Fig. 4: Haplotype phased analysis of ASRT on autosomes.
From: Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability
a Chromosome 5 RT profile from the 6 EB3_2 clones, highlighting regions with standard deviation (SD) > 1 from both the “combined allele RT profile” (Hap1 and Hap2) and from the “allele-restricted RT profile” separately (Hap1 or Hap2). b–i Representative examples of regions present in both GM12878 (top panels) and EB3_2 (bottom panels) clones with variable epigenetic replication timing between alleles. Each clone was color coded as shown, with haplotype 1 shown as a solid line, and haplotype 2 shown as a dotted line for both sets of clones. The left Y axis shows the replication timing (Early/Late) profiles. The SD of the replication timing across each locus is shown below each panel. The right Y axis shows the AEI, with smooth rectangles representing TL and the stippled rectangles representing protein coding genes. The opaque rectangles show AEI, while the transparent rectangles show bi-allelic expression of TL and protein coding regions. Chromosome number and genomic positions (megabases) are shown on the X axis. Areas highlighted in gray represent outliers in the SD. f–i The location of rtQTL at VERT regions, with the Early (E) and Late (L) alleles26 for both GM12878 and EB3_2 are shown (also see Supplementary Data 5).
