Mesoscale Modeling of Chromatin Fibers

Gavin D. Bascom, Tamar Schlick

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Although many computational approaches for treating general nucleic acids exist, there are few available for treating the nucleic-acid/protein complex which packages eukaryotic DNA, namely the chromatin fiber. Understanding chromatin structure and its relation to function has been an enduring challenge for biology. Here we describe the evolution, mechanics, and analysis of a computational model on the mesoscale level to investigate chromatin fibers up to several hundred nucleosomes. The rigid nucleosome core particle is considered the basic subunit for modeling, and histone tails, DNA linkers, and linker histones are treated as flexible beads. Following a description of the structure and function of chromatin constituents, including histone core proteins and their protruding tails, we review chromatin secondary and tertiary structures up to the gene level. We briefly describe the evolution of our mesoscale model and its application to a variety of chromatin structure/function problems. Details of all energy functions, model mechanics, sampling methods, and model parameters are given, along with analytical techniques for quantifying both local and global properties of chromatin fibers. Future developments and applications are outlined.

Original languageEnglish (US)
Title of host publicationNuclear Architecture and Dynamics
PublisherElsevier
Pages123-147
Number of pages25
ISBN (Electronic)9780128034804
DOIs
StatePublished - Jan 1 2017

Keywords

  • Chromatin architecture
  • Chromatin fibers
  • Coarse-grained modeling
  • Contact maps
  • Equlilibrium sampling
  • Gene elements
  • Multiscale modeling

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Fingerprint

Dive into the research topics of 'Mesoscale Modeling of Chromatin Fibers'. Together they form a unique fingerprint.

Cite this