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. 2021 Nov 9;12:6365. doi: 10.1038/s41467-021-26576-2

Fig. 4. Deficiency of rRNA biogenesis changed the normal epigenetic state of PNH region.

Fig. 4

a Boxplots demonstrate the averaged H3K9me3 and H3K27me3 levels of 101 Inactive Hub fragments, 578 NAD fragments and 34888 L1 sequences; H3K9me3 of PNH: p = 2.56E−34(***), H3K9me3 of NAD: p = 9.64E−185(***), H3K9me3 of L1: p = 0(***), H3K27me3 of PNH: p = 1.89E−33(***), H3K27me3 of NAD: p = 2.35E−160(***), H3K27me3 of L1: p = 0(***), two-sided, Wilcox signed rank test; N = 1 biologically independent ChIP-seq experiment. GEO accession code GSE166041 . b UCSC Genome Browser viewing of H3K9me3 and H3K27me3 ChIP-seq signals in control and CX-5461 treated mES cells around a representative PNH fragment at chr15:4,699,343–5,778,242. GEO accession code GSE166041. c Boxplots demonstrate the averaged H3K4me3 and H3K27ac levels of 101 Inactive Hub fragments, 578 NAD fragments and 34888 L1 sequences; H3K4me3 on PNH: p = 1.86E−23(***), H3K4me3 on NAD: p = 8.48E−172(***), H3K4me3 on L1: p = 0(***), H3K27ac on PNH: p = 6.46E−26(***), H3K27ac on NAD: p = 2.22E−172(***), H3K27ac on L1: p = 0(***), two-sided, Wilcox signed rank test, N = 1 biologically independent ChIP-seq experiment. GEO accession code GSE166041. d UCSC Genome Browser viewing of H3K4me3 and H3K27ac ChIP-seq signals in control mES cells and CX-5461 treated mES cells around a representative PNH fragment at chr10:3,632,504–3,926,058. GEO accession code GSE166041. e Heatmap plots demonstrate the levels of chromatin accessibility on within 1 mb region around start and end sites of Inactive Hub and NAD, and within 1 kb region around start and end sites of L1. The regions of different lengths of Inactive Hub and NAD fragments were fitted to 1 mb. The regions of different lengths of L1 sequences were fitted to 1 kb. SS: start site of a chromatin fragment of PNH; ES: end site of a chromatin fragment of PNH. The PNH fragment was defined as the L1 contained regions overlapped with Inactive Hub and NAD. GEO accession code GSE166041. f Boxplots demonstrate the averaged chromatin accessibility of 101 Inactive Hub fragments, 578 NAD fragments and 34,888 L1 sequences; chromatin accessibility of PNH: p = 0(***), chromatin accessibility of NAD: p = 2.65E−09(***), chromatin accessibility of L1: p = 9.17E−74(***), two-sided, Wilcox signed rank test, N = 1 biologically independent ChIP-seq experiment. GEO accession code GSE166041. g UCSC Genome Browser viewing of ATAC-seq signals in control and CX-5461 treated mES cells around a representative PNH fragment at chr19:18,666,449–18,747,509. GEO accession code GSE166041. h Boxplots demonstrate the averaged binding signals of NCL and TRIM28 on 101 Inactive Hub fragments, 578 NAD fragments and 34,888 L1 sequences; NCL on PNH: p = 2.56E−34(***), NCL on NAD: p = 1.71E−179(***), NCL on L1: p = 0(***), TRIM28 on PNH: p = 3.16E−34(***), TRIM28 on NAD: p = 1.04E−175(***), TRIM28 on L1: p = 0(***), two-sided, Wilcox signed rank test, N = 1 biologically independent ChIP-seq experiment. GEO accession code GSE166041. i UCSC Genome Browser viewing of NCL and TRIM28 ChIP-seq signals in control and CX-5461 treated mES cells around a representative PNH fragment at chr18:7,718,063–8,074,255. GEO accession code GSE166041. a, c, f, h The center line is the median, the bottom of the box is the 25th percentile boundary, the top of the box is the 75th, and the whiskers define the bounds of the data that are not considered outliers, with outliers defined as greater/lesser than ±1.5× IQR, where IQR inter-quartile range.