Bridging chromatin structure and function over a range of experimental spatial and temporal scales by molecular modeling

Stephanie Portillo-Ledesma, Tamar Schlick

Research output: Contribution to journalReview article

Abstract

Chromatin structure, dynamics, and function are being intensely investigated by a variety of methods, including microscopy, X-ray diffraction, nuclear magnetic resonance, biochemical crosslinking, chromosome conformation capture, and computation. The modeling helps interpret experimental data and generate configurations and mechanisms related to the three-dimensional organization and function of the genome. Experimental contact maps, in particular, as obtained by a variety of chromosome conformation capture methods, are of increasing interest due to their implications on genome structure and regulation on many levels. In this perspective, using seven examples from our group's studies, we illustrate how molecular modeling can help interpret such experimental data. Specifically, we show how computed contact maps related to experimental systems can help interpret structures of nucleosomes, chromatin higher-order folding, domain segregation mechanisms, gene organization, and the effect on chromatin structure of external and internal fiber parameters, such as nucleosome positioning, presence of nucleosome free regions, histone post-translational modifications, and linker histone binding. We argue that such computations on multiple spatial and temporal scales will be increasingly important for the integration of genomic, epigenomic, and biophysical data on chromatin structure and related cellular processes. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics.

Original languageEnglish (US)
Article numbere1434
JournalWiley Interdisciplinary Reviews: Computational Molecular Science
Volume10
Issue number2
DOIs
StatePublished - Mar 1 2020

Keywords

  • chromatin structure and function
  • experimental techniques
  • mesoscale modeling

ASJC Scopus subject areas

  • Biochemistry
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computational Mathematics
  • Materials Chemistry

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