Panel A shows a heatmap of differentially expressed genes between control and Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel B shows a volcano plot highlighting significantly upregulated and downregulated genes in Cd11cCre positive Rxrab deficient mature alveolar macrophages compared with controls. Panel C shows a bubble plot of significantly enriched Gene Ontology biological processes associated with altered transcriptional programs in Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel D shows a heatmap comparing expression of alveolar macrophage core genes and monocyte associated genes between control mature alveolar macrophages and Cd11cCre positive Rxrab deficient immature alveolar macrophages. Panel E shows genomic heatmaps of ATAC sequencing accessibility signals around transcription start sites in control and Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel F shows motif enrichment analysis identifying transcription factor binding motifs enriched in chromatin regions closed in Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel G shows a Venn diagram comparing RXR binding associated genes with significantly upregulated and downregulated genes in Cd11cCre positive Rxrab deficient mature alveolar macrophages. Panel H shows motif enrichment analysis of RXR chromatin immunoprecipitation peaks identifying enriched transcription factor motifs in alveolar macrophages. Panel I shows a donut chart illustrating genomic feature distribution of RXR binding peaks across promoter, intronic, exonic, intergenic, untranslated, and transcription termination regions. Panel J shows a bar graph quantifying associations between RXR peaks and proximal or distal H3K27ac chromatin regions in alveolar macrophages. Panel K shows UCSC genome browser tracks of ATAC sequencing, RXR binding, and H3K27ac chromatin peaks across key alveolar macrophage genes including Ucp3 and Fabp1.
RXRs act as LDTFs in AMs. (A) Heatmap representing all DEGs detected in the comparison of Rxrabfl/fl mAMs (n = 4 mice) with Cd11cCre+Rxrabfl/fl mAMs (n = 3 mice) from 9-wk-old mice. (B) Volcano plot showing global transcriptomic changes in Cd11cCre+Rxrabfl/fl mAMs. Colored dots represent DEGs with significant upregulation (p-adj <0.05 and FC >0; red) or significant downregulation (p-adj <0.05 and FC <0; blue). (C) Significantly enriched GO terms derived from the bulk RNA-seq data comparison between Cd11cCre+Rxrabfl/fl and Rxrabfl/fl mAMs, detected with the PANTHER statistical enrichment test tool (P < 0.05 with Bonferroni correction). (D) Heatmap showing expression values of previously described typical AM-upregulated and -downregulated core genes and monocyte genes [20] in Rxrabfl/fl mAMs (n = 4 mice) versus Cd11cCre+Rxrabfl/fl ImmAMs (n = 3 mice). (E) Genomic heatmap of ATAC-seq signals located in TSS-flanking regions (±5 kb) in sorted mAMs from 9-wk-old Rxrabfl/fl and Cd11cCre+Rxrabfl/fl mice (n = 4 per genotype) (log2(FC) ≤ −1 or ≥1, FDR <0.05). (F) HOMER motif enrichment analysis in closed ATAC-seq peaks in Cd11cCre+Rxrabfl/fl mAMs. (G) Overlapping analysis for the collection of 2,867 genes that were identified as nearest to RXRα HT-ChIPmentation peaks and for the collection of 527 DEGs obtained in bulk RNA-seq. (H) HOMER motif enrichment analysis of RXR peaks. (I) Genome feature distribution analysis of RXR peaks. (J) Bar plot showing the association between RXRα peaks and H3K27ac peaks classified as proximal or distal peaks according to their distance from the nearest gene. (K) UCSC genome browser plots showing ATAC-seq, RXRα and H3K27ac (distal and proximal) HT-ChIPmentation peaks in key AM genes. Blue boxes label differentially accessible regions showing RXR binding in Cd11cCre+Rxrabfl/fl versus Rxrabfl/fl mAMs. *P ≤ 0.05; Test of equal or given proportions (prop.test function in R).