Publication details

Single-Base Resolution Sequence-Directed Nucleosome Mapping


TRIFONOV Eduard Nikolajevič HAPALA Jan

Year of publication 2013
Type Article in Periodical
Magazine / Source Israel Journal of Chemistry
MU Faculty or unit

Central European Institute of Technology

Field Genetics and molecular biology
Keywords DNA; ucleobases; nucleosome positioning; regulation of transcription; TATA box
Description Frequently used nucleosome mapping techniques, both experimental and computational ones, pursue a rather simple task to determine whether a given sequence segment is likely to belong to a nucleosome, thus measuring the nucleosome occupancy along the sequence. A more ambitious task is to determine the position with high resolution, so that not only the approximate translational position of the nucleosome on DNA would be known, but also the rotational setting of the DNA. The rotational setting is important to know since the binding of various transcription factors to the nucleosome DNA crucially depends on the accessibility of the respective recognition sequences. The only experimental technique that provides the highest possible accuracy of the positioning is crystallization of the nucleosomes reconstituted on specific sequences, with subsequent solving of their structures from x-ray diffraction data. Two computational approaches to the accurate positioning of nucleosomes, based on energy calculations and on sequence patterndirected mapping, are currently in different stages of progress.
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