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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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Temporal TF binding correlates with temporal gene expression and function. (A) Proportion of target genes with CRMs bound at different time points (green, early; yellow, mid-stages; red, late stages), divided into groups based on the first stage that they are expressed in the embryo. In all, 33% of genes with CRMs bound at 2–4 h initiate expression at 2–3.5 h, whereas an additional 33% initiate expression at 3.5–6 h. Significantly enriched classes peaking in different time points are marked with asterisks (Fisher's exact test *P<0.05, **P<0.001). (B) Representative examples of expression patterns of genes targeted by temporally bound CRMs. The only expression of the rosy gene in mesodermal and/or muscle occurs at early stages in development, the expression of fasIII initiates in visceral and somatic muscle at mid-embryogenesis, whereas CG5080 is strongly expressed in somatic muscle at late stages. (C) Genes with occupied enhancers early in development have different functions than those that are bound by the same TF at later stages. GO categories (with the number of genes indicated in brackets) showing differential enrichment between target genes grouped by temporal-binding classes. The blue shade corresponds to the –log of the P-value (Benjamini–Hochberg corrected). For the full set of GO terms see Supplementary Table 3. (D) The upper panel displays the number of CRMs bound by Mef2 and/or Biniou out of the 69 CRMs associated with 18 muscle contractile genes. Bottom panel shows the temporal expression pattern of the 18 genes, which initiate at 8–9 h of development, reaching high levels of expression by 11–12 h, reflecting the temporal occupancy of their CRMs. Solid line represents mean expression and dashed lines represent 1 s.d. above and below the mean.
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f3: Temporal TF binding correlates with temporal gene expression and function. (A) Proportion of target genes with CRMs bound at different time points (green, early; yellow, mid-stages; red, late stages), divided into groups based on the first stage that they are expressed in the embryo. In all, 33% of genes with CRMs bound at 2–4 h initiate expression at 2–3.5 h, whereas an additional 33% initiate expression at 3.5–6 h. Significantly enriched classes peaking in different time points are marked with asterisks (Fisher's exact test *P<0.05, **P<0.001). (B) Representative examples of expression patterns of genes targeted by temporally bound CRMs. The only expression of the rosy gene in mesodermal and/or muscle occurs at early stages in development, the expression of fasIII initiates in visceral and somatic muscle at mid-embryogenesis, whereas CG5080 is strongly expressed in somatic muscle at late stages. (C) Genes with occupied enhancers early in development have different functions than those that are bound by the same TF at later stages. GO categories (with the number of genes indicated in brackets) showing differential enrichment between target genes grouped by temporal-binding classes. The blue shade corresponds to the –log of the P-value (Benjamini–Hochberg corrected). For the full set of GO terms see Supplementary Table 3. (D) The upper panel displays the number of CRMs bound by Mef2 and/or Biniou out of the 69 CRMs associated with 18 muscle contractile genes. Bottom panel shows the temporal expression pattern of the 18 genes, which initiate at 8–9 h of development, reaching high levels of expression by 11–12 h, reflecting the temporal occupancy of their CRMs. Solid line represents mean expression and dashed lines represent 1 s.d. above and below the mean.

Mentions: The high degree of temporal TF binding suggests tight regulation, which implies functional importance. To assess this, we examined the relationship between temporal CRM occupancy and temporal patterns of gene expression and developmental progression. As all four factors are transcriptional activators, we compared the timing of TF binding (both on and off) to the time of activation of the associated target genes, using two independent data sets for gene expression. First, using in situ hybridization data from the Berkeley Drosophila Genome Project database (BDGP; Tomancak et al, 2002), which provide an accurate measure of expression timing in the tissue of interest (Figure 3A and B). Second, using a microarray-based developmental time course with finer temporal resolution, restricting our analysis to tissue-specific genes (Supplementary Figure 8B). Both approaches show a significant correlation between the timing of TF binding and gene expression: For early bound CRMs, for example, the largest proportion of target genes are activated during early stages of development, reflecting the transient occupancy of their CRMs at these stages (Figure 3A). Similarly, for CRMs that are occupied during mid-embryogenesis (6–8 h) or later (10–12 h), the majority of their target genes are activated during the respective developmental stages (Figure 3A). This trend holds true for each TF taken separately (Supplementary Figure 8A) and for CRMs occupied very transiently at a single time point, despite potentially containing more noise due to false positives (Supplementary Figure 9). The correlation between dynamic TF binding and the timing of gene expression during development is much higher than what has been observed in yeast (Ni et al, 2009), which is remarkable given that developmental genes typically have multiple CRMs, adding another level of complexity.


