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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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Transcription factors occupy CRMs in highly dynamic patterns. (A) k-Means clustering of binding profiles of four TFs (Twi, Tin, Mef2, and Bin) shows emerging temporal-binding patterns, which are similar in all four cases. Each row represents a TF-bound region, each column a time window of development. The intensity of blue represents the level of ChIP enrichment (log2 of the peak height). Colored vertical bars represent early (green), continuous (yellow), and late (red) bound regions. (B) Hierarchical clustering of total CRM occupancy, using the average TF-binding enrichment at a given time point, for all 2813 unique CRMs. (C) Representative examples of individual CRMs from (B), illustrating that different temporal-binding patterns can occur in the same locus either in a coordinated (CRMs #659, 153, 895, 38) or cascading (CRMs #81, 147, 392, 134) manner. Blue represents the level of ChIP enrichment, yellow represents no binding.
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f1: Transcription factors occupy CRMs in highly dynamic patterns. (A) k-Means clustering of binding profiles of four TFs (Twi, Tin, Mef2, and Bin) shows emerging temporal-binding patterns, which are similar in all four cases. Each row represents a TF-bound region, each column a time window of development. The intensity of blue represents the level of ChIP enrichment (log2 of the peak height). Colored vertical bars represent early (green), continuous (yellow), and late (red) bound regions. (B) Hierarchical clustering of total CRM occupancy, using the average TF-binding enrichment at a given time point, for all 2813 unique CRMs. (C) Representative examples of individual CRMs from (B), illustrating that different temporal-binding patterns can occur in the same locus either in a coordinated (CRMs #659, 153, 895, 38) or cascading (CRMs #81, 147, 392, 134) manner. Blue represents the level of ChIP enrichment, yellow represents no binding.

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)

Transcription factors occupy CRMs in highly dynamic patterns. (A) k-Means clustering of binding profiles of four TFs (Twi, Tin, Mef2, and Bin) shows emerging temporal-binding patterns, which are similar in all four cases. Each row represents a TF-bound region, each column a time window of development. The intensity of blue represents the level of ChIP enrichment (log2 of the peak height). Colored vertical bars represent early (green), continuous (yellow), and late (red) bound regions. (B) Hierarchical clustering of total CRM occupancy, using the average TF-binding enrichment at a given time point, for all 2813 unique CRMs. (C) Representative examples of individual CRMs from (B), illustrating that different temporal-binding patterns can occur in the same locus either in a coordinated (CRMs #659, 153, 895, 38) or cascading (CRMs #81, 147, 392, 134) manner. Blue represents the level of ChIP enrichment, yellow represents no binding.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Transcription factors occupy CRMs in highly dynamic patterns. (A) k-Means clustering of binding profiles of four TFs (Twi, Tin, Mef2, and Bin) shows emerging temporal-binding patterns, which are similar in all four cases. Each row represents a TF-bound region, each column a time window of development. The intensity of blue represents the level of ChIP enrichment (log2 of the peak height). Colored vertical bars represent early (green), continuous (yellow), and late (red) bound regions. (B) Hierarchical clustering of total CRM occupancy, using the average TF-binding enrichment at a given time point, for all 2813 unique CRMs. (C) Representative examples of individual CRMs from (B), illustrating that different temporal-binding patterns can occur in the same locus either in a coordinated (CRMs #659, 153, 895, 38) or cascading (CRMs #81, 147, 392, 134) manner. Blue represents the level of ChIP enrichment, yellow represents no binding.
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