Using long-read sequencing to detect imprinted DNA methylation
- Author(s)
- Gigante, S; Gouil, Q; Lucattini, A; Keniry, A; Beck, T; Tinning, M; Gordon, L; Woodruff, C; Speed, TP; Blewitt, ME; Ritchie, ME;
- 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
- Research Division(s)
- Bioinformatics; Epigenetics And Development; Personalised Oncology
- PubMed ID
- 30793194
- Publisher's Version
- https://doi.org/10.1093/nar/gkz107
- Open Access at Publisher's Site
https://doi.org/10.1093/nar/gkz107- NHMRC Grants
- NHMRC/1104924, NHMRC/1098290, NHMRC/1140976,
- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
- Documents
Creation Date: 2019-03-13 11:54:07
Last Modified: 2019-07-24 02:07:41