Fig. 2: Temporal compartmentalization of the cis- and trans- regulatory landscape during erythropoiesis.
From: Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation
a K-means clustering of 11,805 changing DHS resulted in 5 clusters (E1-E5) with sequential activity profiles for each cluster. Values are z-score of per day average normalized DHS counts from 3 donors. b K-means clustering of 5792 developmentally regulated genes resulted in 5 clusters (G1–G5). Values are z-score of per day average normalized FPKM from 3 donors. c A matrix showing the enrichment score (log2-ratio observed over expected) for any given DHS cluster, around each developmentally regulated DHS ( ± 50 kb from TSS). Highlighted in red is cluster G3 which is enriched for both late downregulated DHS of cluster E3 and early upregulated from cluster E4. Asterisks denote X2 test p-value < 0.05. d Correlation density plot between developmental genes and developmental DHS ± 250 kb around the gene promoter. Gray shaded area highlights enrichment of correlations within ±50 kb around the gene promoter. e DNase I accessibility track of the CDH1 locus during erythroid differentiation, highlighting the accessibility of 3 nearby DHS correlated to CDH1 expression. f DNase I accessibility track of the CDH1 locus in HUDEP-2 cells depicting the genetic knockout of the CDH1 promoter and two upstream DHS (-12, and -5) (above) along with the resulted ablation in CDH1 protein expression as assessed by flow cytometry (below).
