A Multiscale Perspective on Chromatin Architecture through Polymer Physics

Abstract

The spatial organization of chromatin within the eukaryotic nucleus is critical in regulating key cellular functions, such as gene expression, and its disruption can lead to disease. Advances in experimental techniques, such as Hi-C and microscopy, have significantly enhanced our understanding of chromatin's intricate and dynamic architecture, revealing complex patterns of interaction at multiple scales. Along with experimental methods, physics-based computational models, including polymer phase separation and loop-extrusion mechanisms, have been developed to explain chromatin structure in a principled manner. Here, we illustrate genomewide applications of these models, highlighting their ability to predict chromatin contacts across different scales and to spread light on the underlying molecular determinants. Additionally, we discuss how these models provide a framework for understanding alterations in chromosome folding associated with disease states, such as SARS-CoV-2 infection and pathogenic structural variants, providing valuable insights into the role of chromatin architecture in health and disease.

Keywords: SARS-CoV-2; chromatin architecture; multiscale modeling; polymer physics; structural variants.

Figure 1.. Physics models of chromatin contact formation.

a) In the Strings and Binders (SBS) model, chromatin is modeled as a self-avoiding polymer chain, presenting different types of binding sites (represented by different colors) to cognate diffusing molecules (binders). The binders can loop the chain by bridging their cognate binding sites, thus driving phase separation of distinct clusters of sites with enriched levels of self-interactions. b) The PRISMR method infers the minimal number of SBS binding sites required to explain a genomic region’s experimental contact matrix by iteratively minimizing the difference between model and experimental contact matrices. c) In the LE+SBS model, polymer phase separation acts concurrently with loop-extrusion, an active mechanism in which extruding motors translocate along the chromatin chain and extrude loops until they find anchor points such as CTCF sites with opposite orientation.

Figure 2.. SBS model of chromosomes and epigenetic barcode of binding domains.

a) SBS model of chromosome 20 in GM12878 cell line (71). Hi-C data (top) for the entire chromosome 20 at 5 kb resolution is well recapitulated by the SBS model (bottom, r=0.97; r’=0.85). The model binding domains (middle) overlap with each other along the chromosome. Similar results are found across other chromosomes. b) Zoom-in from panel a of the Hi-C (top) and model (bottom) matrices for two 2-Mb regions along chromosome 20, highlighting that the model inferred for the entire chromosome also captures genomic contacts at short ranges, e.g. at TAD scales. c) The model binding domains cluster in nine main epigenetic classes based on their correlations with epigenetic marks. The centroid of each class represents the combinatorial barcode displayed in the heatmap. d) The epigenetic barcode can predict de novo chromatin contacts: SBS binding domains are identified for a test set of independent chromosomes by correlating their epigenetic signals with the epigenetic classes in panel c. Subsequently, the contact matrices are predicted using the SBS model. As an example, de novo predicted contact matrices and their comparison to independent Hi-C matrices (71)for chromosomes 19 (r=0.91, r’=0.47) and 21 (r=0.91, r’=0.63) of GM12878 cell line are shown. Adapted from (53).

Figure 3.. Chromatin is reshaped at A/B compartments and TADs scales in SARS-CoV-2 infected cells.

a) Sketch of the overall A-compartment weakening and increased A/B mixing in the infected genome found from Hi-C data (40). b) Block co-polymer model of chromatin at the A/B compartement level: binders mediate homotypic interactions with affinities E_A-A and E_B-B and heterotypic interactions with affinity E_A-B. c) Hi-C data (40) show intra-TAD contacts weakening in SARS-CoV-2 infected genome with respect to the mock case, together with a general reduction of Cohesin level (40). d) SBS+LE model used to study the effects of SARS-CoV-2 infection at the TAD scale. e) Mock Hi-C data (top) of the genomic region (Chr9:32,3–32,7 Mb, hg19) centered around the interferon response DDX58 gene are well reproduced by the model simulated contact map (bottom). Between the matrices CTCF signal (40) and both anchor point probability and binding domains for the LE+SBS model are shown. f) As in panel e, for SARS-CoV-2 infection case. The viral infection causes structural re-arrangements of the IFN DDX58 locus. Adapted from (39) (Creative Commons CCBY license).

Figure 4.. Chromatin is reshaped at TADs scale under the effect of SVs.

a) By informing the SBS model inferred from WT contact data with a specific rearrangement (e.g. a deletion), the effects of genomic mutations on chromatin architecture can be predicted from only polymer physics. b) Contact matrices from WT cHi-C data (top) (34) and SBS model (bottom) for a 6-Mb long region in human skin fibroblasts around the EPHA4 gene. The model well recapitulates the locus architecture (r=0.93, r’=0.69). c) The model predicts the effects of DelB, a 1.6-Mb heterozygous deletion at the EPHA4 locus (top), as validated by independent cHi-C data (bottom) in human skin fibroblasts carrying this mutation (34) (r=0.93, r’=0.61). Increased interaction is detected between the EPHA4 enhancer region and the gene PAX3 (blue bars), leading to PAX3 misexpression and brachydactyly. The locus genes (rectangles), TAD boundaries (hexagons), enhancers (ovals), and the deletion (gray box) are displayed between the matrices. Adapted from (34).