Evidence map›Paper›PMID 36190595›Full record

ArticleJournal of assisted reproduction and genetics2022

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

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of assisted reproduction and genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.9field-weighted citation impact, top 28% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 11 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 3 institutions in 1 country.

Minghua Liu *Reproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.ORCID http://orcid.org/0000-0002-9850-6311
Peiru Liu *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.
Yunjian Chang *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.
Beiying XuState 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.
Nengzhuang WangReproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.
Lina QinReproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China.
Jufen ZhengReproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China. jf_zheng@sina.cn.
Yun LiuMOE 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.
Ligang WuState 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.
Hongli YanReproductive Medical Center, Changhai Hospital, Naval Medical University, Shanghai, China. hongliyan@smmu.edu.cn.
Second Military Medical University · CNCenter for Excellence in Molecular Cell Science · CNSun Yat-sen University · CN

Funding

Natural Science Foundation of Shanghai 2018YFC1005002
6 · The paper itself

Abstract

backgroundA 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).

methodsWhole-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.

resultsA 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.

conclusionOur 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.

Indexed as

MicroRNAsRNA, Small UntranslatedDNA FragmentationDNA MethylationHumansMaleSemenSpermatozoaMicroRNAsRNA, Small UntranslatedCorrelation matricesDFIDNA methylationsncRNAsSpermWGBS

Identifiers

PMID36190595
PMCPMC9596664
OpenAlexW4300427303

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.