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Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila.

Carl SH, Russell S - BMC Genomics (2015)

Bottom Line: To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites.We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. s.carl@gen.cam.ac.uk.

ABSTRACT

Background: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known.

Results: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.

Conclusion: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

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Pairwise analysis of Dichaete binding site turnover. (A) Quantitative differences in Dichaete binding between D. melanogaster and D. simulans. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. simulans (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. simulans clustered by binding affinity scores. The color key and histogram shows the distribution of binding affinity scores (log of normalised read counts) in all bound intervals in each sample. Darker green corresponds to higher affinity scores or stronger binding, while lighter green corresponds to lower affinity scores or weaker binding. Roughly equal numbers of intervals are preferentially bound in each species. (B) Quantitative differences in Dichaete binding between D. melanogaster and D. yakuba. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. yakuba (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. yakuba clustered by binding affinity scores. The color key and histogram are as in (A). Again, rough equal numbers of intervals are preferentially bound in each species, although more differentially bound intervals are identified overall. (C) Example of Dichaete binding site turnover between D. melanogaster (blue) and D. yakuba (orange) at the reduced ocelli (rdo) locus. Binding profiles represent the normalised log2 fold changes between Dichaete-Dam binding and Dam-only control binding in each GATC fragment. Bars represent bound intervals identified at FDR5. Bound intervals that are positionally conserved are not shown. Strong binding is observed in the third, fourth and eleventh introns in D. yakuba; these binding events are lost in D. melanogaster, but several binding intervals are gained in the first and fourth introns.
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Fig4: Pairwise analysis of Dichaete binding site turnover. (A) Quantitative differences in Dichaete binding between D. melanogaster and D. simulans. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. simulans (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. simulans clustered by binding affinity scores. The color key and histogram shows the distribution of binding affinity scores (log of normalised read counts) in all bound intervals in each sample. Darker green corresponds to higher affinity scores or stronger binding, while lighter green corresponds to lower affinity scores or weaker binding. Roughly equal numbers of intervals are preferentially bound in each species. (B) Quantitative differences in Dichaete binding between D. melanogaster and D. yakuba. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. yakuba (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. yakuba clustered by binding affinity scores. The color key and histogram are as in (A). Again, rough equal numbers of intervals are preferentially bound in each species, although more differentially bound intervals are identified overall. (C) Example of Dichaete binding site turnover between D. melanogaster (blue) and D. yakuba (orange) at the reduced ocelli (rdo) locus. Binding profiles represent the normalised log2 fold changes between Dichaete-Dam binding and Dam-only control binding in each GATC fragment. Bars represent bound intervals identified at FDR5. Bound intervals that are positionally conserved are not shown. Strong binding is observed in the third, fourth and eleventh introns in D. yakuba; these binding events are lost in D. melanogaster, but several binding intervals are gained in the first and fourth introns.

Mentions: We employed DiffBind [87] to perform a differential enrichment analysis, comparing Dichaete-Dam binding profiles between two species for each binding interval, identifying binding intervals that showed significant quantitative differences between each pair of species [87]. For comparisons between D. melanogaster and D. simulans or D. yakuba, we found approximately equal numbers of preferentially bound intervals in each species (Figure 4A-B). In agreement with the PCA plot, 8880 differentially bound intervals were identified between D. melanogaster and D. yakuba at FDR1, while only 5044 were identified between D. melanogaster and D. simulans, indicating a greater amount of quantitative binding divergence between D. melanogaster and D. yakuba. Again, this finding shows that divergence in binding follows the known Drosophila phylogeny and suggests a molecular clock mechanism for Dichaete binding site turnover, as has been proposed for other TFs in Drosophila [77]. Interestingly, the proportion of differentially bound intervals that are present in both species but show quantitative changes in binding strength, as opposed to those that are qualitatively absent in one species, also increases with phylogenetic distance, from 58.0% between D. melanogaster and D. simulans to 63.7% between D. melanogaster and D. yakuba. This also represents an increase in the percentage of the total D. melanogaster Dichaete binding intervals that quantitatively change in another species, from 9.6% in D. simulans to 20.4% in D. yakuba.Figure 4


Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila.

Carl SH, Russell S - BMC Genomics (2015)

