Impact of vitamin D depletion during development on mouse sperm DNA methylation

ABSTRACT

Suboptimal environmental conditions during development can substantially alter the epigenome. Stable environmentally-induced changes to the germline epigenome, in particular, have important implications for the health of the next generation. We showed previously that developmental vitamin D depletion (DVD) resulted in loss of DNA methylation at several imprinted loci over two generations. Here, we assessed the impact of DVD on genome-wide methylation in mouse sperm in order to characterize the number, extent and distribution of methylation changes in response to DVD and to find genes that may be susceptible to this prevalent environmental perturbation. We detected 15,827 loci that were differentially methylated in DVD mouse sperm vs. controls. Most epimutations (69%) were loss of methylation, and the extent of methylation change and number of CpGs affected in a region were associated with genic location and baseline methylation state. Methylation response to DVD at validated loci was only detected in offspring that exhibited a phenotypic response to DVD (increased body and testes weight) suggesting the two types of responses are linked, though a causal relationship is unclear. Epimutations localized to regions enriched for developmental and metabolic genes and pathway analyses showed enrichment for Cadherin, Wnt, PDGF and Integrin signaling pathways. These findings show for the first time that vitamin D status during development leads to substantial DNA methylation changes across the sperm genome and that locus susceptibility is linked to genomic and epigenomic context.

KEYWORDS:

• DOHAD
• vitamin D deficiency
• bisulfite sequencing
• sperm
• DNA methylation

Acknowledgments

We thank the UNC Systems Genetics Core Facility for providing the Collaborative Cross mice; Fernando Pardo Manuel de Villena for advice in selection of the CC strain; Terry Furey for advice in filtering bis-seq reads at repetitive regions and Mark Calaway, Kiristin Clement, Alisha Coffey, Kunjie Hua, Ryan Kuster, Judy Oakes and Sarah Schoenrock for providing technical assistance.

Author contributions

The experimental question and study design was conceived by FI. Mouse crosses and treatment scheme were conceived and supervised by LT and WV. Experimental animal handling, tissue collection, sample selection and preparation were performed by JX and FI. Post-sequencing quality control and data analyses to identify DMCs were performed by RZG and CB. All other data generation, analyses and interpretation were performed by JX and EP under the supervision of FI. The manuscript was drafted by JX and revised by FI with input from all authors. All authors have read and approved this manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Ethical disclosure

All animal handling was performed in accordance with the Guide for the Care and Use of Laboratory Animals under the corresponding animal use protocol at the University of North Carolina at Chapel Hill.

Supplementary material

Supplementary data for this article can be accessed here.

Additional information

Funding

This work was supported by the National Institute of Environmental Health Sciences [grant number KES023849A] and National Institute of Mental Health [grant number R01MH100241].