Fig. 2

Fig. 2

Differential promoter looping between human neural retina and RPE/choroid. a Proportion of differential promoter-associated loops (at 5-kb resolution) in human neural retina (red) and RPE/choroid (blue) according to FitHiChIP (FDR < 0.05). b Aggregate peak analysis centered at HiChIP loops specific of neural retina, RPE/choroid, and stable loops. c Enrichment of RetNet IRD genes, retina-specific RetNet genes, RPE/choroid-specific RetNet genes, and retina-enriched genes from the EyeGEx database within genes specifically contacted in the neural retina (right; Fisher’s exact test, p = 7.713e − 06, p = 2.042e − 07, p = 0.8979, and p = 4.382e − 10, respectively) and RPE/choroid (left; Fisher’s exact test, p = 0.4856, p = 0.1584, p = 0.3647, and p = 0.0046, respectively). d Top-10 enriched GO Biological Process terms associated with differentially HiChIP-contacted promoters in neural retina and RPE/choroid. e Genomic tracks showing the 3D chromatin configuration of the RHO gene locus. For both tissues, HiChIP contact matrices, differential loops, and HiChIP-derived H3K4me3 ChIP-seq signals are represented from top to bottom. f Virtual 4C contact frequencies (viewpoints indicated by a green line) for all genes within the RHO locus derived from the neural retina and RPE/choroid binned HiChIP counts