Poster Presentation 39th Annual Lorne Genome Conference 2018

Using long-read sequencing to detect haplotype-specific differential methylation (#153)

Scott Gigante 1 , Alexis Lucattini 2 , Andrew Keniry 1 , Quentin Gouil 1 , Matthew Tinning 2 , Lavinia Gordon 2 , Chris Woodruff 1 , Matthew E Ritchie 1 , Terry P Speed 1 , Marnie E Blewitt 1
  1. Walter and Eliza Hall Institute, Parkville, VIC, Australia
  2. Australian Genome Research Facility, Parkville, VIC, Australia

Asymmetric expression patterns between the two parental alleles are critical for development of the mammalian embryo. This process known as imprinting involves differential DNA methylation of the parental genomes. We sequence mouse embryonic placental tissue on the Oxford Nanopore MinION and exploit the long reads to determine both haplotype and CpG methylation levels. Comparison with matched Reduced-Representation Bisulfite Sequencing data confirms the accuracy of the methylation calls, and highlights the improvement in haplotyping conferred by the longer reads. We successfully identify known imprinting control regions, as well as novel differentially methylated regions. Based on their proximity to hitherto unknown monoallelically expressed genes, we propose that some of these regions could constitute new imprinting control regions.