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Fig. 1 | Genome Biology

Fig. 1

From: The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos

Fig. 1

Chromatin architecture of pig embryonic fibroblast. a Left: Hi-C contact matrix of chromosome 3 at 100 kb resolution at PEF (pooled data from 2 biological replicates). Middle: the principal component 1 (PC1) values (bottom) and correlation matrix (upper) obtained at 300 kb resolution for chromosome 3. Positive PC1 values represent compartment A regions (yellow), and negative values represent compartment B regions (blue). Right: TADs identified by deDoc are shown (50-kb resolution, chr5: 4–7.5 Mb). Yellow boxes represent TADs. b Relative contact frequency plot showing the percentage of contacts as a function of genome distance in PEF (blue) and MEF (orange). c Ratio of homologous bins classified by A/B compartment status between PEF and MEF. d Comparison of expression level between genes located in A compartments and genes located in B compartments of PEF (P = 1.84E−7, Mann-Whitney U test, one-tailed). e Plots showing H3k27ac and H3k4me3 ChIP-seq signal relative to the compartments (chr3: 14–19 Mb). Gene density is also shown. f Mean value of insulation scores around PEF TAD boundaries (boundaries ± 625 kb). g Average numbers of CTCF ChIP-seq peaks (blue) and gene TSS (orange) around PEF TAD boundaries (boundaries ± 200 kb). h Motif count and orientation of inferred CTCF binding sites relative to PEF TAD boundaries. i Venn graphs showing the overlap of TAD boundaries between PEF and MEF (P = 7.63E−67 compared to random, Fisher’s exact test). j Cumulative curve of TADs according to TAD conservation. TAD conservation was calculated as the probability of two homologous bins located within a TAD of PEF which also co-existence within a TAD of MEF. The same curve under shuffled TADs was shown in gray as control. k Aggregate loop plots showing the strength of PEF CTCF loop (left) and strength of interactions between homologous loop anchors in MEF (right)

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