Novel Insights into DNA Methylation Features in Spermatozoa: Stability and Peculiarities

Abstract

Data about the entire sperm DNA methylome are limited to two sperm donors whereas studies dealing with a greater number of subjects focused only on a few genes or were based on low resolution arrays. This implies that information about what we can consider as a normal sperm DNA methylome and whether it is stable among different normozoospermic individuals is still missing. The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same subject (intra-individual variability) are relevant for a better understanding of pathological conditions. We addressed these questions by using the high resolution Infinium 450K methylation array and compared normal sperm DNA methylomes against somatic and cancer cells. Our study, based on the largest number of subjects (n = 8) ever considered for such a large number of CpGs (n = 487,517), provided clear evidence for i) a highly conserved DNA methylation profile among normozoospermic subjects; ii) a stable sperm DNA methylation pattern in different quality-fractioned sperm populations of the same individual. The latter finding is particularly relevant if we consider that different quality fractioned sperm subpopulations show differences in their structural features, metabolic and genomic profiles. We demonstrate, for the first time, that DNA methylation in normozoospermic men remains highly uniform regardless the quality of sperm subpopulations. In addition, our analysis provided both confirmatory and novel data concerning the sperm DNA methylome, including its peculiar features in respect to somatic and cancer cells. Our description about a highly polarized sperm DNA methylation profile, the clearly distinct genomic and functional organization of hypo- versus hypermethylated loci as well as the association of histone-enriched hypomethylated loci with embryonic development, which we now extended also to hypomethylated piRNAs-linked genes, provides solid basis for future basic and clinical research.

Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation

“…5B. A similar approach was taken to examine genes found to have altered methylation in sperm due to infertility (Krausz et al, 2012) and paternal age (Jenkins et al, 2014). Folic acid supplements in our study did not significantly affect methylation of the eight infertility-associated or the 48 paternal aging-associated gene promoters (Supplemental Figure S7).…”

High-density array analysis of DNA methylation in Tamoxifen-resistant breast cancer cell lines

“…3D). 13,14 The relationship of shared hyperand hypomethylated CpG sites in the Tamoxifen-selected lines to the canonical CpG islands is shown in Figure 3E and F. The pattern of the hypermethylated sites deviates from their representation on the HM450 BeadChip. Only 10% of hypermethylated CpG sites lie within the CpG islands, while 31% of the CpGs included on the BeadChip are within an island ( Fig.…”

Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors

“…It is well established that distinct epigenetic profiles exemplified by DNA methylation signify pluripotent as well as divergent somatic lineage states (Krausz et al 2012;Nazor et al 2012;Reinius et al 2012;Yuen et al 2013;Anton et al 2014;Court et al 2014;He et al 2014). The germ lineage also bears a unique developmentally regulated state, with transient erasure of genomic imprints that ensues from a post-inner cell mass wave of methylome erasure (Tada et al 1998), followed by the establishment of male or female gametic epigenetic sexual dimorphism required for physiological reproduction (Gkountela et al 2015;Guo et al 2015;Tang et al 2015).…”