Dynamic CRM occupancy reflects a temporal map of developmental progression.

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

Temporal TF binding correlates with temporal gene expression and function. (A) Proportion of target genes with CRMs bound at different time points (green, early; yellow, mid-stages; red, late stages), divided into groups based on the first stage that they are expressed in the embryo. In all, 33% of genes with CRMs bound at 2–4 h initiate expression at 2–3.5 h, whereas an additional 33% initiate expression at 3.5–6 h. Significantly enriched classes peaking in different time points are marked with asterisks (Fisher's exact test *P<0.05, **P<0.001). (B) Representative examples of expression patterns of genes targeted by temporally bound CRMs. The only expression of the rosy gene in mesodermal and/or muscle occurs at early stages in development, the expression of fasIII initiates in visceral and somatic muscle at mid-embryogenesis, whereas CG5080 is strongly expressed in somatic muscle at late stages. (C) Genes with occupied enhancers early in development have different functions than those that are bound by the same TF at later stages. GO categories (with the number of genes indicated in brackets) showing differential enrichment between target genes grouped by temporal-binding classes. The blue shade corresponds to the –log of the P-value (Benjamini–Hochberg corrected). For the full set of GO terms see Supplementary Table 3. (D) The upper panel displays the number of CRMs bound by Mef2 and/or Biniou out of the 69 CRMs associated with 18 muscle contractile genes. Bottom panel shows the temporal expression pattern of the 18 genes, which initiate at 8–9 h of development, reaching high levels of expression by 11–12 h, reflecting the temporal occupancy of their CRMs. Solid line represents mean expression and dashed lines represent 1 s.d. above and below the mean.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Temporal TF binding correlates with temporal gene expression and function. (A) Proportion of target genes with CRMs bound at different time points (green, early; yellow, mid-stages; red, late stages), divided into groups based on the first stage that they are expressed in the embryo. In all, 33% of genes with CRMs bound at 2–4 h initiate expression at 2–3.5 h, whereas an additional 33% initiate expression at 3.5–6 h. Significantly enriched classes peaking in different time points are marked with asterisks (Fisher's exact test *P<0.05, **P<0.001). (B) Representative examples of expression patterns of genes targeted by temporally bound CRMs. The only expression of the rosy gene in mesodermal and/or muscle occurs at early stages in development, the expression of fasIII initiates in visceral and somatic muscle at mid-embryogenesis, whereas CG5080 is strongly expressed in somatic muscle at late stages. (C) Genes with occupied enhancers early in development have different functions than those that are bound by the same TF at later stages. GO categories (with the number of genes indicated in brackets) showing differential enrichment between target genes grouped by temporal-binding classes. The blue shade corresponds to the –log of the P-value (Benjamini–Hochberg corrected). For the full set of GO terms see Supplementary Table 3. (D) The upper panel displays the number of CRMs bound by Mef2 and/or Biniou out of the 69 CRMs associated with 18 muscle contractile genes. Bottom panel shows the temporal expression pattern of the 18 genes, which initiate at 8–9 h of development, reaching high levels of expression by 11–12 h, reflecting the temporal occupancy of their CRMs. Solid line represents mean expression and dashed lines represent 1 s.d. above and below the mean.
Mentions: The high degree of temporal TF binding suggests tight regulation, which implies functional importance. To assess this, we examined the relationship between temporal CRM occupancy and temporal patterns of gene expression and developmental progression. As all four factors are transcriptional activators, we compared the timing of TF binding (both on and off) to the time of activation of the associated target genes, using two independent data sets for gene expression. First, using in situ hybridization data from the Berkeley Drosophila Genome Project database (BDGP; Tomancak et al, 2002), which provide an accurate measure of expression timing in the tissue of interest (Figure 3A and B). Second, using a microarray-based developmental time course with finer temporal resolution, restricting our analysis to tissue-specific genes (Supplementary Figure 8B). Both approaches show a significant correlation between the timing of TF binding and gene expression: For early bound CRMs, for example, the largest proportion of target genes are activated during early stages of development, reflecting the transient occupancy of their CRMs at these stages (Figure 3A). Similarly, for CRMs that are occupied during mid-embryogenesis (6–8 h) or later (10–12 h), the majority of their target genes are activated during the respective developmental stages (Figure 3A). This trend holds true for each TF taken separately (Supplementary Figure 8A) and for CRMs occupied very transiently at a single time point, despite potentially containing more noise due to false positives (Supplementary Figure 9). The correlation between dynamic TF binding and the timing of gene expression during development is much higher than what has been observed in yeast (Ni et al, 2009), which is remarkable given that developmental genes typically have multiple CRMs, adding another level of complexity.

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