Extended Data Fig. 9: ATAC-seq shows differential chromatin accessibility in response to corpse-derived lysophosphatidylcholine and arachidonic acid dependent on RXRα.
From: Stem cells tightly regulate dead cell clearance to maintain tissue fitness
a, Representative histograms of fragment lengths in base pairs (bp) detected for cultured Rxra HFSCs ATAC-seq replicates. recomb, 9-cis retinoic acid +all-trans retinoic acid +lysophosphatidylcholine +arachidonic acid; WT, wild type; cKO, conditional knockout. b, Pearson correlation (R2) values for reads mapped to peaks on cultured Rxra HFSCs ATAC-seq replicates. n = 2 each (Media, Recomb) and n = 4 each (Corpses+Veh, Corpses+BEL) biological replicates per genotype. c, Principal component analysis on reads mapped to peaks. Biological replicates as in (b). d, Heatmap showing all peaks with significantly altered accessibility between Rxra WT and cKO pooled replicates exposed to corpses with (+Veh, vehicle) or without (+BEL, bromoenol lactone) lysophosphatidylcholine + arachidonic acid. Signal for pooled replicate samples is in reads per genome coverage (RPGC) (colour bar legend, right). Each row corresponds to a detected peak, centered and extended +/− 1 kb. Peaks are clustered based on differential accessibility relative to Rxra WT+Veh corpses, and summarized as the mean accessibility signal per region in a dark blue line (peaks that close in BEL and Rxra cKO), a light blue line (peaks that close in cKO only), a green line (peaks that close in BEL only), a yellow line (peaks that open in cKO only) or a red line (peaks that open in BEL only) in the graph at top. e, Venn diagram representation comparing peaks that open in response to corpses with those gained in response to retinoic acid (RA) + lysophosphatidylcholine (LPC) + arachidonic acid (AA) (‘Recomb’ condition) in Rxra WT HFSCs. Arrows indicate the percentage of peaks that require RXRα for accessibility within each category. Notably, enhancer peaks associated to phagocytic genes fall within the 32% of peaks gained in response to both corpses and recombinant signal that require Rxra for accessibility, which are shown in Fig. 4g. f, Top, ATAC-seq replicate-pooled peak tracks for lysosomal gene enhancers in cultured Rxra WT and cKO HFSCs exposed to apoptotic corpses with (+Veh) or without (+BEL) secreted LPC and FAs, or treated with RA + LPC + AA (+Recomb signals) for 4 hrs. Peaks with differential accessibility highlighted in light blue. Bottom, Cut & Run-seq for RXRα replicate pooled peak tracks for same enhancers above, in cultured Rxra WT HFSCs exposed to apoptotic corpses with (+Veh) or without (+BEL) secreted LPC and FAs, or treated with RA + LPC + AA (+Recomb signals) for 4 hrs. Peak tracks in reads per genome coverage (RPGC). No peak enrichment was observed in Rxra cKO HFSCs at these loci.
