Genome-wide DNA methylation profiles and small noncoding RNA signatures in sperm with a high DNA fragmentation index

Minghua Liu; Peiru Liu; Yunjian Chang; Beiying Xu; Nengzhuang Wang; Lina Qin; Jufen Zheng; Yun Liu; Ligang Wu; Hongli Yan

doi:10.1007/s10815-022-02618-6

Genome-wide DNA methylation profiles and small noncoding RNA signatures in sperm with a high DNA fragmentation index

J Assist Reprod Genet. 2022 Oct;39(10):2255-2274. doi: 10.1007/s10815-022-02618-6. Epub 2022 Oct 3.

Authors

Minghua Liu^#¹, Peiru Liu^#², Yunjian Chang^#³, Beiying Xu³, Nengzhuang Wang¹, Lina Qin¹, Jufen Zheng⁴, Yun Liu⁵, Ligang Wu⁶, Hongli Yan⁷

Affiliations

¹ Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.
² MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China.
³ State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
⁴ Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China. jf_zheng@sina.cn.
⁵ MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, China. yliu39@fudan.edu.cn.
⁶ State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. lgwu@sibcb.ac.cn.
⁷ Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China. hongliyan@smmu.edu.cn.

^# Contributed equally.

Abstract

Background: A growing number of studies have reported that sperm DNA fragmentation (SDF) is associated with male infertility. However, no studies have compared genome-wide DNA methylation profiles and sncRNA signatures between sperm with high and low sperm DNA fragmentation indices (DFIs).

Methods: Whole-genome bisulfite sequencing (WGBS) was performed on sperm samples from a weak group (DFI ≥ 30%, n = 6) and normal group (DFI ≤ 15%, n = 7). Small noncoding RNA (sncRNA) deep sequencing was conducted for sperm samples from the weak (DFI ≥ 30%, n = 13) and normal (DFI ≤ 15%, n = 17) groups.

Results: A total of 4939 differentially methylated regions (DMRs) were identified in the weak group sperm samples relative to normal group sperm samples, with 2072 (41.95%) of them located in promoter regions. The percentages of hypermethylated DMRs were higher than those of hypomethylated DMRs in all seven examined gene annotation groups. Hypermethylated DMRs were significantly enriched in terms associated with neurons and microtubules. Compared with the normal group, the global DNA methylation level of the weak group sperm showed a downward trend, with lower correlation for methylation in the weak group sperm; therefore, the chromosomes of high-DFI sperm may be loose. On average, 40.5% of sncRNAs were annotated as rsRNAs, 19.3% as tsRNAs, 10.4% as yRNAs, and 7.1% as miRNAs. A total of 27 miRNAs, 151 tsRNAs, and 70 rsRNAs were differentially expressed between the two groups of sperm samples. Finally, 7 sncRNAs were identified as candidate sperm quality biomarkers, and the target genes of the differentially expressed miRNAs are involved in nervous system development.

Conclusion: Our findings suggest that genome-wide DNA methylation profiles and sncRNA signatures are significantly altered in high-DFI sperm. Our study provides potential biomarkers for sperm quality.

Keywords: Correlation matrices; DFI; DNA methylation; Sperm; WGBS; sncRNAs.

MeSH terms

DNA Fragmentation
DNA Methylation / genetics
Humans
Male
MicroRNAs* / metabolism
RNA, Small Untranslated* / genetics
Semen
Spermatozoa / metabolism

Substances

RNA, Small Untranslated
MicroRNAs

Grants and funding

2018YFC1005002/Natural Science Foundation of Shanghai