Fig. 3: 3D genome mapping of variant–gene interactions in fat and lean broiler chicken lines. | Nature Communications

Fig. 3: 3D genome mapping of variant–gene interactions in fat and lean broiler chicken lines.

From: Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens

Fig. 3: 3D genome mapping of variant–gene interactions in fat and lean broiler chicken lines.

a Hi–C contact matrices at varying resolutions for chromosomes in the FL and LL genomes, with darker shades indicating higher chromatin interaction frequencies. b Three-dimensional average models of FL and LL chromatin structures, color-coded to represent different chromosomes at a 500 kb resolution, illustrating average inter-chromosomal spatial relationships rather than specific diploid configurations. c Box plots of Von Neumann entropy comparing chromatin conformational looseness in the FL and LL genomes. Boxplot center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range and data beyond that threshold indicated as outliers. P values were obtained using unpaired two-tailed Student’s t-test, n = 40 biologically independent samples. d Log–log plot of contact frequency versus distance, highlighting structural differences between the FL and LL genomic architectures. e Chromatin A/B compartment distribution maps for specific chromosomal regions in the FL and LL genomes at 100 kb resolution. f Frequency charts of A/B compartment transitions, showing the proportion of transitions between A/B compartments in the FL and LL genomes. g Aggregate peak analysis (APA) of all topologically associating domains (TADs) within the FL and LL genomes at 10 kb resolution. h Statistical summary of specific and shared TAD boundaries, including counts and percentages. i APA for a comparative analysis of all chromatin loops within the FL and LL genomes at resolutions of 1, 5, 10, and 25 kb. j Distribution charts summarizing the number and percentage of specific and shared chromatin loops. k Schematic diagrams illustrating how functional variants influence gene interactions through changes in proximal and distal RE activity and in TAD and loop structures. l Table detailing 2559 variant–gene interactions identified, categorized by interaction type, variant number, REs, and target genes involved. Source data are provided as a Source Data file.

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