Genome Structure Determination via 3C-based Data Integration by the Integrative Modeling Platform

Methods. 2012 Nov;58(3):300-6. doi: 10.1016/j.ymeth.2012.04.004. Epub 2012 Apr 13.

Abstract

The three-dimensional (3D) architecture of a genome determines the spatial localization of regulatory elements and the genes they regulate. Thus, elucidating the 3D structure of a genome may result in significant insights about how genes are regulated. The current state-of-the art in experimental methods, including light microscopy and cell/molecular biology, are now able to provide detailed information on the position of genes and their interacting partners. However, such methods by themselves are not able to determine the high-resolution 3D structure of genomes or genomic domains. Here we describe a computational module of the Integrative Modeling Platform (IMP, http://www.integrativemodeling.org) that uses chromosome conformation capture data to determine the 3D architecture of genomic domains and entire genomes at unprecedented resolutions. This approach, through the visualization of looping interactions between distal regulatory elements, allows characterizing global chromatin features and their relation to gene expression. We illustrate our work by outlining the determination of the 3D architecture of the α-globin domain in the human genome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Calibration
  • Chromatin / genetics*
  • Chromatin / ultrastructure
  • Chromosome Mapping*
  • Cluster Analysis
  • Epistasis, Genetic
  • Humans
  • Markov Chains
  • Models, Genetic
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Protein Structure, Tertiary
  • alpha-Globins / genetics

Substances

  • Chromatin
  • alpha-Globins