Intergenic and Intronic DNA Hypomethylated Regions as Putative Regulators of Imprinted Domains

Abstract

Aim: To investigate the regulatory potential of intergenic/intronic hypomethylated regions (iHMRs) within imprinted domains. Materials & methods: Based on the preliminary results of the histone modification and conservation profiles, we conducted reporter assays on the Peg3 and H19 domain iHMRs. The in vitro results were confirmed by the in vivo deletion of Peg3-iHMR designed to test its function in the Peg3 imprinted domain. Results & conclusion: Initial bioinformatic analyses suggested that some iHMRs may be noncanonical enhancers for imprinted genes. Consistent with this, Peg3- and H19-iHMRs showed context-dependent promoter and enhancer activity. Further, deletion of Peg3-iHMR resulted in allele- and sex-specific misregulation of several imprinted genes within the domain. Taken together, these results suggest that some iHMRs may function as domain-wide regulators for the associated imprinted domains.

Graphical abstract

Keywords::

• DNA methylation
• iHMR
• imprinted domains
• imprinted gene regulation
• imprinted genes
• imprinting
• intergenic hypomethylated region

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-2017-0125

Acknowledgements

The authors thank H Kim for her assistance with the cell culture and reporter assay experiments, and C Pesson for his help with the DNA methylation analyses of the human tumor panel. The authors also thank H Kim and W Frey for their thoughtful feedback and discussion over the manuscript.

Financial & competing interests disclosure

This work was supported by NIH (R01-GM066225 and R01-GM097074 to J Kim). 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

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

This work was supported by NIH (R01-GM066225 and R01-GM097074 to J Kim). 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.