Integrative DNA Methylation and Gene Expression Analyses Identify DNA Packaging and Epigenetic Regulatory Genes Associated with Low Motility Sperm

Abstract

BackgroundIn previous studies using candidate gene approaches, low sperm count (oligospermia) has been associated with altered sperm mRNA content and DNA methylation in both imprinted and non-imprinted genes. We performed a genome-wide analysis of sperm DNA methylation and mRNA content to test for associations with sperm function.Methods and ResultsSperm DNA and mRNA were isolated from 21 men with a range of semen parameters presenting to a tertiary male reproductive health clinic. DNA methylation was measured with the Illumina Infinium array at 27,578 CpG loci. Unsupervised clustering of methylation data differentiated the 21 sperm samples by their motility values. Recursively partitioned mixture modeling (RPMM) of methylation data resulted in four distinct methylation profiles that were significantly associated with sperm motility (P = 0.01). Linear models of microarray analysis (LIMMA) was performed based on motility and identified 9,189 CpG loci with significantly altered methylation (Q<0.05) in the low motility samples. In addition, the majority of these disrupted CpG loci (80%) were hypomethylated. Of the aberrantly methylated CpGs, 194 were associated with imprinted genes and were almost equally distributed into hypermethylated (predominantly paternally expressed) and hypomethylated (predominantly maternally expressed) groups. Sperm mRNA was measured with the Human Gene 1.0 ST Affymetrix GeneChip Array. LIMMA analysis identified 20 candidate transcripts as differentially present in low motility sperm, including HDAC1 (NCBI 3065), SIRT3 (NCBI 23410), and DNMT3A (NCBI 1788). There was a trend among altered expression of these epigenetic regulatory genes and RPMM DNA methylation class.ConclusionsUsing integrative genome-wide approaches we identified CpG methylation profiles and mRNA alterations associated with low sperm motility.

Sperm nucleus decondensation, hyaluronic acid (HA) binding and oocyte activation capacity: different markers of sperm immaturity? Case reports

“…An additional interesting observation is that our treatment of Zn and vitamins of the group B are able to rescue the HA binding as it does for the DNA packaging. In any case, our observations confirm that in human sperm, fertility potential is highly dependent of méthylation [16,17] the major non-genetic contributions of the sperm nucleus to embryonic development. This observation confirms that homocysteine recycling i.e.…”

Genomic imprints as a model for the analysis of epigenetic stability during assisted reproductive technologies

“…However, other genes have now been identified with differential gametic DNA methylation that is retained through early preimplantation development (Smallwood et al 2011, Kobayashi et al 2012. Furthermore, while genome-wide methylation analyses are limited, altered DNA methylation has been detected at both imprinted and non-imprinted genes in ART-conceived children (Katari et al 2009), in vitro cultured mouse blastocysts (Wright et al 2011), and sperm from infertile men (Houshdaran et al 2007, Pacheco et al 2011, Aston et al 2012, as well as globally in two-cell mouse embryos from superovulated mothers and sperm from men with infertility (Shi & Haaf 2002, Benchaib et al 2003. Thus, aberrant imprinted methylation may be an indicator of more global epigenetic instability arising from ARTs or underlying infertility.…”

Effectiveness of Assisted Reproduction Techniques as an Answer to Male Infertility

“…This event is associated with spedific disease syndrome. In a recent study (Pacheco et al 2011), CpG methylation profiles and mRNA alterations have been associated with low sperm motility.…”