Fig. 6: rRNA biogenesis defect drove 3D chromatin structure reorganization of PNH region towards the 2C-like state. | Nature Communications

Fig. 6: rRNA biogenesis defect drove 3D chromatin structure reorganization of PNH region towards the 2C-like state.

From: rRNA biogenesis regulates mouse 2C-like state by 3D structure reorganization of peri-nucleolar heterochromatin

Fig. 6

a Hi-C contact maps of Inactive Hub and 1.5 Mb genomic regions around Dux at 150 kb resolution. GEO accession code GSE166041. b Hi-C contact maps of NAD and 1.5 Mb genomic regions around Dux at 150 kb resolution. GEO accession code GSE166041. c Hi-C contact maps of L1 and 1.5 Mb genomic regions around Dux at 150 kb resolution. The zoomed-in regions aim to demonstrate the change of Hi-C contacts between Dux and chromosome 10 in control mES cells and CX-5461 treated mES cells. GEO accession code GSE166041. d Hi-C pearson correlation coefficient (PCC) heat maps of Inactive Hub and 1.5 Mb genomic regions around Dux at 150 kb resolution. GEO accession code GSE166041. e Hi-C pearson correlation heat maps of NAD and 1.5 Mb genomic regions around Dux at 150 kb resolution. GEO accession code GSE166041. f Hi-C pearson correlation heat maps of L1 and 1.5 Mb genomic regions around Dux at 150 kb resolution. The zoomed-in regions aim to demonstrate the change of Hi-C PCC between Dux and chromosome 10 in control mES cells and CX-5461 treated mES cells. GEO accession code GSE166041. g Scatter plot demonstrates the log2(fold change) of Hi-C contacts between Inactive Hub and different types of genes in control and CX-5461 treated mES cells. GEO accession code GSE166041. h Scatter plot demonstrates the log2(fold change) of Hi-C contacts between NAD and different types of genes in control and CX-5461 treated mES cells. GEO accession code GSE166041. i Scatter plot demonstrates the log2(fold change) of Hi-C contacts between L1 and different types of genes in control and CX-5461 treated mES cells. GEO accession code GSE166041. j Scatter plot demonstrates the PCC difference between Inactive Hub and different types of genes in control and CX-5461 treated mES cells. GEO accession code GSE166041. k Scatter plot demonstrates the PCC difference between NAD and different types of genes in control and CX-5461 treated mES cells. GEO accession code GSE166041. l Scatter plot demonstrates the PCC difference between L1 and different types of genes in control and CX-5461 treated mES cells. The difference of PCC is defined as the average (PCC) of Inactive Hub regions and different types of genes in CX-5461 treated mES cells minus the average PCC of Inactive Hub regions and different types of genes in wild type mES cells. PCC Pearson correlation coefficient, MERVL-int: upregulated MERVL-int genes, MT2_Mm upregulated MT2_Mm genes, UG upregulated genes, DG downregulated genes. GEO accession code GSE166041. m DNA FISH analysis with a Dux locus probe and Inactive Hub locus probe, and co-immunostained with NCL protein. The percentage of Nucleolus-localized (overlapped with NCL) and Nucleoplasm-localized (nonoverlapped with NCL) of FISH signals is calculated. Dux: p = 3.67E−05(***), Inactive Hub: p = 4.13E−05(***), chi-square test; N denotes the number of observed mES cells; N = 11 biologically independent observations; Data are presented as mean values +/− SEM. SEM standard error of mean. GEO accession code GSE166041. Source data are provided as a Source Data file.

Back to article page