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Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers.

Crocker J, Potter N, Erives A - Nat Commun (2010)

Bottom Line: However, NEEs also possess dense clusters of variant Dl sites.Here, we show that these increasingly variant sites are eclipsed relic elements, which were superseded by more recently evolved threshold encodings.Given the divergence in egg size during Drosophila lineage evolution, the observed characteristic clusters of divergent sites indicate a history of frequent selection for changes in threshold responses to the Dl morphogen gradient and confirm the NEE structure/function model.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.

ABSTRACT
Concentration gradients of morphogenic proteins pattern the embryonic axes of Drosophila by activating different genes at different concentrations. The neurogenic ectoderm enhancers (NEEs) activate different genes at different threshold levels of the Dorsal (Dl) morphogen, which patterns the dorsal/ventral axis. NEEs share a unique arrangement of highly constrained DNA-binding sites for Dl, Twist (Twi), Snail (Sna) and Suppressor of Hairless (Su(H)), and encode the threshold variable in the precise length of DNA that separates one well-defined Dl element from a Twi element. However, NEEs also possess dense clusters of variant Dl sites. Here, we show that these increasingly variant sites are eclipsed relic elements, which were superseded by more recently evolved threshold encodings. Given the divergence in egg size during Drosophila lineage evolution, the observed characteristic clusters of divergent sites indicate a history of frequent selection for changes in threshold responses to the Dl morphogen gradient and confirm the NEE structure/function model.

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Recently evolved NEEs have not accumulated relic element clusters.(a–d) NEE-driven lacZ in situ hybridization experiments for D. ananassae (D. ana.) NEEs. Shown are lateral stripe expression patterns that are typical of multiple transgenic D. melanogaster lines made with the D. ananassae NEEs from vn (a), vnd (b), rho (c) and brk (d). (e) Diagram of relic site clusters for the Delta and vnd NEEs from D. ananassae. Matches to CA satellite on either strand (black), Su(H)-binding motif (red), E(CA)T (orange), Dβ (dark blue) and a Dβ motif spectrum (light blue) are visualized in separate numbered tracks (1–7) at the top and described in more detail below. CA satellite is defined here as sequences matching two CA-dinucleotide repeats or longer given by the perl regular expression: 'A?(CA){2,}C?'. (f) The typical lacZ in situ hybridization experiment for D. ananassae Delta NEE. (g) A comparison of the Delta NEE Su(H)-binding site and downstream flanking sequence and the Dα motif for D. ananassae. The flanking sequence at the Delta site (black lettering) is unrelated to a Dl half-site.
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f7: Recently evolved NEEs have not accumulated relic element clusters.(a–d) NEE-driven lacZ in situ hybridization experiments for D. ananassae (D. ana.) NEEs. Shown are lateral stripe expression patterns that are typical of multiple transgenic D. melanogaster lines made with the D. ananassae NEEs from vn (a), vnd (b), rho (c) and brk (d). (e) Diagram of relic site clusters for the Delta and vnd NEEs from D. ananassae. Matches to CA satellite on either strand (black), Su(H)-binding motif (red), E(CA)T (orange), Dβ (dark blue) and a Dβ motif spectrum (light blue) are visualized in separate numbered tracks (1–7) at the top and described in more detail below. CA satellite is defined here as sequences matching two CA-dinucleotide repeats or longer given by the perl regular expression: 'A?(CA){2,}C?'. (f) The typical lacZ in situ hybridization experiment for D. ananassae Delta NEE. (g) A comparison of the Delta NEE Su(H)-binding site and downstream flanking sequence and the Dα motif for D. ananassae. The flanking sequence at the Delta site (black lettering) is unrelated to a Dl half-site.

Mentions: From the D. ananassae genome, we cloned and assayed both a functional set of canonical NEEs (Fig. 7a–d) and a new NEE at the Delta locus (Fig. 7e–f). Delta encodes a ligand for the Notch receptor, whose signalling is relayed by Su(H)4748. In D. melanogaster embryos, Delta is expressed in a narrow lateral stripe in the mesectoderm and ventral-most row of the neurogenic ectoderm using sequences that are unrelated to the unique NEEDelta sequence of D. ananassae49. This NEEDelta sequence has not acquired either CA-satellite fragments or Dl relic sequences (Fig. 7e). Nonetheless, this enhancer is functional in D. melanogaster embryos (Fig. 7f). Furthermore, its Su(H)-binding site does not overlap the ghost Dα motif that characterizes the canonical NEEs of the genus (Fig. 7g). Altogether, our data on the NEEDelta sequence suggest a shorter period of evolutionary maintenance, as is consistent with its more recent phylogenetic origin relative to canonical NEEs.


Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers.

Crocker J, Potter N, Erives A - Nat Commun (2010)

Recently evolved NEEs have not accumulated relic element clusters.(a–d) NEE-driven lacZ in situ hybridization experiments for D. ananassae (D. ana.) NEEs. Shown are lateral stripe expression patterns that are typical of multiple transgenic D. melanogaster lines made with the D. ananassae NEEs from vn (a), vnd (b), rho (c) and brk (d). (e) Diagram of relic site clusters for the Delta and vnd NEEs from D. ananassae. Matches to CA satellite on either strand (black), Su(H)-binding motif (red), E(CA)T (orange), Dβ (dark blue) and a Dβ motif spectrum (light blue) are visualized in separate numbered tracks (1–7) at the top and described in more detail below. CA satellite is defined here as sequences matching two CA-dinucleotide repeats or longer given by the perl regular expression: 'A?(CA){2,}C?'. (f) The typical lacZ in situ hybridization experiment for D. ananassae Delta NEE. (g) A comparison of the Delta NEE Su(H)-binding site and downstream flanking sequence and the Dα motif for D. ananassae. The flanking sequence at the Delta site (black lettering) is unrelated to a Dl half-site.
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f7: Recently evolved NEEs have not accumulated relic element clusters.(a–d) NEE-driven lacZ in situ hybridization experiments for D. ananassae (D. ana.) NEEs. Shown are lateral stripe expression patterns that are typical of multiple transgenic D. melanogaster lines made with the D. ananassae NEEs from vn (a), vnd (b), rho (c) and brk (d). (e) Diagram of relic site clusters for the Delta and vnd NEEs from D. ananassae. Matches to CA satellite on either strand (black), Su(H)-binding motif (red), E(CA)T (orange), Dβ (dark blue) and a Dβ motif spectrum (light blue) are visualized in separate numbered tracks (1–7) at the top and described in more detail below. CA satellite is defined here as sequences matching two CA-dinucleotide repeats or longer given by the perl regular expression: 'A?(CA){2,}C?'. (f) The typical lacZ in situ hybridization experiment for D. ananassae Delta NEE. (g) A comparison of the Delta NEE Su(H)-binding site and downstream flanking sequence and the Dα motif for D. ananassae. The flanking sequence at the Delta site (black lettering) is unrelated to a Dl half-site.
Mentions: From the D. ananassae genome, we cloned and assayed both a functional set of canonical NEEs (Fig. 7a–d) and a new NEE at the Delta locus (Fig. 7e–f). Delta encodes a ligand for the Notch receptor, whose signalling is relayed by Su(H)4748. In D. melanogaster embryos, Delta is expressed in a narrow lateral stripe in the mesectoderm and ventral-most row of the neurogenic ectoderm using sequences that are unrelated to the unique NEEDelta sequence of D. ananassae49. This NEEDelta sequence has not acquired either CA-satellite fragments or Dl relic sequences (Fig. 7e). Nonetheless, this enhancer is functional in D. melanogaster embryos (Fig. 7f). Furthermore, its Su(H)-binding site does not overlap the ghost Dα motif that characterizes the canonical NEEs of the genus (Fig. 7g). Altogether, our data on the NEEDelta sequence suggest a shorter period of evolutionary maintenance, as is consistent with its more recent phylogenetic origin relative to canonical NEEs.

Bottom Line: However, NEEs also possess dense clusters of variant Dl sites.Here, we show that these increasingly variant sites are eclipsed relic elements, which were superseded by more recently evolved threshold encodings.Given the divergence in egg size during Drosophila lineage evolution, the observed characteristic clusters of divergent sites indicate a history of frequent selection for changes in threshold responses to the Dl morphogen gradient and confirm the NEE structure/function model.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.

ABSTRACT
Concentration gradients of morphogenic proteins pattern the embryonic axes of Drosophila by activating different genes at different concentrations. The neurogenic ectoderm enhancers (NEEs) activate different genes at different threshold levels of the Dorsal (Dl) morphogen, which patterns the dorsal/ventral axis. NEEs share a unique arrangement of highly constrained DNA-binding sites for Dl, Twist (Twi), Snail (Sna) and Suppressor of Hairless (Su(H)), and encode the threshold variable in the precise length of DNA that separates one well-defined Dl element from a Twi element. However, NEEs also possess dense clusters of variant Dl sites. Here, we show that these increasingly variant sites are eclipsed relic elements, which were superseded by more recently evolved threshold encodings. Given the divergence in egg size during Drosophila lineage evolution, the observed characteristic clusters of divergent sites indicate a history of frequent selection for changes in threshold responses to the Dl morphogen gradient and confirm the NEE structure/function model.

Show MeSH