Seminar

Latest on the chromatin code - high resolution sequence positioning of the nucleosomes.

Prof. Edward N.Trifonov

After 30 years of agony of many labs in attempts to derive sequence rules that determine nucleosome positions, the positioning pattern is finally established by three different approaches. The signal is exceptionally weak, so that only when genome-wide database of nucleosome DNA sequences recently became available, it became also possible to extract the pattern. Applied to sequences on which the nucleosomes have been formed and crystallized, the pattern allows to identify the nucleosome centers with only 1 base uncertainty. High resolution mapping allowed to discover preferential protective orientation of gene splice junctions in nucleosome DNA, and to demonstrate that the nucleosomes are formed on regions encoding synchronized amphipathic helices. One period of the typical ideal nucleosome DNA (making deadly strong nucleosomes) is described by the motif CGGAAATTTCCG. The pattern in G+C rich isochores is rather CGGGGGCCCCCG, while in A+T rich isochores it is TAAAAATTTTTA. All conform to YRRRRRYYYYYR, the motif corresponding to minimal bending energy cost.