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A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA.

O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM - Elife (2015)

Bottom Line: An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish.Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates.Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

View Article: PubMed Central - PubMed

Affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.

ABSTRACT
Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

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All low-plated populations share a single base pair change in thegenetic region controlling armor plates.Genome-wide comparisons of low- and high-plated fish reveal a T → Gbase pair change (black box) that is shared between all low-platedpopulations tested, including the low-plated Japanese NAKA fish thatotherwise shows a primarily marine-like haplotype in theEDA region. Geographic population codes and DNAsequences from marine high-plated populations and freshwater low-platedpopulations are shown in red and blue, respectively, along withrepresentative Alizarin Red stained fish showing typical armor platepatterns in different fish. The 16 kb candidate interval controlling armorplate number (blue bar, Colosimo et al.,2005) is shown beneath predicated genes in the region. Also shownare the numbered positions (4–16) of previously identified SNPs thatdifferentiate most low- and high-plated sticklebacks other than NAKA (Colosimo et al., 2005). These numberedSNPs correspond to positions chrIV: 12800508, 12808303, 12808630, 12811933,12813328, 12813394, 12815024, 12815027, 12816201, 12816202, 12816360,12816402, and 12816464 in the stickleback genome assembly (Jones et al., 2012). Blank positionsrepresent occasional gaps in sequence coverage for individual fish fromlarge population surveys (Colosimo et al.,2005; Jones et al.,2012). The position of the shared T → G change(chrIV:12811481) is indicated with a short black vertical line in theoverall genomic interval, and in a 3.2 kb region that was used to test forpossible regulatory enhancers in the EDA region (orangebar, chrIV:12808949–12812120).DOI:http://dx.doi.org/10.7554/eLife.05290.004
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fig2: All low-plated populations share a single base pair change in thegenetic region controlling armor plates.Genome-wide comparisons of low- and high-plated fish reveal a T → Gbase pair change (black box) that is shared between all low-platedpopulations tested, including the low-plated Japanese NAKA fish thatotherwise shows a primarily marine-like haplotype in theEDA region. Geographic population codes and DNAsequences from marine high-plated populations and freshwater low-platedpopulations are shown in red and blue, respectively, along withrepresentative Alizarin Red stained fish showing typical armor platepatterns in different fish. The 16 kb candidate interval controlling armorplate number (blue bar, Colosimo et al.,2005) is shown beneath predicated genes in the region. Also shownare the numbered positions (4–16) of previously identified SNPs thatdifferentiate most low- and high-plated sticklebacks other than NAKA (Colosimo et al., 2005). These numberedSNPs correspond to positions chrIV: 12800508, 12808303, 12808630, 12811933,12813328, 12813394, 12815024, 12815027, 12816201, 12816202, 12816360,12816402, and 12816464 in the stickleback genome assembly (Jones et al., 2012). Blank positionsrepresent occasional gaps in sequence coverage for individual fish fromlarge population surveys (Colosimo et al.,2005; Jones et al.,2012). The position of the shared T → G change(chrIV:12811481) is indicated with a short black vertical line in theoverall genomic interval, and in a 3.2 kb region that was used to test forpossible regulatory enhancers in the EDA region (orangebar, chrIV:12808949–12812120).DOI:http://dx.doi.org/10.7554/eLife.05290.004

Mentions: Previous studies narrowed the minimal candidate interval controlling armor plates toa 16 kb interval containing EDA and flanking regions (Colosimo et al., 2005). To look for possibleshared molecular changes that might account for the regulatory difference betweenmarine and freshwater sticklebacks, we amplified and sequenced theEDA candidate interval from low-plated Japanese NAKA fish, andcompared it to other high- and low-plated stickleback populations (Figure 2 and ‘Materials andmethods’). This analysis identified a single T → G nucleotide change,located at position chrIV:12811481 (gasAcu1 assembly, Jones et al., 2012) in the intergenic region downstream ofEDA, that was shared between NAKA and all other low-platedsticklebacks examined.10.7554/eLife.05290.004Figure 2.All low-plated populations share a single base pair change in thegenetic region controlling armor plates.


A recurrent regulatory change underlying altered expression and Wnt response of the stickleback armor plates gene EDA.

