Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

Chris A Brackley, Jill M Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R Hughes, Veronica J Buckle, Davide Marenduzzo

Research output: Contribution to journalArticlepeer-review

Abstract

The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops. To test the model, we perform FISH experiments and compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.

Original languageEnglish
Article number59
JournalGenome Biology
Volume17
Issue number1
DOIs
Publication statusPublished - 31 Mar 2016

Keywords

  • Chromosome conformation
  • Polymer model
  • Fluorescence in situ hybridization
  • cis-regulation

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