Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Proc Natl Acad Sci U S A
2005 Aug 16;10233:11769-74. doi: 10.1073/pnas.0505291102.
Show Gene links
Show Anatomy links
An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules.
Cameron RA
,
Chow SH
,
Berney K
,
Chiu TY
,
Yuan QA
,
Krämer A
,
Helguero A
,
Ransick A
,
Yun M
,
Davidson EH
.
???displayArticle.abstract???
The DNA of functional cis-regulatory modules displays extensive sequence conservation in comparisons of genomes from modestly distant species. Patches of sequence that are several hundred base pairs in length within these modules are often seen to be 80-95% identical, although the flanking sequence cannot even be aligned. However, it is unlikely that base pairs located between the transcription factor target sites of cis-regulatory modules have sequence-dependent function, and the mechanism that constrains evolutionary change within cis-regulatory modules is incompletely understood. We chose five functionally characterized cis-regulatory modules from the Strongylocentrotus purpuratus (sea urchin) genome and obtained orthologous regulatory and flanking sequences from a bacterial artificial chromosome genome library of a congener, Strongylocentrotus franciscanus. As expected, single-nucleotide substitutions and small indels occur freely at many positions within the regulatory modules of these two species, as they do outside the regulatory modules. However, large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence. The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA.
Altschul,
Basic local alignment search tool.
1990, Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Arnone,
The hardwiring of development: organization and function of genomic regulatory systems.
1997,
Pubmed
,
Echinobase
Balhoff,
Evolutionary analysis of the well characterized endo16 promoter reveals substantial variation within functional sites.
2005,
Pubmed
,
Echinobase
Biermann,
Phylogeny and development of marine model species: strongylocentrotid sea urchins.
2003,
Pubmed
,
Echinobase
Britten,
Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels.
2002,
Pubmed
Britten,
Majority of divergence between closely related DNA samples is due to indels.
2003,
Pubmed
,
Echinobase
Britten,
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty.
1971,
Pubmed
Brown,
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
2005,
Pubmed
Cameron,
A sea urchin genome project: sequence scan, virtual map, and additional resources.
2000,
Pubmed
,
Echinobase
Chapman,
Comparative and functional analyses of LYL1 loci establish marsupial sequences as a model for phylogenetic footprinting.
2003,
Pubmed
Davidson,
A genomic regulatory network for development.
2002,
Pubmed
,
Echinobase
Davidson,
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.
2002,
Pubmed
,
Echinobase
Erives,
Coordinate enhancers share common organizational features in the Drosophila genome.
2004,
Pubmed
Ewing,
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
1998,
Pubmed
Ewing,
Base-calling of automated sequencer traces using phred. II. Error probabilities.
1998,
Pubmed
Fujiyama,
Construction and analysis of a human-chimpanzee comparative clone map.
2002,
Pubmed
Gonzalez,
Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 echinoid species.
1999,
Pubmed
,
Echinobase
Gordon,
Consed: a graphical tool for sequence finishing.
1998,
Pubmed
Griffin,
New 3' elements control Pax6 expression in the developing pretectum, neural retina and olfactory region.
2002,
Pubmed
Göttgens,
Analysis of vertebrate SCL loci identifies conserved enhancers.
2000,
Pubmed
Göttgens,
Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences.
2001,
Pubmed
Hall,
Evolution of sea urchin non-repetitive DNA.
1980,
Pubmed
,
Echinobase
Hardison,
Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights.
1997,
Pubmed
Istrail,
Logic functions of the genomic cis-regulatory code.
2005,
Pubmed
,
Echinobase
Kammandel,
Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity.
1999,
Pubmed
Kim,
Hox cluster genomics in the horn shark, Heterodontus francisci.
2000,
Pubmed
Kim,
Macro-evolution of the hairy enhancer in Drosophila species.
2001,
Pubmed
Kimura-Yoshida,
Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification.
2004,
Pubmed
Kirchhamer,
Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples.
