Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
The coexistence of the DNA organization code with the protein code on the DNA double helix
It is now known that there are several codes residing simultaneously on the DNA double helix. The two best characterized codes are the genetic code ? the code for protein production, and the code for DNA organization, or packaging into nucleosomes. Since these codes have to co-exist simultaneously on the same DNA region, there must be degeneracy in both codes to allow their co-existence. Adenine tracts (?A-tracts?) are homopolymeric stretches of several adjacent adenosines on one strand of the double helix, having unusual structural properties, which were shown to be important in influencing DNA organization in nucleosomes. A-tracts were shown to exclude nucleosomes and as such are instrumental in setting the translational positioning of DNA within nucleosomes. This enables the coding regions to be densely packaged within nucleosomes, whereas regulatory regions are usually devoid of nucleosomes, or packaged less densely. In our study we observe that long A-tracts deficiency characterize only the exon regions within coding regions. Moreover we observe, cross kingdoms, a strong codon bias towards the avoidance of long A-tracts in coding regions, which enables the formation of high density of nucleosomes in these regions. We show that this bias in codon usage is sufficient for enabling DNA organization within nucleosomes without constrains on the actual protein code. Thus, there is a co-dependency, or inter-dependency, of the two major codes within DNA to allow their simultaneous co-existence. In addition, we will discuss a new model for the higher order organization of nucleosomes in coding regions.
Department of Biology