Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci.
Mol Cell 2018;
72:786-797.e11. [PMID:
30344096 PMCID:
PMC6242782 DOI:
10.1016/j.molcel.2018.09.016]
[Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/28/2018] [Accepted: 09/13/2018] [Indexed: 01/01/2023]
Abstract
Chromatin folded into 3D macromolecular structures is often analyzed by chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) techniques, but these frequently provide contradictory results. Chromatin can be modeled as a simple polymer composed of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), chromatin accessibility (assay for transposase-accessible chromatin using sequencing [ATAC-seq]), and structural anchors (CCCTC-binding factor [CTCF]), we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fiber varied along its length; combined with diffusing protein bridges and loop extrusion, this model predicted the 3D organization of genomic loci at a population and single-cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3D and enable predictions of chromatin folding paths.
HiP-HoP: highly predictive heteromorphic polymer model to analyze chromatin structure
Polymer simulations use widely available epigenetic and protein binding data as input
Validate HiP-HoP model at complex loci using 3D FISH and Capture-C
Simulations uncover striking conformational variability in chromatin fiber folding
Collapse