ArticlePLoS computational biology2011
Formation of regulatory modules by local sequence duplication.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 18 citations in OpenAlex.
- The genetic basis of mimicry in the snowy bumble bee (Bombus niveatus) in Anatolia with insights from a color polymorphic gynandromorph.PLoS genetics · 2026Article
- Exploring the complexity of genome size reduction in angiosperms.Plant molecular biology · 2024Review
- Evolutionary Origins of Pseudogenes and Their Association with Regulatory Sequences in Plants.The Plant cell · 2019Article
- Evolution of complex adaptations in molecular systems.Nature ecology & evolution · 2017Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- Dynamics of Transcription Factor Binding Site Evolution.PLoS genetics · 2015Article
- What does it take to evolve an enhancer? A simulation-based study of factors influencing the emergence of combinatorial regulation.Genome biology and evolution · 2015Article
- Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.Computational and structural biotechnology journal · 2014Review
- Natural insertions in rice commonly form tandem duplications indicative of patch-mediated double-strand break induction and repair.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Physical constraints determine the logic of bacterial promoter architectures.Nucleic acids research · 2014Article
- Simulations of enhancer evolution provide mechanistic insights into gene regulation.Molecular biology and evolution · 2014Article
- Lessons from the modular organization of the transcriptional regulatory network of Bacillus subtilis.BMC systems biology · 2013Article
- Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development.Nucleic acids research · 2013Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a common sequence origin by local duplications. This mode of evolution is found to produce regulatory information: duplications can seed new sites in the neighborhood of existing sites. Duplicate seeds evolve subsequently by point mutations, often towards binding a different factor than their ancestral neighbor sites. These results are based on a statistical analysis of 346 cis-regulatory modules in the Drosophila melanogaster genome, and a comparison set of intergenic regulatory sequence in Saccharomyces cerevisiae. In fly regulatory modules, pairs of binding sites show significantly enhanced sequence similarity up to distances of about 50 bp. We analyze these data in terms of an evolutionary model with two distinct modes of site formation: (i) evolution from independent sequence origin and (ii) divergent evolution following duplication of a common ancestor sequence. Our results suggest that pervasive formation of binding sites by local sequence duplications distinguishes the complex regulatory architecture of higher eukaryotes from the simpler architecture of unicellular organisms.
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