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Evolution acts on enhancer organization to fine-tune gradient threshold readouts.

Crocker J, Tamori Y, Erives A - PLoS Biol. (2008)

Bottom Line: Furthermore, by precisely altering the organization of NEEs with different morphogen gradient threshold readouts, we show that CRM organizational evolution is sufficient for explaining changes in enhancer activity.Thus, evolution can act on CRM organization to fine-tune morphogen gradient threshold readouts over a wide dynamic range.Our study demonstrates that equivalence classes of CRMs are powerful tools for detecting lineage-specific adaptations by gene regulatory sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH, USA.

ABSTRACT
The elucidation of principles governing evolution of gene regulatory sequence is critical to the study of metazoan diversification. We are therefore exploring the structure and organizational constraints of regulatory sequences by studying functionally equivalent cis-regulatory modules (CRMs) that have been evolving in parallel across several loci. Such an independent dataset allows a multi-locus study that is not hampered by nonfunctional or constrained homology. The neurogenic ectoderm enhancers (NEEs) of Drosophila melanogaster are one such class of coordinately regulated CRMs. The NEEs share a common organization of binding sites and as a set would be useful to study the relationship between CRM organization and CRM activity across evolving lineages. We used the D. melanogaster transgenic system to screen for functional adaptations in the NEEs from divergent drosophilid species. We show that the individual NEE modules across a genome in any one lineage have independently evolved adaptations to compensate for lineage-specific developmental and/or genomic changes. Specifically, we show that both the site composition and the site organization of NEEs have been finely tuned by distinct, lineage-specific selection pressures in each of the three divergent species that we have examined: D. melanogaster, D. pseudoobscura, and D. virilis. Furthermore, by precisely altering the organization of NEEs with different morphogen gradient threshold readouts, we show that CRM organizational evolution is sufficient for explaining changes in enhancer activity. Thus, evolution can act on CRM organization to fine-tune morphogen gradient threshold readouts over a wide dynamic range. Our study demonstrates that equivalence classes of CRMs are powerful tools for detecting lineage-specific adaptations by gene regulatory sequences.

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Configurations of D. melanogaster, D. pseudoobscura, and D. virilis NEE SequencesSequences of NEE cis-elements described in this study were aligned from the vnd, rho, vn, brk, and sog loci from D. pseudoobscura (top aligned sequence), D. melanogaster (middle aligned sequence), and D. virilis sequences (bottom aligned sequence). Particular details (circled numbers) are discussed in the text. Dorsal motifs are shown in blue, Twist CA-core E-boxes are depicted in green, and Su(H) motifs are depicted in red. Overlap between Dorsal and Su(H) motifs are depicted in purple. Only the regions containing these motifs are shown. Ellipses (“…”) indicate intervening sequences that are not shown. See Table S1 for the full-length sequence.
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pbio-0060263-g002: Configurations of D. melanogaster, D. pseudoobscura, and D. virilis NEE SequencesSequences of NEE cis-elements described in this study were aligned from the vnd, rho, vn, brk, and sog loci from D. pseudoobscura (top aligned sequence), D. melanogaster (middle aligned sequence), and D. virilis sequences (bottom aligned sequence). Particular details (circled numbers) are discussed in the text. Dorsal motifs are shown in blue, Twist CA-core E-boxes are depicted in green, and Su(H) motifs are depicted in red. Overlap between Dorsal and Su(H) motifs are depicted in purple. Only the regions containing these motifs are shown. Ellipses (“…”) indicate intervening sequences that are not shown. See Table S1 for the full-length sequence.

Mentions: We identified NEE-type sequences across the D. melanogaster, D. pseudoobscura, and D. virilis genomes in order to determine how a set of coordinately regulated gene loci co-evolve in a given lineage. We found that the NEE signatures of paired Dorsal–Twist binding sites (5′-SGGAAADYCSS and 5′-CACATGT, respectively) and a Su(H) site overlapping a separate Dorsal site (5′-CGTGGGAAAWDCSM, Su(H) site underlined) were present together in a single CRM across many loci (Figures 1A, 1B, and 2). We refer to such loci as “NEE-bearing” genes. Interestingly, the D. melanogaster NEE signature of an oriented and positioned μ motif (5′-CTGRCCBKSMM) was not discernable in enhancers from either the D. virilis or the D. pseudoobscura genomes.


