The DNA Methylation Landscape of Enhancers in The Guinea Pig Hippocampus

Abstract

Aim: 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.

Keywords::

• ChIP-bisulfite sequencing
• DNA methylation
• enhancers
• H3K4me1
• RNAPII
• RNAPII-Ser5
• transcription onset

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2017-0064

Author’s contributions

M Szyf and SG Matthews conceived and supervised the study; M Szyf, SG Matthews, L Boureau and A Constantinof wrote the main manuscript text; L Boureau, A Constantinof and VG Moisiadis designed and performed experiments; L Boureau and A Constantinof analyzed the data.

Acknowledgements

Illumina sequencing was performed at Institut de Recherches Cliniques de Montreal. The raw sequencing data were submitted to GEO, accession number: GSE Accession number GSE98549.

Financial & competing interests disclosure

Supported by a grant from the Canadian Institute of Health Research (CIHR) MOP-126166 to SG Matthews & M Szyf and CIHR MOP-42411 to M Szyf. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

Brains were derived from animals that sacrificed as controls for other experiments that were approved by Ethical Committee for Animal Experimentation of the University of Toronto.