Advanced search
1 file | 374.52 KB

Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus

(2009) Journal of Molecular Evolution. 69(3). p.249-259
Author
Organization
Abstract
We used a phylogenetic footprinting approach, adapted to high levels of divergence, to estimate the level of constraint in intergenic regions of the extremely gene dense Ostreococcus algae genomes (Chlorophyta, Prasinophyceae). We first benchmarked our method against the Saccharomyces sensu stricto genome data and found that the proportion of conserved non-coding sites was consistent with those obtained with methods using calibration by the neutral substitution rate. We then applied our method to the complete genomes of Ostreococcus tauri and O. lucimarinus, which are the most divergent species from the same genus sequenced so far. We found that 77% of intergenic regions in Ostreococcus still contain some phylogenetic footprints, as compared to 88% for Saccharomyces, corresponding to an average rate of constraint on intergenic region of 17% and 30%, respectively. A comparison with some known functional cis-regulatory elements enabled us to investigate whether some transcriptional regulatory pathways were conserved throughout the green lineage. Strikingly, the size of the phylogenetic footprints depends on gene orientation of neighboring genes, and appears to be genus-specific. In Ostreococcus, 5' intergenic regions contain four times more conserved sites than 3' intergenic regions, whereas in yeast a higher frequency of constrained sites in intergenic regions between genes on the same DNA strand suggests a higher frequency of bidirectional regulatory elements. The phylogenetic footprinting approach can be used despite high levels of divergence in the ultrasmall Ostreococcus algae, to decipher structure of constrained regulatory motifs, and identify putative regulatory pathways conserved within the green lineage.
Keywords
Ostreococcus, Saccharomyces, cis-regulatory elements, Phylogenetic footprinting, Non-coding DNA

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 374.52 KB

Citation

Please use this url to cite or link to this publication:

Chicago
Piganeau, Gwenael, Klaas Vandepoele, Sébastien Gourbière, Yves Van de Peer, and Hervé Moreau. 2009. “Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus.” Journal of Molecular Evolution 69 (3): 249–259.
APA
Piganeau, Gwenael, Vandepoele, K., Gourbière, S., Van de Peer, Y., & Moreau, H. (2009). Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus. Journal of Molecular Evolution, 69(3), 249–259.
Vancouver
1.
Piganeau G, Vandepoele K, Gourbière S, Van de Peer Y, Moreau H. Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus. Journal of Molecular Evolution. New York, NY: Springer; 2009;69(3):249–59.
MLA
Piganeau, Gwenael, Klaas Vandepoele, Sébastien Gourbière, et al. “Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus.” Journal of Molecular Evolution 69.3 (2009): 249–259. Print.
@article{771437,
  abstract     = {We used a phylogenetic footprinting approach, adapted to high levels of divergence, to estimate the level of constraint in intergenic regions of the extremely gene dense Ostreococcus algae genomes (Chlorophyta, Prasinophyceae). We first benchmarked our method against the Saccharomyces sensu stricto genome data and found that the proportion of conserved non-coding sites was consistent with those obtained with methods using calibration by the neutral substitution rate. We then applied our method to the complete genomes of Ostreococcus tauri and O. lucimarinus, which are the most divergent species from the same genus sequenced so far. We found that 77\% of intergenic regions in Ostreococcus still contain some phylogenetic footprints, as compared to 88\% for Saccharomyces, corresponding to an average rate of constraint on intergenic region of 17\% and 30\%, respectively. A comparison with some known functional cis-regulatory elements enabled us to investigate whether some transcriptional regulatory pathways were conserved throughout the green lineage. Strikingly, the size of the phylogenetic footprints depends on gene orientation of neighboring genes, and appears to be genus-specific. In Ostreococcus, 5' intergenic regions contain four times more conserved sites than 3' intergenic regions, whereas in yeast a higher frequency of constrained sites in intergenic regions between genes on the same DNA strand suggests a higher frequency of bidirectional regulatory elements. The phylogenetic footprinting approach can be used despite high levels of divergence in the ultrasmall Ostreococcus algae, to decipher structure of constrained regulatory motifs, and identify putative regulatory pathways conserved within the green lineage.},
  author       = {Piganeau, Gwenael and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Van de Peer, Yves and Moreau, Herv{\'e}},
  issn         = {0022-2844},
  journal      = {Journal of Molecular Evolution},
  language     = {eng},
  number       = {3},
  pages        = {249--259},
  publisher    = {Springer},
  title        = {Unravelling cis-Regulatory Elements in the Genome of the Smallest Photosynthetic Eukaryote: Phylogenetic Footprinting in Ostreococcus},
  url          = {http://dx.doi.org/10.1007/s00239-009-9271-0},
  volume       = {69},
  year         = {2009},
}

Altmetric
View in Altmetric
Web of Science
Times cited: