Fig 2: Performing functional examinations on GATA2-mediated nucleosome states switching and GATA2-regulated Wnt/β-catenin signaling genes.a Nucleosomes containing 16 different sequences were bound to increase amounts of GATA2 protein and separated by native PAGE. Nucleosomes with 30, 90, and 270 nM of GATA2 and the major supershift bands (Ss-1, Ss-2, Ss-3) were indicated and quantified by qPCR relative to the input nucleosomes. Experiments were repeated independently three times with similar results. Each bar represents the mean value with the standard deviation as error bars. b ATAC-seq reads density maps around GATA2-associated RAS loci within 0.5 Kb up/down-stream in siCtrl LNCaP cell line and siGATA2 subline. c RT-qPCR measurement on a set of 20 Wnt/β-catenin signaling genes in siGATA2 before and after DHT treatment. The center for the error bars represents the mean value and the error bars represent the standard deviation with three experiments with a “***” showing p < 0.001 (two-tailed Student’s t-test) between Veh and DHT groups for each gene loci. d A working model showing GATA2 initially binds at the edge of a nucleosome at a crowding array (S4) and reconfigures it to an accessible primed state (S3/S2) upon androgen (DHT) stimulation, subsequently directly regulates or recruits other TFs to coregulate Wnt/β-catenin signaling genes. Source data are provided as a Source Data file.

Fig 3: GATA2-associated functional nucleosome states in Veh and DHT-treated conditions.a Identification of GATA2 borders and a distribution of gaps between borders showing a bimodal pattern for each of two biological replicates. b GATA2 border distribution within different chromosomes in the conditions of Veh and DHT treatment. c The number of GATA2 borders located on nucleosomes and distributed on different nucleosome states for each of two replicates. d An enrichment plot of GATA2 borders in different nucleosome states for each of two replicates. e Two screenshots showing the changes of GATA2 borders along with nucleosome states switching.

Fig 4: GATA2 governing nucleosome states switching from Veh to DHT-treated conditions.a Open chromatin was detected by ATAC-seq for GATA2 binding sites associated with nucleosome states switching in Veh and DHT-treated conditions respectively. b Overlapping between GATA2-associated nucleosome state switching genes and AR-regulated differentially expressed genes in DHT-treated condition. Differentially expressed genes were detected with p value <0.05 and | log2(Fold Change)| > 1. c KEGG pathway analyses showing the top pathways in S4-RAS1 and S3-RAS2 respectively. d The location of the GATA2 motif between ChIP-exo borders relative to the density map of MNase-seq reads for positioned nucleosomes. e The prediction of regulatory features and modules by i-cisTarget illustrating several top enriched TF motifs in unique GATA2-associated nucleosome state switching genes. f SOX9 is the most enriched co-binding TF on WNT signaling genes identified by a publicly available database that collected all ChIP-seq of TFs from ENCODE and ChEA.