O'Brown NM, Summers BR, Jones FC, Brady SD, Kingsley DM - Elife (2015)

All low-plated populations share a single base pair change in thegenetic region controlling armor plates.Genome-wide comparisons of low- and high-plated fish reveal a T → Gbase pair change (black box) that is shared between all low-platedpopulations tested, including the low-plated Japanese NAKA fish thatotherwise shows a primarily marine-like haplotype in theEDA region. Geographic population codes and DNAsequences from marine high-plated populations and freshwater low-platedpopulations are shown in red and blue, respectively, along withrepresentative Alizarin Red stained fish showing typical armor platepatterns in different fish. The 16 kb candidate interval controlling armorplate number (blue bar, Colosimo et al.,2005) is shown beneath predicated genes in the region. Also shownare the numbered positions (4–16) of previously identified SNPs thatdifferentiate most low- and high-plated sticklebacks other than NAKA (Colosimo et al., 2005). These numberedSNPs correspond to positions chrIV: 12800508, 12808303, 12808630, 12811933,12813328, 12813394, 12815024, 12815027, 12816201, 12816202, 12816360,12816402, and 12816464 in the stickleback genome assembly (Jones et al., 2012). Blank positionsrepresent occasional gaps in sequence coverage for individual fish fromlarge population surveys (Colosimo et al.,2005; Jones et al.,2012). The position of the shared T → G change(chrIV:12811481) is indicated with a short black vertical line in theoverall genomic interval, and in a 3.2 kb region that was used to test forpossible regulatory enhancers in the EDA region (orangebar, chrIV:12808949–12812120).DOI:http://dx.doi.org/10.7554/eLife.05290.004
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4384742&req=5

fig2: All low-plated populations share a single base pair change in thegenetic region controlling armor plates.Genome-wide comparisons of low- and high-plated fish reveal a T → Gbase pair change (black box) that is shared between all low-platedpopulations tested, including the low-plated Japanese NAKA fish thatotherwise shows a primarily marine-like haplotype in theEDA region. Geographic population codes and DNAsequences from marine high-plated populations and freshwater low-platedpopulations are shown in red and blue, respectively, along withrepresentative Alizarin Red stained fish showing typical armor platepatterns in different fish. The 16 kb candidate interval controlling armorplate number (blue bar, Colosimo et al.,2005) is shown beneath predicated genes in the region. Also shownare the numbered positions (4–16) of previously identified SNPs thatdifferentiate most low- and high-plated sticklebacks other than NAKA (Colosimo et al., 2005). These numberedSNPs correspond to positions chrIV: 12800508, 12808303, 12808630, 12811933,12813328, 12813394, 12815024, 12815027, 12816201, 12816202, 12816360,12816402, and 12816464 in the stickleback genome assembly (Jones et al., 2012). Blank positionsrepresent occasional gaps in sequence coverage for individual fish fromlarge population surveys (Colosimo et al.,2005; Jones et al.,2012). The position of the shared T → G change(chrIV:12811481) is indicated with a short black vertical line in theoverall genomic interval, and in a 3.2 kb region that was used to test forpossible regulatory enhancers in the EDA region (orangebar, chrIV:12808949–12812120).DOI:http://dx.doi.org/10.7554/eLife.05290.004
Mentions: Previous studies narrowed the minimal candidate interval controlling armor plates toa 16 kb interval containing EDA and flanking regions (Colosimo et al., 2005). To look for possibleshared molecular changes that might account for the regulatory difference betweenmarine and freshwater sticklebacks, we amplified and sequenced theEDA candidate interval from low-plated Japanese NAKA fish, andcompared it to other high- and low-plated stickleback populations (Figure 2 and ‘Materials andmethods’). This analysis identified a single T → G nucleotide change,located at position chrIV:12811481 (gasAcu1 assembly, Jones et al., 2012) in the intergenic region downstream ofEDA, that was shared between NAKA and all other low-platedsticklebacks examined.10.7554/eLife.05290.004Figure 2.All low-plated populations share a single base pair change in thegenetic region controlling armor plates.

Bottom Line: An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish.Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates.Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

View Article: PubMed Central - PubMed

Affiliation: Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.

ABSTRACT
Armor plate changes in sticklebacks are a classic example of repeated adaptive evolution. Previous studies identified ectodysplasin (EDA) gene as the major locus controlling recurrent plate loss in freshwater fish, though the causative DNA alterations were not known. Here we show that freshwater EDA alleles have cis-acting regulatory changes that reduce expression in developing plates and spines. An identical T → G base pair change is found in EDA enhancers of divergent low-plated fish. Recreation of the T → G change in a marine enhancer strongly reduces expression in posterior armor plates. Bead implantation and cell culture experiments show that Wnt signaling strongly activates the marine EDA enhancer, and the freshwater T → G change reduces Wnt responsiveness. Thus parallel evolution of low-plated sticklebacks has occurred through a shared DNA regulatory change, which reduces the sensitivity of an EDA enhancer to Wnt signaling, and alters expression in developing armor plates while preserving expression in other tissues.

Show MeSH