Journal article

Using long-read sequencing to detect imprinted DNA methylation

Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence P Speed, Marnie E Blewitt, Matthew E Ritchie

NUCLEIC ACIDS RESEARCH | OXFORD UNIV PRESS | Published : 2019

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 ∼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 no..

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Grants

Awarded by Australian National Health and Medical Research Council (NHMRC) Fellowship


Awarded by NHMRC


Funding Acknowledgements

Bellberry-Viertel Senior Medical Research Fellowship (to M.E.B.); Australian National Health and Medical Research Council (NHMRC) Fellowship [GNT1104924 to M.E.R.]; NHMRC Project Grants [GNT1098290, GNT1140976 to M.E.B., M.E.R.]; Victorian State Government Operational Infrastructure Support; NHMRC Research Institute Infrastructure Support Scheme. Funding for open access charge: Walter and Eliza Hall Institute of Medical Research