Evolution acts on enhancer organization to fine-tune gradient threshold readouts.

Crocker J, Tamori Y, Erives A - PLoS Biol. (2008)

Configurations of D. melanogaster, D. pseudoobscura, and D. virilis NEE SequencesSequences of NEE cis-elements described in this study were aligned from the vnd, rho, vn, brk, and sog loci from D. pseudoobscura (top aligned sequence), D. melanogaster (middle aligned sequence), and D. virilis sequences (bottom aligned sequence). Particular details (circled numbers) are discussed in the text. Dorsal motifs are shown in blue, Twist CA-core E-boxes are depicted in green, and Su(H) motifs are depicted in red. Overlap between Dorsal and Su(H) motifs are depicted in purple. Only the regions containing these motifs are shown. Ellipses (“…”) indicate intervening sequences that are not shown. See Table S1 for the full-length sequence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2577699&req=5

pbio-0060263-g002: Configurations of D. melanogaster, D. pseudoobscura, and D. virilis NEE SequencesSequences of NEE cis-elements described in this study were aligned from the vnd, rho, vn, brk, and sog loci from D. pseudoobscura (top aligned sequence), D. melanogaster (middle aligned sequence), and D. virilis sequences (bottom aligned sequence). Particular details (circled numbers) are discussed in the text. Dorsal motifs are shown in blue, Twist CA-core E-boxes are depicted in green, and Su(H) motifs are depicted in red. Overlap between Dorsal and Su(H) motifs are depicted in purple. Only the regions containing these motifs are shown. Ellipses (“…”) indicate intervening sequences that are not shown. See Table S1 for the full-length sequence.
Mentions: We identified NEE-type sequences across the D. melanogaster, D. pseudoobscura, and D. virilis genomes in order to determine how a set of coordinately regulated gene loci co-evolve in a given lineage. We found that the NEE signatures of paired Dorsal–Twist binding sites (5′-SGGAAADYCSS and 5′-CACATGT, respectively) and a Su(H) site overlapping a separate Dorsal site (5′-CGTGGGAAAWDCSM, Su(H) site underlined) were present together in a single CRM across many loci (Figures 1A, 1B, and 2). We refer to such loci as “NEE-bearing” genes. Interestingly, the D. melanogaster NEE signature of an oriented and positioned μ motif (5′-CTGRCCBKSMM) was not discernable in enhancers from either the D. virilis or the D. pseudoobscura genomes.

Bottom Line: Furthermore, by precisely altering the organization of NEEs with different morphogen gradient threshold readouts, we show that CRM organizational evolution is sufficient for explaining changes in enhancer activity.Thus, evolution can act on CRM organization to fine-tune morphogen gradient threshold readouts over a wide dynamic range.Our study demonstrates that equivalence classes of CRMs are powerful tools for detecting lineage-specific adaptations by gene regulatory sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, NH, USA.

ABSTRACT
The elucidation of principles governing evolution of gene regulatory sequence is critical to the study of metazoan diversification. We are therefore exploring the structure and organizational constraints of regulatory sequences by studying functionally equivalent cis-regulatory modules (CRMs) that have been evolving in parallel across several loci. Such an independent dataset allows a multi-locus study that is not hampered by nonfunctional or constrained homology. The neurogenic ectoderm enhancers (NEEs) of Drosophila melanogaster are one such class of coordinately regulated CRMs. The NEEs share a common organization of binding sites and as a set would be useful to study the relationship between CRM organization and CRM activity across evolving lineages. We used the D. melanogaster transgenic system to screen for functional adaptations in the NEEs from divergent drosophilid species. We show that the individual NEE modules across a genome in any one lineage have independently evolved adaptations to compensate for lineage-specific developmental and/or genomic changes. Specifically, we show that both the site composition and the site organization of NEEs have been finely tuned by distinct, lineage-specific selection pressures in each of the three divergent species that we have examined: D. melanogaster, D. pseudoobscura, and D. virilis. Furthermore, by precisely altering the organization of NEEs with different morphogen gradient threshold readouts, we show that CRM organizational evolution is sufficient for explaining changes in enhancer activity. Thus, evolution can act on CRM organization to fine-tune morphogen gradient threshold readouts over a wide dynamic range. Our study demonstrates that equivalence classes of CRMs are powerful tools for detecting lineage-specific adaptations by gene regulatory sequences.

Show MeSH