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Sequence rules for nucleosome positioning and chromatin architecture

Orateur :

Edward N. Trifonov, Genome Diversity Center, Institute of Evolution, University of Haifa, Israel

Salle :

C023 (RDC LR6 côté CECAM)

Sujet :

It is commonly believed that the sequence pattern responsible for nucleosome positioning is periodical alternation of AA and TT dinucleotides. While it is true, indeed, for the nucleosomes of yeast, human nucleosomes display a very different pattern - periodicity of GG and CC dinucleotides. Actually, there are at least four patterns, all suitable for the nucleosomes. The customary pattern is counter-phase oscillation of AA and TT dinucleotides, that is explained by the strong influence of sequence biases due to amphipathic alpha helices encoded in DNA. At the same time yeast and other eukaryotic genomes display an in-phase 10.4 base periodicity of AA and TT, not related to the alpha helices, which we consider as second major nucleosome sequence pattern. A strong 10.4 base counter-phase RR/YY periodicity is discovered in human DNA, with major contribution of GG/CC dinucleotides, and only marginal contribution of AA/TT. It appears, thus, that there are several strong periodical patterns that suit the histone octamers : 1)Counter-phase AA/TT, 2)Counter-phase GG/CC, 3)Counter-phase RR/YY and 4)In-phase AA/TT. These four patterns are not inconsistent with one another, and can be combined in a dinucleotide matrix of bendability which, thus, may serve as universal nucleosome positioning pattern. Other important issues to be discussed : structural DNA periodicity in the nucleosome ; physics of in-phase and counter-phase preferences ; sterical exclusion rules and linker lengths ; species-specificity of the nucleosome patterns ; protective role of the nucleosomes ; chromatin structure of promoter regions.

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