Fig. 4

H2a.z was required to maintain the proper chromatin environment within CAR-downTSS and to support the ability of CAR-downTSS-associated genes to increase their expression levels. (A) Bar plot showing normalized mRNA levels of H2az1, H2az1 after shRNA knockdown of H2az1, and H2az2. (B) Western blot and immunostaining results showing H2a.z protein was knocked down after shRNA treatment. (C-D) Histograms showing signal intensity of H3K27ac (C) and H3K4me3 (D) within CAR-downTSS before and after H2a.z knockdown. (E) Density plot showing the fragment size distribution of H3K4me3 Cut&Tag sequencing reads falling within CAR-down before and after H2a.z knockdown. (F) Histogram showing signal intensity of Pol II within CAR-downTSS before (with or without cholesterol treatment) and after (with or without cholesterol treatment) H2a.z knockdown. (G) Box plots showing log₂(fold change) of genes whose expression were increased after cholesterol treatment (left panel), and log₂(fold change) of the same genes under the same condition after additional H2a.z knockdown (right panel). (H) Bar plot showing fold changes of gene expression after cholesterol treatment with or without H2a.z knockdown. (I) Bar plot showing normalized Srcap mRNA level after Srcap shRNA treatment. (J) Bar plot showing fold changes of gene expression after cholesterol treatment with or without Srcap knockdown