Long range clustering of oligonucleotides containing the CG signal

P. Katsaloulis (1, 2) , T. Theoharis (1) , A. Provata (2)

1 Department of Informatics and Telecommunications
2 NCSR - National Center for Scientific Research "Demokritos"

The distance distributions between successive occurrences of the same oligonucleotides in chromosomal DNA are studied, in different classes of higher eucaryotic organisms. A two-parameter modeling is undertaken and applied on the distance distribution of quintuplets (sequences of size five bps) and hexaplets (sequences of size six bps); the first parameter refers to the short range exponential decay of the distributions, whereas the second parameter m refers to the power law behavior. A 2-dimensional scatter plot representing the model equation demonstrates that the points corresponding to the distance distribution of oligonucleotides containing the CG consensus sequence (promoter of the RNA polymerase II) cluster together (group α), apart from all other oligonucleotides (group β). This is shown for the available chordata Homosapiens, Pantroglodytes, Musmusculus, Rattusnorvegicus, Gallusgallus and Daniorerio. This clustering is less evident in lower Animalia and plants, such as Drosophilamelanogaster, Caenorhabditiselegans and Arabidopsisthaliana. Moreover, in all organisms the oligonucleotides which contain any consensus sequence are found to be described by long range distributions, whereas all others have a stronger influence of short range decay. Various measures are introduced and evaluated, to numerically characterize the clustering of the two groups. The one which most clearly discriminates the two classes is shown to be the Proximity Factor.

Mots clés: Long-range correlations; Genome organisation; Power law distributions; Promoters

P. Katsaloulis, T. Theoharis, A. Provata. Long range clustering of oligonucleotides containing the CG signal. Journal of Theoretical Biology, 2009, 258 (1), pp.18. ⟨10.1016/j.jtbi.2009.01.014⟩. ⟨hal-00554563⟩