title: Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions.
abstract: BACKGROUND
  Phenotypic variability among inbred littermates reared in controlled environments remains poorly understood. Metastable epialleles refer to loci that intrinsically behave in this way and a few examples have been described. They display differential methylation in association with differential expression. For example, inbred mice carrying the agouti viable yellow (A (vy) ) allele show a range of coat colours associated with different DNA methylation states at the locus. The availability of next-generation sequencing, in particular whole genome sequencing of bisulphite converted DNA, allows us, for the first time, to search for metastable epialleles at base pair resolution.
  
  
  RESULTS
  Using whole genome bisulphite sequencing of DNA from the livers of five mice from the A (vy) colony, we searched for sites at which DNA methylation differed among the mice. A small number of loci, 356, were detected and we call these inter-individual Differentially Methylated Regions, iiDMRs, 55 of which overlap with endogenous retroviral elements (ERVs). Whole genome resequencing of two mice from the colony identified very few differences and these did not occur at or near the iiDMRs. Further work suggested that the majority of ERV iiDMRs are metastable epialleles; the level of methylation was maintained in tissue from other germ layers and the level of mRNA from the neighbouring gene inversely correlated with methylation state. Most iiDMRs that were not overlapping ERV insertions occurred at tissue-specific DMRs and it cannot be ruled out that these are driven by changes in the ratio of cell types in the tissues analysed.
  
  
  CONCLUSIONS
  Using the most thorough genome-wide profiling technologies for differentially methylated regions, we find very few intrinsically epigenetically variable regions that we term iiDMRs. The most robust of these are at retroviral elements and appear to be metastable epialleles. The non-ERV iiDMRs cannot be described as metastable epialleles at this stage but provide a novel class of variably methylated elements for further study.
authors.affiliation: Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086 Australia.|University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, QLD 4102 Australia.
authors.forename: Harald
authors.initials: H
authors.lastname: Oey
authors.affiliation: Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086 Australia.
authors.forename: Luke
authors.initials: L
authors.lastname: Isbel
authors.affiliation: Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052 Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: Hickey
authors.affiliation: Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086 Australia.
authors.forename: Basant
authors.initials: B
authors.lastname: Ebaid
authors.affiliation: Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC 3086 Australia.
authors.forename: Emma
authors.initials: E
authors.lastname: Whitelaw
keywords: DNA methylation; Genetic variation; Inbred mice; Metastable epiallele