Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

Genomic imprinting is a form of epigenetic regulation that results in the expression of either the maternally or paternally inherited allele of a subset of genes (Ramowitz and Bartolomei 2011). This imprinted expression of transcripts is crucial for normal mammalian development. In humans, loss-of-imprinting of specific loci results in a number of diseases exemplified by the reciprocal growth phenotypes of the Beckwith-Wiedemann and Silver-Russell syndromes, and the behavioral disorders Angelman and Prader-Willi syndromes (Kagami et al. 2008; Buiting 2010; Choufani et al. 2010; Eggermann 2010; Kelsey 2010; Mackay and Temple 2010). In addition, aberrant imprinting also contributes to multigenic disorders associated with various complex traits and cancer (Kong et al. 2009; Monk 2010). Imprinted loci contain differentially methylated regions (DMRs) where cytosine methylation marks one of the parental alleles, providing cis-acting regulatory elements that influence the allelic expression of surrounding genes. Some DMRs acquire their allelic methylation during gametogenesis, when the two parental genomes are separated, resulting from the cooperation of the de novo methyltransferase DNMT3A and its cofactor DNMT3L (Bourc'his et al. 2001; Hata et al. 2002). These primary, or germline imprinted DMRs are stably maintained throughout somatic development, surviving the epigenetic reprogramming at the oocyte-to-embryo transition (Smallwood et al. 2011; Smith et al. 2012). To confirm that an imprinted DMR functions as an imprinting control region (ICR), disruption of the imprinted expression upon genetic deletion of that DMR, either through experimental targeting in mouse or that which occurs spontaneously in humans, is required. A subset of DMRs, known as secondary DMRs, acquire methylation during development and are regulated by nearby germline DMRs in a hierarchical fashion (Coombes et al. 2003; Lopes et al. 2003; Kagami et al. 2010). With the advent of large-scale, base-resolution methylation technologies, it is now possible to discriminate allelic methylation dictated by sequence variants from imprinted methylation. Yet our knowledge of the total number of imprinted DMRs in humans, and their developmental dynamics, remains incomplete, hampered by genetic heterogeneity of human samples. Here we present high-resolution mapping of human imprinted methylation. We performed whole-genome-wide bisulfite sequencing (WGBS) on leukocyte-, brain-, liver-, and placenta-derived DNA samples to identify partially methylated regions common to all tissues consistent with imprinted DMRs. We subsequently confirmed the partial methylated states in tissues using high-density methylation microarrays. The parental origin of methylation was determined by comparing microarray data for DNA samples from reciprocal genome-wide uniparental disomy (UPD) samples, in which all chromosomes are inherited from one parent (Lapunzina and Monk 2011), and androgenetic hydatidiform moles, which are created by the fertilization of an oocyte lacking a nucleus by a sperm that endoreduplicates. The use of uniparental disomies and hydatidiform moles meant that our analyses were not subjected to genotype influences, enabling us to characterize all known imprinted DMRs at base-pair resolution and to identify 21 imprinted domains, which we show are absent in mice. Lastly, we extended our analyses to determine the methylation profiles of all imprinted DMRs in sperm, stem cells derived from parthenogenetically activated metaphase-2 oocyte blastocytes (phES) (Mai et al. 2007; Harness et al. 2011), and stem cells (hES) generated from both six-cell blastomeres and the inner cell mass of blastocysts, delineating the extent of embryonic reprogramming that occurs at these loci during human development.