Comparative Hi-C analysis between human neural retina and RPE/choroid. a Generation of tissue-specific 3D contact matrices using in situ Hi-C on adult human donor neural retina and RPE/choroid samples (n = 4) and strategy for comparative 3D genome analysis. b Results of CHESS comparative analysis between the neural retina and RPE/choroid Hi-C contact matrices (z-ssim similarity scores obtained for chromosome 1 using 1-Mb window sizes, z-ssim < − 1.2, signal/noise (SN) > 2). c Enrichment of retina-enriched genes from the EyeGEx database and RetNet IRD genes compared to Ensembl genes within CHESS differential regions (Fisher’s exact test, p = 0.000273 and p = 0.000658 respectively). d Clustered heatmap of genes within CHESS differential windows using GTEx tissue expression data. e Overlap between genes at (differential) Hi-C loop anchors identified in neural retina and RPE/choroid and EyeGEx retina-enriched genes and RetNet IRD genes. f Enrichment of RetNet IRD genes, retina-specific IRD genes, RPE/choroid-specific IRD genes, and retina-enriched genes from the EyeGEx database compared to Ensembl genes at Hi-C loops in neural retina (Fisher’s exact test, p = 4.312e − 13, p = 4.875e − 12, p = 0.2024 and p = 0.0001 respectively), differential Hi-C loops in the neural retina (Fisher’s exact test, p = 1.149e − 05, p = 1.254e − 06, p = 0.7515 and p = 3.826e − 13 respectively) and Hi-C loops in RPE/choroid (Fisher’s exact test, p = 0.4705, p = 0.2559, p = 0.0991 and p = 0.8237 respectively). g Single-cell RNA expression within adult human retina of clusters of genes identified at differential loops in neural retina and RPE/choroid. The figure in panel a was partly created using BioRender
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