Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.

Logie, Colin

The van Noort (Leiden) and Logie (NCMLS) groups  report a statistical mechanics model that captures DNA sequence preferences for nucleosome positioning in the Proceedings of the National Academy of Science (USA) issue of 20th August. Essentially, upon DNA wrapping around the histone octamer, AA, TT and TA dinucleotides are favored on the inner surface of the DNA superhelix , while GC dinucleotides preferentially face outwards. In combination with Percus' equation, a system of  three parameters (period, amplitude and chemical potential) accurately predicts experimentally defined nucleosome positions. Hence, a new DNA code is identified which dictates where nucleosomes are positioned, predicting (regulatory) DNA sequences that are occluded or accessible in nucleosome arrays. Deviations from predictions are likely due to enzyme mediated chromatin remodeling, as shown for the +1 nucleosome of transcription units. An on-line tool to analyze your DNA sequence of interest is available: link.  

Read more (dutch): link

van der Heijden T, van Vugt JJ, Logie C, van Noort J. Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy. Proc Natl Acad Sci U S A. 2012 Aug 20.


<< back to overview news items