Pairwise analysis of Dichaete binding site turnover. (A) Quantitative differences in Dichaete binding between D. melanogaster and D. simulans. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. simulans (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. simulans clustered by binding affinity scores. The color key and histogram shows the distribution of binding affinity scores (log of normalised read counts) in all bound intervals in each sample. Darker green corresponds to higher affinity scores or stronger binding, while lighter green corresponds to lower affinity scores or weaker binding. Roughly equal numbers of intervals are preferentially bound in each species. (B) Quantitative differences in Dichaete binding between D. melanogaster and D. yakuba. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. yakuba (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. yakuba clustered by binding affinity scores. The color key and histogram are as in (A). Again, rough equal numbers of intervals are preferentially bound in each species, although more differentially bound intervals are identified overall. (C) Example of Dichaete binding site turnover between D. melanogaster (blue) and D. yakuba (orange) at the reduced ocelli (rdo) locus. Binding profiles represent the normalised log2 fold changes between Dichaete-Dam binding and Dam-only control binding in each GATC fragment. Bars represent bound intervals identified at FDR5. Bound intervals that are positionally conserved are not shown. Strong binding is observed in the third, fourth and eleventh introns in D. yakuba; these binding events are lost in D. melanogaster, but several binding intervals are gained in the first and fourth introns.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
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Fig4: Pairwise analysis of Dichaete binding site turnover. (A) Quantitative differences in Dichaete binding between D. melanogaster and D. simulans. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. simulans (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. simulans clustered by binding affinity scores. The color key and histogram shows the distribution of binding affinity scores (log of normalised read counts) in all bound intervals in each sample. Darker green corresponds to higher affinity scores or stronger binding, while lighter green corresponds to lower affinity scores or weaker binding. Roughly equal numbers of intervals are preferentially bound in each species. (B) Quantitative differences in Dichaete binding between D. melanogaster and D. yakuba. MA plot shows binding intervals that are preferentially bound in D. melanogaster (pink, fold change > 0) or D. yakuba (pink, fold change < 0) at FDR1. Heatmap shows differentially bound Dichaete-Dam intervals between D. melanogaster and D. yakuba clustered by binding affinity scores. The color key and histogram are as in (A). Again, rough equal numbers of intervals are preferentially bound in each species, although more differentially bound intervals are identified overall. (C) Example of Dichaete binding site turnover between D. melanogaster (blue) and D. yakuba (orange) at the reduced ocelli (rdo) locus. Binding profiles represent the normalised log2 fold changes between Dichaete-Dam binding and Dam-only control binding in each GATC fragment. Bars represent bound intervals identified at FDR5. Bound intervals that are positionally conserved are not shown. Strong binding is observed in the third, fourth and eleventh introns in D. yakuba; these binding events are lost in D. melanogaster, but several binding intervals are gained in the first and fourth introns.
Mentions: We employed DiffBind [87] to perform a differential enrichment analysis, comparing Dichaete-Dam binding profiles between two species for each binding interval, identifying binding intervals that showed significant quantitative differences between each pair of species [87]. For comparisons between D. melanogaster and D. simulans or D. yakuba, we found approximately equal numbers of preferentially bound intervals in each species (Figure 4A-B). In agreement with the PCA plot, 8880 differentially bound intervals were identified between D. melanogaster and D. yakuba at FDR1, while only 5044 were identified between D. melanogaster and D. simulans, indicating a greater amount of quantitative binding divergence between D. melanogaster and D. yakuba. Again, this finding shows that divergence in binding follows the known Drosophila phylogeny and suggests a molecular clock mechanism for Dichaete binding site turnover, as has been proposed for other TFs in Drosophila [77]. Interestingly, the proportion of differentially bound intervals that are present in both species but show quantitative changes in binding strength, as opposed to those that are qualitatively absent in one species, also increases with phylogenetic distance, from 58.0% between D. melanogaster and D. simulans to 63.7% between D. melanogaster and D. yakuba. This also represents an increase in the percentage of the total D. melanogaster Dichaete binding intervals that quantitatively change in another species, from 9.6% in D. simulans to 20.4% in D. yakuba.Figure 4

Bottom Line: To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites.We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Cambridge Systems Biology Centre, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK. s.carl@gen.cam.ac.uk.

ABSTRACT

Background: Group B Sox proteins are a highly conserved group of transcription factors that act extensively to coordinate nervous system development in higher metazoans while showing both co-expression and functional redundancy across a broad group of taxa. In Drosophila melanogaster, the two group B Sox proteins Dichaete and SoxNeuro show widespread common binding across the genome. While some instances of functional compensation have been observed in Drosophila, the function of common binding and the extent of its evolutionary conservation is not known.

Results: We used DamID-seq to examine the genome-wide binding patterns of Dichaete and SoxNeuro in four species of Drosophila. Through a quantitative comparison of Dichaete binding, we evaluated the rate of binding site turnover across the genome as well as at specific functional sites. We also examined the presence of Sox motifs within binding intervals and the correlation between sequence conservation and binding conservation. To determine whether common binding between Dichaete and SoxNeuro is conserved, we performed a detailed analysis of the binding patterns of both factors in two species.

Conclusion: We find that, while the regulatory networks driven by Dichaete and SoxNeuro are largely conserved across the drosophilids studied, binding site turnover is widespread and correlated with phylogenetic distance. Nonetheless, binding is preferentially conserved at known cis-regulatory modules and core, independently verified binding sites. We observed the strongest binding conservation at sites that are commonly bound by Dichaete and SoxNeuro, suggesting that these sites are functionally important. Our analysis provides insights into the evolution of group B Sox function, highlighting the specific conservation of shared binding sites and suggesting alternative sources of neofunctionalisation between paralogous family members.

Show MeSH
Related in: MedlinePlus