Profiling the DNA methylation patterns of imprinted genes in abnormal semen samples by next-generation bisulfite sequencing

Purpose Changes in DNA methylation modifications have been associated with male infertility. With the development of assisted reproductive technologies (ARTs), abnormal DNA methylation in sperm, especially in imprinted genes, may impact the health of offspring and requires an in-depth study. Methods In this study, we collected abnormal human semen samples, including asthenospermic, oligospermic, oligoasthenospermic and deformed sperm, and investigated the methylation of imprinted genes by reduced representation bisulfite sequencing (RRBS) and bisulfite amplicon sequencing on the Illumina platform. Results The differentially methylated regions (DMRs) of imprinted genes, includingH19,GNAS,MEG8andSNRPN, were different in the abnormal semen groups.MEG8DMR methylation in the asthenospermic group was significantly increased. Furthermore, higher methylation levels ofMEG8,GNASandSNRPNDMR in the oligospermic and oligoasthenospermic groups and a decrease in theH19DMR methylation level in the oligospermic group were observed. However, the methylation levels of these regions varied greatly among the different semen samples and among individual sperm within the same semen sample. The SNP rs2525883 genotype in theH19DMR affected DNA methylation. Moreover, DNA methylation levels differed in the abnormal semen groups in the non-imprinted genomic regions, including repetitive sequence DNA transposons and long/short interspersed nuclear elements (LINEsandSINEs). Conclusion Our study established that imprinted gene DMRs, such asH19,GNAS,SNRPNandMEG8, were differentially methylated in the abnormal semen groups with obvious inter- and intra-sample heterogeneities. These results suggest that special attention needs to be paid to possible epigenetic risks during reproduction.