Using long-read sequencing to detect imprinted DNA methylation
Details
Publication Year 2019-05-07, Volume 47, Issue #8, Page e46
Journal Title
Nucleic Acids Research
Publication Type
Journal Article
Abstract
Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of approximately 10, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterize, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data. Our analysis successfully identifies known imprinting control regions (ICRs) as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new ICRs.
Publisher
Oxford Academic
WEHI Research Division(s)
Bioinformatics; Epigenetics And Development; Personalised Oncology; Bioinformatics
PubMed ID
30793194
Open Access at Publisher's Site
https://doi.org/10.1093/nar/gkz107
NHMRC Grants
NHMRC/1104924 NHMRC/1098290 NHMRC/1140976
Rights Notice
Refer to copyright notice on published article.


Creation Date: 2019-03-13 11:54:07
Last Modified: 2019-07-24 02:07:41
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