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Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm JO, Xu F, Ronne H, Komorowski J - BMC Bioinformatics (2008)

Bottom Line: We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression.We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. jakub@lcb.uu.se

ABSTRACT

Background: The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation.

Results: In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.

Conclusion: We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

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Related in: MedlinePlus

Influence of motif location on gene expression in deletion strains. A) Expression in the Gcn4 deletion strain compared to the wild type, for genes without the Gcn4 motif, with the motif outside the preferred location (200–400 bp upstream) and with the motif in the preferred position. B) Expression in Mbp1 deletion strain compared to the wild type, for genes without the Mbp1 motif, with the motif outside the preferred location (100–200 bp upstream) and with the motif in the preferred position.
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Figure 2: Influence of motif location on gene expression in deletion strains. A) Expression in the Gcn4 deletion strain compared to the wild type, for genes without the Gcn4 motif, with the motif outside the preferred location (200–400 bp upstream) and with the motif in the preferred position. B) Expression in Mbp1 deletion strain compared to the wild type, for genes without the Mbp1 motif, with the motif outside the preferred location (100–200 bp upstream) and with the motif in the preferred position.

Mentions: To test if the observed bias in motif location within promoters that actually bind a given TF correlates with TF-specific effects on gene expression, we used available data on gene expression in different knockout strains [30]. We found such data for four of the TFs that showed a significant location bias: Cin5, Gcn4, Mbp1 and Swi4. For each of these TFs we compared expression of three sets of genes a) all genes without the motif in the promoter, b) all genes with the motif but not in the preferred location, and c) all genes where the promoter contains the motif in the preferred location. Gcn4 is an activator of genes that are induced in response to amino acid starvation, and as expected genes with the Gcn4-binding motif in their promoters have a reduced expression in the Gcn4 deletion strain. Notably, genes with a Gcn4 motif at 200–400 bp upstream of the start codon have a significantly lower (p = 9.4e-3) expression in the deletion strain than genes with the motif in other locations (Figure 2a). This shows that the location of the Gcn4-binding motif is important not only for Gcn4 binding, but also for Gcn4-dependent regulation in vivo. Mbp1 is a repressor involved in regulation of cell cycle progression, and as expected genes with the Mbp1-binding motif in their promoters have a higher level of expression in the Mbp1 deletion strain. Also in this case, we found that genes where the Mbp1 motif is found in a preferential location for DNA binding (101–200 bp upstream of the start codon) have a significantly higher (p = 8.4e-6) level of expression in the Mbp1 deletion strain than genes which have Mbp1 motifs elsewhere in their promoters (Figure 2b), suggesting that the location of the Mbp1 motif also is important for Mbp1-dependent repression. For Swi4 the results were inconclusive (p-value 0.095), and for Cin5 no expression differences were observed for different motif locations (data not shown).


Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm JO, Xu F, Ronne H, Komorowski J - BMC Bioinformatics (2008)

Influence of motif location on gene expression in deletion strains. A) Expression in the Gcn4 deletion strain compared to the wild type, for genes without the Gcn4 motif, with the motif outside the preferred location (200–400 bp upstream) and with the motif in the preferred position. B) Expression in Mbp1 deletion strain compared to the wild type, for genes without the Mbp1 motif, with the motif outside the preferred location (100–200 bp upstream) and with the motif in the preferred position.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2629780&req=5

Figure 2: Influence of motif location on gene expression in deletion strains. A) Expression in the Gcn4 deletion strain compared to the wild type, for genes without the Gcn4 motif, with the motif outside the preferred location (200–400 bp upstream) and with the motif in the preferred position. B) Expression in Mbp1 deletion strain compared to the wild type, for genes without the Mbp1 motif, with the motif outside the preferred location (100–200 bp upstream) and with the motif in the preferred position.
Mentions: To test if the observed bias in motif location within promoters that actually bind a given TF correlates with TF-specific effects on gene expression, we used available data on gene expression in different knockout strains [30]. We found such data for four of the TFs that showed a significant location bias: Cin5, Gcn4, Mbp1 and Swi4. For each of these TFs we compared expression of three sets of genes a) all genes without the motif in the promoter, b) all genes with the motif but not in the preferred location, and c) all genes where the promoter contains the motif in the preferred location. Gcn4 is an activator of genes that are induced in response to amino acid starvation, and as expected genes with the Gcn4-binding motif in their promoters have a reduced expression in the Gcn4 deletion strain. Notably, genes with a Gcn4 motif at 200–400 bp upstream of the start codon have a significantly lower (p = 9.4e-3) expression in the deletion strain than genes with the motif in other locations (Figure 2a). This shows that the location of the Gcn4-binding motif is important not only for Gcn4 binding, but also for Gcn4-dependent regulation in vivo. Mbp1 is a repressor involved in regulation of cell cycle progression, and as expected genes with the Mbp1-binding motif in their promoters have a higher level of expression in the Mbp1 deletion strain. Also in this case, we found that genes where the Mbp1 motif is found in a preferential location for DNA binding (101–200 bp upstream of the start codon) have a significantly higher (p = 8.4e-6) level of expression in the Mbp1 deletion strain than genes which have Mbp1 motifs elsewhere in their promoters (Figure 2b), suggesting that the location of the Mbp1 motif also is important for Mbp1-dependent repression. For Swi4 the results were inconclusive (p-value 0.095), and for Cin5 no expression differences were observed for different motif locations (data not shown).

Bottom Line: We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression.We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

View Article: PubMed Central - HTML - PubMed

Affiliation: The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden. jakub@lcb.uu.se

ABSTRACT

Background: The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation.

Results: In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy.

Conclusion: We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

Show MeSH
Related in: MedlinePlus