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. 2022 Jul 5;11:e77898. doi: 10.7554/eLife.77898

Figure 9. Mutual exclusive allelic H3K36me3 and H3K27me3 histone marks at seven parent-of-origin (PofO) methylation-biased blocks.

All blocks demonstrate allelic H3K36me3 on hypermethylated allele and H3K27me3 on hypomethylated allele. For NA12878 and NA19240, allele1 is the paternal and allele2 is maternal. For sake of visualization in other four cell lines without parental information, allele1 for H3K36me3 mark demonstrates the allele with more mapped reads at all blocks except ZNF597/NAA60. Therefore, for H3K36me3 we swapped the reference allele read count with the alternative allele read count if the reference allele count was less than the alternative allele count. At ZNF597/NAA60, we swapped the reference allele read count with the alternative allele read count if the reference had higher read count. We also swapped the reference and the alternative allele counts for the same SNVs for H3K27me3. Each point represents a heterozygous SNV. Lines are connecting SNVs that have mapped reads for both histone modifications.

Figure 9—source data 1. H3K36me3 and H3K27me3 allelic read counts for the heterozygous single-nucleotide variants (SNVs) mapped to the detected PofO-biased methylation blocks.

Figure 9.

Figure 9—figure supplement 1. Allelic H3K36me3 and H3K27me3 histone marks read count at seven test blocks.

Figure 9—figure supplement 1.

Test blocks do not display allelic bias for H3K36me3 or H3K27me3 histone modifications. For NA12878 and NA19240, allele1 is the paternal and allele2 is maternal. For sake of visualization in other four cell lines without parental information, allele1 for H3K36me3 mark demonstrates the allele with more mapped reads. Therefore, for H3K36me3 we swapped reference allele read count with alternative allele read count if reference allele count was less than alternative allele count. We also swapped reference and alternative allele counts for the same SNVs for H3K27me3. Each point represents a heterozygous SNV. Lines are connecting SNVs that have mapped reads for both histone modifications.
Figure 9—figure supplement 1—source data 1. H3K36me3 and H3K27me3 allelic read counts for the heterozygous single-nucleotide variants (SNVs) mapped to the test blocks.
Figure 9—figure supplement 2. IGV screenshot of the PPIEL imprinted cluster.

Figure 9—figure supplement 2.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Red box shows known germline DMR. The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 3. IGV screenshot of the MEG3 imprinted cluster.

Figure 9—figure supplement 3.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Black box shows known somatic differentially methylated region (DMR). The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 4. IGV screenshot of the MEST imprinted cluster.

Figure 9—figure supplement 4.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Red box shows known germline differentially methylated region (DMR). The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 5. IGV screenshot of the DIRAS3 imprinted cluster.

Figure 9—figure supplement 5.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Red box shows known germline differentially methylated region (DMR). The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 6. IGV screenshot of the IGF2 imprinted cluster.

Figure 9—figure supplement 6.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Black box represents known somatic differentially methylated region (DMR) and red box shows known germline DMR. The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 7. IGV screenshot of the MTRNR2L4 imprinted cluster.

Figure 9—figure supplement 7.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Black box represents known somatic differentially methylated region (DMR). The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.
Figure 9—figure supplement 8. IGV screenshot of the ADNP2 imprinted cluster.

Figure 9—figure supplement 8.

The histone mark tracks are representing allelic read counts for H3K36me3 and H3K27me3 modifications. The range for all histone mark tracks is 0–20. In H3K27 and H3K36 tracks, for NA12878 and NA19240 the parent-of-origin (PofO) could be determined and specified by maternal (Mat) and paternal (Pat) alleles. While the other samples are specified by reference (Ref) and alternative (Alt) alleles. Red box shows known germline differentially methylated region (DMR). The range for all methylation tracks is 0–1. In PofO ASE track, positive or upward bars represent paternal expression bias and negative or downward bars represent maternal expression bias.