, as their expression decreased following pal-1 RNAi. However, unc-120 expression appears to increase following pal-1 RNAi. This result is at odds with multiple microarray and reporter gene experiments and may indicate either a transient response to pal-1 inhibition that is subsequently resolved (Baugh et al, 2005a; Fukushige et al, 2006), or could be due to the mex-3 mutant background used for these studies. The other exception is elt-1, which despite the microarray data, we have validated as a pal-1 target by analysis of reporter constructs (see below). In addition, the known dependence of elt-3 and lin-26 expression upon elt-1 function (Gilleard et al, 1999b; Landmann et al, 2004) and the positive regulation of vab-7 by tbx-8,9 (Pocock et al, 2004b) are readily apparent in the data (Figure 2).

Bottom Line: Based on these results, we define and characterize two modules composed of muscle- and epidermal-specifying transcription factors that function together within a single cell lineage to robustly specify multiple cell types.The expression of these two modules, although positively regulated by a common factor, is reliably segregated among daughter cells.The coupling of asynchronous and topologically distinct modules may be a general principle of module assembly that functions to potentiate genetic switches.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
Biological networks are inherently modular, yet little is known about how modules are assembled to enable coordinated and complex functions. We used RNAi and time series, whole-genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage-specific transcriptional regulatory network. These data are supported by selected reporter gene analyses and comprehensive yeast one-hybrid and promoter sequence analyses. Based on these results, we define and characterize two modules composed of muscle- and epidermal-specifying transcription factors that function together within a single cell lineage to robustly specify multiple cell types. The expression of these two modules, although positively regulated by a common factor, is reliably segregated among daughter cells. Our analyses indicate that these modules repress each other, and we propose that this cross-inhibition coupled with their relative time of induction function to enhance the initial asymmetry in their expression patterns, thus leading to the observed invariant gene expression patterns and cell lineage. The coupling of asynchronous and topologically distinct modules may be a general principle of module assembly that functions to potentiate genetic switches.

Show MeSH