Fig. 2: Application of SnapHiC to sn-m3C-seq data from human prefrontal cortex uncovered chromatin loops in diverse brain cell types.
From: SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data
a, Scatter plot showing the numbers of cells and SnapHiC-identified loops in each of the 14 major cell types identified in human prefrontal cortex in Lee et al.3. ODC, oligodendrocyte. Astro, astrocyte. MG, microglia. OPC, oligodendrocyte progenitor cell. Endo, endothelial cell. L2/3, L4, L5 and L6 denote excitatory neuron subtypes located in different cortical layers. Pvalb and Sst, medial ganglionic eminence-derived inhibitory subtypes. Ndnf and Vip, CGE-derived inhibitory subtypes. NN1, nonneuronal cell type 1. b, Boxplot of ATAC-seq log2(CPM+1) value (left), H3K27ac ChIP–seq log2(CPM+1) value (middle) and RNA-seq log2(FPKM+1) value (right) at Astro-specific, MG-specific, ODC-specific and L2/3-specific SnapHiC loops. For each set of SnapHiC loops, the values are calculated using ATAC-seq/H3K27ac ChIP–seq/RNA-seq data generated from astrocyte, microglia, oligodendrocytes and neurons, respectively (Methods). ***P < 2.2 × 10−16, two-sided P values by the paired Wilcoxon signed-rank test. In each box, the upper edge, horizontal center line and lower edge represent the 75th percentile, median and 25th percentile, respectively. The upper whiskers represent the 75th percentile + 1.5× the interquartile range (IQR). The lower whiskers represent the minimum values (0). Data points with a value above the 75th percentile + 1.5× the IQR are outliers and reported as dots. c, SnapHiC-identified loops from astrocyte and microglia around gene APOE. There is no loop identified in this genomic region from oligodendrocytes or L2/3 excitatory neurons, so no corresponding tracks are shown. Two astrocyte-specific loops linking the APOE promoter (highlighted in gray) and the active enhancers in astrocyte (highlighted in pink) containing two Alzheimer’s disease (AD) -associated GWAS SNPs are marked by black arrows. Only APOE transcription start site-distal Alzheimer’s disease-associated GWAS SNPs are shown in the figures (residing in the region chr19: 45,440,000–45,630,000).
