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Dynamic CRM occupancy reflects a temporal map of developmental progression.

Wilczyński B, Furlong EE - Mol. Syst. Biol. (2010)

Bottom Line: CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves.The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development.Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

ABSTRACT
Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

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Relationship between TF binding, motif quality, and temporal occupancy. (A) The distribution of quantitative-binding signal (log2 ChIP peak height) for different temporal classes of CRMs bound by the TF Twist shows that there is a clear distinction between early, continuous, and late CRMs. All TFs are shown in Supplementary Figure 3. (B) Average enrichment of all motifs in CRM classes defined by binding of respective TFs. The appropriate motif is significantly enriched in bound CRMs compared with non-bound CRMs (NB). There is no difference in motif enrichment between the three temporal classes. (C) Quantitative TF binding (ChIP enrichment) is only weakly correlated (Pearson's r=0.192) with motif strength as measured by the PWM log-odds score. Exemplified using Twi binding at 4–6 h, where each dot represents a single CRM (all TFs shown in Supplementary Figures 5 and 6). A number of CRMs with no detectable Twist binding (blue dots) contain high-affinity motifs. (D) Motifs in bound CRMs are significantly more conserved than in non-bound CRMs, but there is no significant difference in motif conservation between temporal classes. NB, non-bound CRMs.
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f2: Relationship between TF binding, motif quality, and temporal occupancy. (A) The distribution of quantitative-binding signal (log2 ChIP peak height) for different temporal classes of CRMs bound by the TF Twist shows that there is a clear distinction between early, continuous, and late CRMs. All TFs are shown in Supplementary Figure 3. (B) Average enrichment of all motifs in CRM classes defined by binding of respective TFs. The appropriate motif is significantly enriched in bound CRMs compared with non-bound CRMs (NB). There is no difference in motif enrichment between the three temporal classes. (C) Quantitative TF binding (ChIP enrichment) is only weakly correlated (Pearson's r=0.192) with motif strength as measured by the PWM log-odds score. Exemplified using Twi binding at 4–6 h, where each dot represents a single CRM (all TFs shown in Supplementary Figures 5 and 6). A number of CRMs with no detectable Twist binding (blue dots) contain high-affinity motifs. (D) Motifs in bound CRMs are significantly more conserved than in non-bound CRMs, but there is no significant difference in motif conservation between temporal classes. NB, non-bound CRMs.

Mentions: We first assessed the temporal occupancy of each TF independently, focusing on regions bound by a TF in at least two consecutive time points (see Materials and methods). As these criteria will eliminate CRMs bound at only a single time point, it provides a very stringent set of combinatorially bound modules (Supplementary Table 1). Even within this conservative definition, unsupervised clustering of binding profiles revealed extensive temporal dynamics (Figure 1A), confirming our earlier findings (Sandmann et al, 2006, 2007; Jakobsen et al, 2007), while extending the analysis genome wide. All TFs examined target three broad classes of CRMs with different temporal occupancy (Figure 1A; Supplementary Figure 2): early bound modules, having TF binding during the first two time points for a given TF, but not later, continuous, occupied at all time points (representing about 50% of CRMs bound by a TF) and late, having binding only at the last two time points and not at earlier stages of development. Therefore, each TF occupies ∼50% of its targeted CRMs in a transient manner; being bound either at early or late stages of development (Supplementary Figure 2). Defining transient occupancy is inherently difficult due to potential false negatives, which can lead to a misclassification of continuous binding. However, measuring the quantitative signal for all CRMs revealed very low levels of occupancy on ‘early' CRMs at late developmental stages and conversely a low-binding signal for ‘late' CRMs at early stages of development (Figure 2A; Supplementary Figure 3), demonstrating that transient binding is not an effect of thresholding of the ChIP signal (see Materials and methods).


Dynamic CRM occupancy reflects a temporal map of developmental progression.

