Part of the Imprinting track collection, this track shows differentially methylated regions (DMRs) between the maternal and the paternal haplotype. They were identified from 123 trio-phased assemblies of the HPRC release 2. The track has more than 4800 regions with an absolute methylation difference above 0.05. A region where the maternal copy is more methylated than the paternal copy is a candidate for a locus that is imprinted by methylation of the maternal allele, and the reverse holds for the paternal copy.
The authors calculated the regions on the CHM13v2.0 reference. They were lifted to hg38 for this track, see Methods for details.
Each region is colored by the parent whose haplotype has the higher methylation level:
| Red: higher methylation on the maternal haplotype | |
| Blue: higher methylation on the paternal haplotype |
The methylation difference, maternal minus paternal, is shown on the details page and when the mouse is moved over a region. It is positive for red and negative for blue regions. The track can be filtered by haplotype and by the size of the methylation difference.
Methylation was called from Oxford Nanopore reads with modkit v0.4.1 and the reads were aligned to the personalized assemblies with Winnowmap v2.03 (-x map-ont -I 8G --MD --cs -y -a -Y -L --eqx), keeping primary alignments. Each diploid assembly was split by haplotype and chain files from haplotype to CHM13v2.0 were built with a Nextflow pipeline running nf-LO and minimap2. Methylation calls were lifted to CHM13v2.0 with CrossMap v0.7.0, using a shift of 1 bp on the negative strand so that the methylation tag stays on the C of the CpG. Maternal and paternal groups were compared per chromosome with DSS v2.58.0 in R v4.5.3: DSS::DMLtest with smoothing (span 500 bp) and unequal dispersion identified differentially methylated CpGs (delta 0, p-value below 0.001), and callDMR (p-value below 0.001, delta 0, minimum length 50 bp, at least 3 CpGs, merge distance 100 bp, at least half of the sites significant) grouped them into regions. Only regions with an absolute methylation difference above 0.05 were kept. See Lucas et al. for details on the HPRC data.
The data files were provided by the authors, who also lifted the regions from CHM13v2.0 to hg38 with the chain files of the CHM13 project. The lifted BED file contains 4827 regions. We converted it to a bigBed file and added the haplotype and the methylation difference as separate fields, see the makeDoc file and the scripts. No region was dropped.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-sep tables. From scripts, the data can be accessed through our API, track=hprcDmr.
For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called hprcDmr.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, e.g. bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/imprinting/hprcImprint/hprcDmr.bb -chrom=chr21 -start=0 -end=100000000 stdout
The original annotation source data was provided by the authors and is available on request.
Thanks to Juhyun Kim and Brandon D. Pickett for providing this track.
Lucas JK, Hebbar P, Liao WW, Macias-Velasco JF, Novak AM, Asri M, Balacco JR, Blair AP, Bolognini D, Ebler J et al. HPRC2: A human pangenome reference with near-complete coverage of common genetic variation. bioRxiv. 2026 Jul 22;. PMID: 42539208; PMC: PMC13419748
Feng H, Wu H. Differential methylation analysis for bisulfite sequencing using DSS. Quant Biol. 2019 Dec 31;7(4):327-334. PMID: 34084562; PMC: PMC8171293
Talenti A, Prendergast J. nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over. Genome Biol Evol. 2021 Sep 1;13(9). PMID: 34383887; PMC: PMC8412297
Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1;30(7):1006-7. PMID: 24351709; PMC: PMC3967108