Fig. 4
From: Dark and camouflaged genomic regions remain challenging in CHM13
Dark regions obscure epigenetic assay results. (a) Whole genome bisulfite sequencing is a common genome-wide short-read sequencing assay that identifies CpG methylation sites by converting unmethylated cytosines to uracils. (b) ChIP-Seq is an assay that pulls down DNA bound to a target protein. (c) HiC data identifies the location of chromatin loops in nuclear DNA. (d) Compared to 100 bp Illumina data, the whole-genome bisulfite sequencing samples have more dark-by-depth and less dark-by-MAPQ. Most of the ChIP data, as expected, are dark-by-depth; however, 1.2 Mb (3.4%) are dark-by-MAPQ. (e) Due to close paralogs few, if any, CpG sites in AMY1C can be quantified using short-read sequencing because AMY1C is dark-by-MAPQ and camouflaged by AMY1A and AMY1B. (f) H2AC18/19 camouflage each other and, as a result, the promoter associated histone mark H3K4me3 peaks are obscured and left unanalyzed. (g) The CR1 tandem domain repeats completely obscure DNA looping data in HiC data.