1996,
Pubmed
,
Echinobase
Kirchhamer,
Spatial and temporal information processing in the sea urchin embryo: modular and intramodular organization of the CyIIIa gene cis-regulatory system.
1996,
Pubmed
,
Echinobase
Kleinjan,
Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription.
2004,
Pubmed
Kurokawa,
Regulation of Otx2 expression and its functions in mouse epiblast and anterior neuroectoderm.
2004,
Pubmed
Langeland,
Conservation of regulatory elements controlling hairy pair-rule stripe formation.
1993,
Pubmed
Lee,
Expression of Spgatae, the Strongylocentrotus purpuratus ortholog of vertebrate GATA4/5/6 factors.
2004,
Pubmed
,
Echinobase
Lee,
Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida.
2003,
Pubmed
,
Echinobase
Levine,
Gene regulatory networks for development.
2005,
Pubmed
,
Echinobase
Li,
Requirement of SpOtx in cell fate decisions in the sea urchin embryo and possible role as a mediator of beta-catenin signaling.
1999,
Pubmed
,
Echinobase
Littlewood,
A combined morphological and molecular phylogeny for sea urchins (Echinoidea: Echinodermata).
1995,
Pubmed
,
Echinobase
Ludwig,
Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.
1998,
Pubmed
Margulies,
Detecting highly conserved regions of the human genome by multispecies sequence comparisons.
2003,
Pubmed
Oda-Ishii,
Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis.
2005,
Pubmed
Oliveri,
Gene regulatory network controlling embryonic specification in the sea urchin.
2004,
Pubmed
,
Echinobase
Pennacchio,
Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome.
2003,
Pubmed
Ransick,
New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization.
2002,
Pubmed
,
Echinobase
Revilla-i-Domingo,
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres.
2004,
Pubmed
,
Echinobase
Romano,
Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation.
2003,
Pubmed
,
Echinobase
Shashikant,
Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element.
1998,
Pubmed
,
Echinobase
Soltysik-Española,
Endo16, a large multidomain protein found on the surface and ECM of endodermal cells during sea urchin gastrulation, binds calcium.
1994,
Pubmed
,
Echinobase
Springer,
Phylogeny, rates of evolution, and patterns of codon usage among sea urchin retroviral-like elements, with implications for the recognition of horizontal transfer.
1995,
Pubmed
,
Echinobase
Sweet,
LvDelta is a mesoderm-inducing signal in the sea urchin embryo and can endow blastomeres with organizer-like properties.
2002,
Pubmed
,
Echinobase
Thompson,
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
1997,
Pubmed
Tümpel,
Conservation and diversity in the cis-regulatory networks that integrate information controlling expression of Hoxa2 in hindbrain and cranial neural crest cells in vertebrates.
2002,
Pubmed
Uchikawa,
Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals.
2003,
Pubmed
Wikramanayake,
Nuclear beta-catenin-dependent Wnt8 signaling in vegetal cells of the early sea urchin embryo regulates gastrulation and differentiation of endoderm and mesodermal cell lineages.
2004,
Pubmed
,
Echinobase
Williams,
Organization of wing formation and induction of a wing-patterning gene at the dorsal/ventral compartment boundary.
1994,
Pubmed
Yuh,
Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.
2001,
Pubmed
,
Echinobase
Yuh,
An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network.
2004,
Pubmed
,
Echinobase
Yuh,
Complexity and organization of DNA-protein interactions in the 5'-regulatory region of an endoderm-specific marker gene in the sea urchin embryo.
1994,
Pubmed
,
Echinobase
Yuh,
Modular cis-regulatory organization of Endo16, a gut-specific gene of the sea urchin embryo.
1996,
Pubmed
,
Echinobase
Yuh,
Quantitative functional interrelations within the cis-regulatory system of the S. purpuratus Endo16 gene.
1996,
Pubmed
,
Echinobase
Yuh,
Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.
1998,
Pubmed
,
Echinobase
