The role of transcript regions and amino acid choice in nucleosome positioning.

Eukaryotic DNA is organized and compacted in a string of nucleosomes, DNA-wrapped protein cylinders. The positions of nucleosomes along DNA are not random but show well-known base pair sequence preferences that result from the sequence-dependent elastic and geometric properties of the DNA double helix. Here, we focus on DNA around transcription start sites, which are known to typically attract nucleosomes in multicellular life forms through their high GC content.

Multiplexing mechanical and translational cues on genes.

The genetic code gives precise instructions on how to translate codons into amino acids. Due to the degeneracy of the genetic code-18 out of 20 amino acids are encoded for by more than one codon-more information can be stored in a basepair sequence. Indeed, various types of additional information have been discussed in the literature, e.

Shortest paths through synonymous genomes.

The elasticity of the DNA double helix varies with the underlying base pair sequence. This allows one to put mechanical cues into sequences that in turn influence the packaging of DNA into nucleosomes, DNA-wrapped protein cylinders. Nucleosomes dictate a broad range of biological processes, ranging from gene regulation, recombination, and replication to chromosome condensation.

Physics behind the mechanical nucleosome positioning code.

The positions along DNA molecules of nucleosomes, the most abundant DNA-protein complexes in cells, are influenced by the sequence-dependent DNA mechanics and geometry. This leads to the "nucleosome positioning code", a preference of nucleosomes for certain sequence motives. Here we introduce a simplified model of the nucleosome where a coarse-grained DNA molecule is frozen into an idealized superhelical shape.