Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

The epigenome is a complex assortment of proteins and chemical modifications that are associated with DNA, control its transcription (Brink 1960; Bernstein et al. 2007), and mediate stable phenotypic states as exemplified by cell differentiation. The genome and the epigenome are associated in the chromosomes and are inherited together, but the degree to which the epigenome is encoded by the genome is not known. Furthermore, it is not clear to what extent the epigenome is maintained in the germline and transmitted between generations (Feng et al. 2010). It might be reset in each generation using genetically encoded information, but persistence of epigenetic states in the germline creates the potential for semi-independent inheritance of epigenetic information (Rakyan and Beck 2006; Richards 2006). Finally, it is not clear if epigenetic states that are present in the germline influence somatic epigenotypes, or conversely, if somatic epigenetic states are generated during cell differentiation using genetically encoded information. We have explored the use of comparative epigenomic analysis (“phyloepigenomics”) to obtain insights into changes in the epigenome in human evolution. Epigenetic differences provide a means to modulate the regulatory activity of noncoding regions. Functionally significant changes may be more readily identified in the epigenome than in the genome: Sequence change is not always associated with functional change (Boffelli et al. 2004), but the epigenome mediates genome function by controlling transcription (Brink 1960; Bernstein et al. 2007), and so changes in it are more likely to reflect functional changes. Epigenomic comparison might thus complement the evidence of potentially adaptive genomic changes identified with multiple sequence-based approaches (Pollard et al. 2006; Prabhakar et al. 2006; Grossman et al. 2010; Yi et al. 2010). This study focuses on one component of the epigenome, cytosine methylation, a covalent modification of DNA that acts as a focal point in mechanisms that suppress transcription initiation (Klose and Bird 2006). We have compared the methylomes of human and chimpanzee in a homogeneous somatic cell type, the neutrophil, using the orangutan as an outgroup. Our comparison uses a “methyltyping” assay based on digestion with the methylation-sensitive restriction enzyme HpaII and deep sequencing (MethylSeq) (Ball et al. 2009; Brunner et al. 2009). MethylSeq data was analyzed with MetMap (Singer et al. 2010), a computational method that we developed to correct bias in MethylSeq data and infer the true methylation status of all HpaII sites within the scope of the experiment. The combination of MethylSeq and MetMap obtains very deep sequence data focused on regions of the genome that are not methylated and can reliably detect methylation changes in these regions (Singer et al. 2010). Compared to methods that use methylation-independent restriction enzymes, MethylSeq retrieves information spanning more of the genome because of a more favorable profile of fragment sizes (Singer et al. 2010). We find that, while the methylomes of human and chimp are similar, a set of ∼1500 stable differences in CpG island-like regions distinguishes human from chimp; these differences identify regions that may have diverged in gene regulatory function. The methylation states can be used to build a tree that recapitulates the phylogenetic relationship of the three species. Analysis of CG substitution patterns in CpG island-like regions that have conserved their methylated state in human, chimp, and orang indicates that methylation in the neutrophil reflects germline methylation. Our findings demonstrate that methyltyping can identify differences that distinguish human from chimp and that these differences exist in the germline. This raises the question of whether a germline epigenome is transmitted along with the genome, and if so, whether it is completely determined by genome sequence.