Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach

Abstract

Background: The three-dimensional organization of the genome is tightly connected to its biological function. The Hi-C approach was recently introduced as a method that can be used to identify higher-order chromatin interactions genome-wide. The aim of this study was to determine genome-wide chromatin interaction frequencies using the Hi-C approach in mouse sperm cells and embryonic fibroblasts.

Results: The obtained data demonstrate that the three-dimensional genome organizations of sperm and fibroblast cells show a high degree of similarity both with each other and with the previously described mouse embryonic stem cells. Both A- and B-compartments and topologically associated domains are present in spermatozoa and fibroblasts. Nevertheless, sperm cells and fibroblasts exhibit statistically significant differences between each other in the contact probabilities of defined loci. Tight packaging of the sperm genome results in an enrichment of long-range contacts compared with the fibroblasts. However, only 30% of the differences in the number of contacts are based on differences in the densities of their genome packages; the main source of the differences is the gain or loss of contacts that are specific for defined genome regions. We find that the dependence of the contact probability on genomic distance for sperm is close to the dependence predicted for the fractal globular folding of chromatin.

Conclusions: Overall, we can conclude that the three-dimensional structure of the genome is passed through generations without being dramatically changed in sperm cells.

Figure 1

Relative Hi-C contact probability maps. Whole-genome (A,D) and chromosome 19 (B,E) maps at a 1 Mb resolution for sperm cells and fibroblasts. The color of each dot represents the log of the interaction probability for the corresponding genome bins. The graphs under the heatmaps show E1 values for chromosome 19 in sperm cells and fibroblasts. The two-dimensional contact correlation matrices constructed as in [10] (C,F) demonstrate the characteristic plaid patterns for both sperm cells and fibroblasts.

Figure 2

Comparison of the E1 values for sperms cells, fibroblasts, cortex and ES cells. (A-F) Scatter plots of eigenvectors. The E1 values are highly similar in fibroblasts and sperm cells. The x- and y-axes indicate the E1 values from sperm and fibroblasts (A); sperm and ES cells (ESC) (B); sperm and cortex (C); fibroblasts and ES cells (D); fibroblasts and cortex (E); ES cells and cortex (F). The line represents the linear trend for the obtained values.

Figure 3

TADs are present in fibroblasts and sperm cells. The TAD signal is shown as a green line (for sperm cells) or a blue line (for fibroblasts) for a region on chromosome 19. The fragments of the heatmaps for sperm cells and fibroblasts (binned at a resolution of 40 kb) display the enrichment of contacts inside the TAD domains. The TAD signal shows visible similarity between sperm cells and fibroblasts.

Figure 4

Identification of regions distinguishing sperm cells and fibroblasts. (A) E1 values, Euclidean distance and Pearson and Spearman correlation coefficients for chromosome 1 of both sperm cells (green line for E1 values) and fibroblasts (blue line for E1 values). All graphs indicate high similarities between sperm cells and fibroblasts (that is, similar E1 values, small Euclidean distance and high correlation coefficients). However, some regions display less similarity than others. (B) The two-dimensional heatmaps for the whole genome and for chromosome 19 (binned at a 1 Mb resolution) indicate the significance of the differences in the contact probability between fibroblasts and sperm cells. Each dot represents a single contact. Regions in red are not mappable, those in yellow are significantly different, those in cerulean are significantly different with a difference of more than two times, and those in blue are contacts where no significant difference was found.

Figure 5

The genome of sperm cells is packed more tightly than that of fibroblasts. (A) The dependence of the contact probability on the genomic distance P(s) averaged over all chromosomes, compared with P ~ 1/s. The blue line indicates fibroblasts (P ~ s^-1.27), and the green line indicates sperm cells (P ~ s^-1.07). (B) The ratio between sperm cells’ and fibroblasts’ contact probabilities at different genomic distances. The x-axis indicates genomic distance, and the y-axis indicates the ratio of contact probabilities. The black lines show a 1:1 ratio.

Figure 6

Analysis of intrachromosomal contacts in sperm cells and fibroblasts. (A) The ratio between intra- and interchromosomal contact numbers for sperm cells (green) and fibroblasts (blue). (B,C) The two-dimensional heatmaps show the observed number of interactions between any pair of chromosomes divided by the expected number of interactions between those chromosomes for sperm cells (B) and fibroblasts (C). The color of each dot represents the enrichment (red) or depletion (blue) of contacts compared with the expected values. (D) The observed number of interactions between any pair of chromosomes plotted against the difference in the lengths of those chromosomes. The dotted lined represents the linear trend for obtained values.