Physics behind the mechanical nucleosome positioning code

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Martijn Zuiddam - , Leiden University (Author)
  • Ralf Everaers - , École normale supérieure de Lyon (Author)
  • Helmut Schiessel - , Leiden University (Author)

Abstract

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. We calculate the exact sequence preferences of our nucleosome model and find it to reproduce qualitatively all the main features known to influence nucleosome positions. Moreover, using well-controlled approximations to this model allows us to come to a detailed understanding of the physics behind the sequence preferences of nucleosomes.

Details

Original languageEnglish
Article number052412
JournalPhysical Review E
Volume96
Issue number5
Publication statusPublished - 28 Nov 2017
Peer-reviewedYes
Externally publishedYes

External IDs

PubMed 29347769