Fig. 1
From: Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease
Three-dimensional chromatin architecture datasets for aging and Alzheimer’s disease. (a) Post-mortem brain tissue from female AD patients and cognitively normal elderly and females were studied using Hi-C; other data were also generated or collected to facilitate the understanding of Hi-C results, e.g., ATAC-seq, H3K27ac ChIP-seq, and GWAS SNPs. (b) The loops identified by HiCCUPS for three groups of samples. (c) Chromosome interactions heatmap for an exemplary region around BIN1 at chr2 of AD sample. (d) Integrative analysis results, including an interaction histogram, compartment score, loops predicted by HiCCUPS, H3K27ac peaks, open chromatin regions by ATAC-seq, contacts of active regions, AD risk SNPs, SNP-promoter interactions, eQTLs, and protein-coding genes. The height of loops indicated the log2 transformed contact frequency. Note that eQTLs of non-coding genes were also displayed in the eQTL track and no eQTL was identified for the BIN1 gene at p < 1e-5. Note that the used data are from different sources. Track 1 from entorhinal cortex samples of AD cases and matched controls [23]; Track 2 from prefrontal cortex region of Chinese AD samples; Track 3 is inferred regions by integrative analysis of Track 1 and Track 2; Track 4 is collected from a published meta-analysis on PGC-ALZ, IGAP, ADSP, and UKB8,9; Track 5 are downloaded from the GTEx database (https://gtexportal.org/).