Wilczyński B, Furlong EE - Mol. Syst. Biol. (2010)

Relationship between TF binding, motif quality, and temporal occupancy. (A) The distribution of quantitative-binding signal (log2 ChIP peak height) for different temporal classes of CRMs bound by the TF Twist shows that there is a clear distinction between early, continuous, and late CRMs. All TFs are shown in Supplementary Figure 3. (B) Average enrichment of all motifs in CRM classes defined by binding of respective TFs. The appropriate motif is significantly enriched in bound CRMs compared with non-bound CRMs (NB). There is no difference in motif enrichment between the three temporal classes. (C) Quantitative TF binding (ChIP enrichment) is only weakly correlated (Pearson's r=0.192) with motif strength as measured by the PWM log-odds score. Exemplified using Twi binding at 4–6 h, where each dot represents a single CRM (all TFs shown in Supplementary Figures 5 and 6). A number of CRMs with no detectable Twist binding (blue dots) contain high-affinity motifs. (D) Motifs in bound CRMs are significantly more conserved than in non-bound CRMs, but there is no significant difference in motif conservation between temporal classes. NB, non-bound CRMs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2913398&req=5

f2: Relationship between TF binding, motif quality, and temporal occupancy. (A) The distribution of quantitative-binding signal (log2 ChIP peak height) for different temporal classes of CRMs bound by the TF Twist shows that there is a clear distinction between early, continuous, and late CRMs. All TFs are shown in Supplementary Figure 3. (B) Average enrichment of all motifs in CRM classes defined by binding of respective TFs. The appropriate motif is significantly enriched in bound CRMs compared with non-bound CRMs (NB). There is no difference in motif enrichment between the three temporal classes. (C) Quantitative TF binding (ChIP enrichment) is only weakly correlated (Pearson's r=0.192) with motif strength as measured by the PWM log-odds score. Exemplified using Twi binding at 4–6 h, where each dot represents a single CRM (all TFs shown in Supplementary Figures 5 and 6). A number of CRMs with no detectable Twist binding (blue dots) contain high-affinity motifs. (D) Motifs in bound CRMs are significantly more conserved than in non-bound CRMs, but there is no significant difference in motif conservation between temporal classes. NB, non-bound CRMs.
Mentions: We first assessed the temporal occupancy of each TF independently, focusing on regions bound by a TF in at least two consecutive time points (see Materials and methods). As these criteria will eliminate CRMs bound at only a single time point, it provides a very stringent set of combinatorially bound modules (Supplementary Table 1). Even within this conservative definition, unsupervised clustering of binding profiles revealed extensive temporal dynamics (Figure 1A), confirming our earlier findings (Sandmann et al, 2006, 2007; Jakobsen et al, 2007), while extending the analysis genome wide. All TFs examined target three broad classes of CRMs with different temporal occupancy (Figure 1A; Supplementary Figure 2): early bound modules, having TF binding during the first two time points for a given TF, but not later, continuous, occupied at all time points (representing about 50% of CRMs bound by a TF) and late, having binding only at the last two time points and not at earlier stages of development. Therefore, each TF occupies ∼50% of its targeted CRMs in a transient manner; being bound either at early or late stages of development (Supplementary Figure 2). Defining transient occupancy is inherently difficult due to potential false negatives, which can lead to a misclassification of continuous binding. However, measuring the quantitative signal for all CRMs revealed very low levels of occupancy on ‘early' CRMs at late developmental stages and conversely a low-binding signal for ‘late' CRMs at early stages of development (Figure 2A; Supplementary Figure 3), demonstrating that transient binding is not an effect of thresholding of the ChIP signal (see Materials and methods).

Bottom Line: CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves.The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development.Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Genome Biology, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.

ABSTRACT
Development is driven by tightly coordinated spatio-temporal patterns of gene expression, which are initiated through the action of transcription factors (TFs) binding to cis-regulatory modules (CRMs). Although many studies have investigated how spatial patterns arise, precise temporal control of gene expression is less well understood. Here, we show that dynamic changes in the timing of CRM occupancy is a prevalent feature common to all TFs examined in a developmental ChIP time course to date. CRMs exhibit complex binding patterns that cannot be explained by the sequence motifs or expression of the TFs themselves. The temporal changes in TF binding are highly correlated with dynamic patterns of target gene expression, which in turn reflect transitions in cellular function during different stages of development. Thus, it is not only the timing of a TF's expression, but also its temporal occupancy in refined time windows, which determines temporal gene expression. Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression.

Show MeSH
Related in: MedlinePlus