ArticleProceedings of the National Academy of Sciences of the United States of America2005
An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Complex signatures of genomic variation of two non-model marine species in a homogeneous environment.BMC genomics · 2018Article
- A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer.Nature communications · 2017Article
- Convergent occurrence of the developmental hourglass in plant and animal embryogenesis?Annals of botany · 2016Review
- Evolutionary Footprints of Short Tandem Repeats in Avian Promoters.Scientific reports · 2016Article
- Do echinoderm genomes measure up?Marine genomics · 2015Review
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- Theory of the origin, evolution, and nature of life.Life (Basel, Switzerland) · 2011Article
- Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites.BMC evolutionary biology · 2009Article
- Evolution of regulatory sequences in 12 Drosophila species.PLoS genetics · 2009Article
- Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.Genome research · 2008Article
- Noncanonical DNA motifs as transactivation targets by wild type and mutant p53.PLoS genetics · 2008Article
- A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.Developmental biology · 2008Article
- Recent computational approaches to understand gene regulation: mining gene regulation in silico.Current genomics · 2007Article
- Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication.Plant physiology · 2006Article
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Authors and funding
10 authors.
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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.
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