Over het archief
Het OWA, het open archief van het Waterbouwkundig Laboratorium heeft tot doel alle vrij toegankelijke onderzoeksresultaten van dit instituut in digitale vorm aan te bieden. Op die manier wil het de zichtbaarheid, verspreiding en gebruik van deze onderzoeksresultaten, alsook de wetenschappelijke communicatie maximaal bevorderen.
Dit archief wordt uitgebouwd en beheerd volgens de principes van de Open Access Movement, en het daaruit ontstane Open Archives Initiative.
Basisinformatie over ‘Open Access to scholarly information'.
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic Eukaryote: phylogenetic footprinting in Ostreococcus
Piganeau, G.; 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. J. Mol. Evol. 69(3): 249-259. https://dx.doi.org/10.1007/s00239-009-9271-0
In: Journal of Molecular Evolution. Springer-Verlag: New York. ISSN 0022-2844; e-ISSN 1432-1432, meer
|  |
| Trefwoorden |
Ostreococcus C.Courties & M.-J.Chrétiennot-Dinet, 1995 [WoRMS]; Saccharomyces Meyen ex E.C. Hansen, 1838 [WoRMS]
Marien/Kust |
| Author keywords |
Phylogenetic footprinting Non-coding DNA cis-regulatory elements Saccharomyces Ostreococcus |
| Auteurs | | Top |
- Piganeau, G.
- Vandepoele, K., meer
- Gourbière, S.
|
- Van de Peer, Y., meer
- Moreau, H.
|
|
| 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. |
IMIS is ontwikkeld en wordt gehost door het VLIZ.
