Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence.

the exact positions of nucleosomes play crucial roles in chromatin function.

DNA molecules are much longer than the cells that contain them. This requires their compaction, which introduces also an opportunity: the regulation of transcription through a differentiated fashion of DNA packaging. In eukaryotes DNA molecules can guide their own packaging into nucleosomes by having the desired mechanical properties (stiffnesses and intrinsic curvature) written into their base-pair (bp) sequence. This has been referred to as the “nucleosome positioning code”

As the DNA is strongly deformed when wrapped around the histones, sequence-dependent geometrical and mechanical properties could—at least locally—overrule other effects that also influence nucleosome positioning like the presence of proteins that compete for the same DNA stretch or the action of chromatin remodellers

Nucleosomes can thus be considered as a highly diverse class of DNA-protein complexes with a near continuous range of physical properties.