The DNA methylation landscape of enhancers in the guinea pig hippocampus.

To determine the state of methylation of DNA molecules in the guinea pig hippocampus that are associated with either poised or active enhancers. Methods: We used sequential chromatin immunoprecipitation-bisulfite-sequencing with an antibody to H3K4me1 to map the state of methylation of DNA that is found within enhancers. Actively transcribing transcription start sites were mapped by chromatin immunoprecipitation-sequencing with an antibody to RNApolII-PS5. Total DNA methylation was mapped using reduced representation bisulfite sequencing. Results: DNA that overlaps with H3K4me1 binding regions in the genome is heavily methylated. However, DNA molecules that are found in H3K4me1 chromatin are hypomethylated, while DNA found in enhancers that are associated with active transcription is further demethylated. Differential methylation in enhancers is spotted in single CGs, bimodal and corresponds to transcription factor binding sites. Conclusion: Our study delineates the DNA methylation status of H3K4 me1-bound regions in the hippocampus in active and inactive genes.