Journal article
Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts
PLoS biology, Vol.6(11), pp.2576-2587
11/2008
DOI: 10.1371/journal.pbio.0060263
PMCID: PMC2577699
PMID: 18986212
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.
Characterizing neuroectodermal enhancers located throughout the genomes of three
Drosophila
species reveals that each enhancer evolved functional adaptations that compensate for the evolutionary changes specific to each lineage.
Details
- Title: Subtitle
- Evolution Acts on Enhancer Organization to Fine-Tune Gradient Threshold Readouts
- Creators
- Justin Crocker - Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America University of California, Berkeley, United States of AmericaYoichiro Tamori - Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America University of California, Berkeley, United States of AmericaAlbert Erives - Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America University of California, Berkeley, United States of America
- Resource Type
- Journal article
- Publication Details
- PLoS biology, Vol.6(11), pp.2576-2587
- DOI
- 10.1371/journal.pbio.0060263
- PMID
- 18986212
- PMCID
- PMC2577699
- NLM abbreviation
- PLoS Biol
- ISSN
- 1544-9173
- eISSN
- 1545-7885
- Publisher
- Public Library of Science
- Alternative title
- Adaptations Stored in Enhancer Organization
- Language
- English
- Date published
- 11/2008
- Academic Unit
- Biology
- Record Identifier
- 9984217533502771
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