Fig. 4: Accurate and allele-specific functional genomics analyses using the targeted haplotype-resolved assembly.

a Examples of C/T variants on CpG sites. b The CpG variant density plot throughout the targeted MHC region. The positions of three MHC class I genes and three MHC class II genes are indicated at the top. c The effect of CpG variants on DNA methylation analysis. Data are represented from three independent experiments, P values: shared P = 0.851, Hap1 unique P = 0.000496, Hap2 unique P = 0.000318 (***P < 0.001, ns: not significant, paired Student’s t-test, two-sided). d Allele-specific transcriptional regulation of the HLA-DPA1 gene. Top part: allele-specific methylation in the promoter region of the HLA-DPA1 gene. The differentially methylated region (DMR-DPA1) between two haplotypes is indicated as a pink bar. The shared CpGs between two haplotypes are shown as black short lines, while haplotype-specific CpGs are indicated as blue or red short lines. The Y-axis indicates the DNA methylation level for each haplotype, separately. Three replicates are shown. Bottom part: allele-specific expression of the HLA-DPA1 gene. The expression level for haplotype 1 and 2 is indicated as blue and red, respectively. Three replicates are shown. e Pyrosequencing of two polymorphic positions within the exons of the HLA-DPA1 gene of GM12878 cells. Y-axis indicates the ratio of the targeted SNPs between the two haplotypes. Data are represented from three independent experiments, P values: rs2308931 (C/T) P = 0.0177, rs2308930 (A/G) P = 0.0056 (*0.01  < P < 0.05, **0.001  < P < 0.01, paired Student’s t-test, two-sided). f Bisulfite Sanger sequencing of PCR clones for part of the DMR-DPA1 region, containing one haplotype 1-specific CpG and two haplotype-shared CpGs. Each line represents one read where black or white circles illustrate methylated or unmethylated CpGs, respectively. g DMR-DPA1 exerted methylation-dependent promoter activity on gene expression. Dual-luciferase reporter assays were performed. Data are represented as mean ± SEM from three independent experiments, P values: Unmethylated/No insert P = 0.0035, Methylated/Unmethylated P = 0.0036 (**0.001  < P < 0.01, Student’s t-test, two-sided). Source data are provided as a Source Data file.