Figure 5.
QPD results in ectopic enhancer-gene interactions specific to the disease chromosome. (A) H3K27ac tracks from control megakaryocytes, CTCF ChIA-PET tracks from K562, and gray-dashed boxes marking sub-TADPLAU and sub-TADVCL are shown, as in Figure 4. Black horizontal bar marks the position of the QPD duplication. (B) Individual 4C-Seq contact profiles from QPD and control megakaryocytes generated using a bait (restriction fragment) at the PLAU promoter (top) and EHNQPD (bottom), marked by black and red anchor symbols, respectively. For domainograms, the black trendline shows the median contact frequency in 5-kb windows tiled across 1-kb increments normalized to the maximum median value at 5-kb resolution; shaded area indicates the 20th to 80th percentiles. The heat map color-scale shows median contact frequency in the windows of increasing size from 2 to 50 kb tiled across 1-kb increments, normalized relative to the maximum median value at 12-kb resolution. Bar plots below domainograms depict log2 fold enrichment in 4C contacts in QPD vs control samples calculated for 5-kb bins tiled across 1-kb increments. Counts for bins falling within the duplicated region were divided by 1.5 to adjust for the copy number in the QPD samples. Red and black bars signify windows of nominally significantly increased interaction in QPD and control samples, respectively (nonadjusted P < .1; 2-tailed Student t test). (C) The 4C-seq design used to assess allele-specific contacts from the ENHQPD perspective. (D) Genome browser view (top) of PLAU DpnII fragments (black rectangles below the gene model) and SNPs rs1916341 and rs2227574 (vertical black bars). Fragments harboring SNPs are outlined in red. The percentage of reads (bottom) from each 4C sample at 2 SNPs that contain either the allele from the disease chromosome or the other allele. Dashed black line show the expected frequency of QPD alleles based on 1.5 copy (ie, 0.66). Numbers below bars correspond to the total number of reads mapped to a given SNP. (E) Sanger sequencing chromatographs of 4C prelibrary PCR products from 2 control and 3 QPD samples. Genotypes are displayed in the format control allele > QPD allele. *P < .01; **P < .001; ***P < .0001 by 2-tailed binomial test.

QPD results in ectopic enhancer-gene interactions specific to the disease chromosome. (A) H3K27ac tracks from control megakaryocytes, CTCF ChIA-PET tracks from K562, and gray-dashed boxes marking sub-TADPLAU and sub-TADVCL are shown, as in Figure 4. Black horizontal bar marks the position of the QPD duplication. (B) Individual 4C-Seq contact profiles from QPD and control megakaryocytes generated using a bait (restriction fragment) at the PLAU promoter (top) and EHNQPD (bottom), marked by black and red anchor symbols, respectively. For domainograms, the black trendline shows the median contact frequency in 5-kb windows tiled across 1-kb increments normalized to the maximum median value at 5-kb resolution; shaded area indicates the 20th to 80th percentiles. The heat map color-scale shows median contact frequency in the windows of increasing size from 2 to 50 kb tiled across 1-kb increments, normalized relative to the maximum median value at 12-kb resolution. Bar plots below domainograms depict log2 fold enrichment in 4C contacts in QPD vs control samples calculated for 5-kb bins tiled across 1-kb increments. Counts for bins falling within the duplicated region were divided by 1.5 to adjust for the copy number in the QPD samples. Red and black bars signify windows of nominally significantly increased interaction in QPD and control samples, respectively (nonadjusted P < .1; 2-tailed Student t test). (C) The 4C-seq design used to assess allele-specific contacts from the ENHQPD perspective. (D) Genome browser view (top) of PLAU DpnII fragments (black rectangles below the gene model) and SNPs rs1916341 and rs2227574 (vertical black bars). Fragments harboring SNPs are outlined in red. The percentage of reads (bottom) from each 4C sample at 2 SNPs that contain either the allele from the disease chromosome or the other allele. Dashed black line show the expected frequency of QPD alleles based on 1.5 copy (ie, 0.66). Numbers below bars correspond to the total number of reads mapped to a given SNP. (E) Sanger sequencing chromatographs of 4C prelibrary PCR products from 2 control and 3 QPD samples. Genotypes are displayed in the format control allele > QPD allele. *P < .01; **P < .001; ***P < .0001 by 2-tailed binomial test.

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