Analysis of DNA variants in miRNAs and miRNA 3ʼUTR binding sites in female infertility patients

Abstract

Early human embryogenesis relies on maternal gene products accumulated during oocyte growth and maturation, until around day-3 post-fertilization when human zygotic genome activation occurs. The maternal-to-zygotic transition (MZT) is a tightly coordinated process of selective maternal transcript clearance and new zygotic transcript production. If MZT is disrupted, it will lead to developmental arrest and pregnancy loss. It is well established that microRNA (miRNA) mutations disrupt regulation of their target transcripts. We hypothesize that some cases of embryonic arrest and pregnancy loss could be explained by the mutations in the maternal genome that affect miRNA-target transcript pairs. To this end, we examined mutations within miRNAs or miRNA binding sites in the 3ʼ untranslated regions (3ʼUTR) of target transcripts. Using whole-exome sequencing data from 178 women undergoing in vitro fertilization (IVF) procedures, we identified 1197 variants in miRNA genes, including 93 single nucleotide variants (SNVs) and 19 small insertions/deletions (INDELs) within the seed region of 100 miRNAs. Eight miRNA seed-region variants were significantly enriched among our patients when compared to a normal population. Within predicted 3ʼUTR miRNA binding sites, we identified 7393 SNVs and 1488 INDELs. Between our patients and a normal population, 52 SNVs and 30 INDELs showed significant association in the single-variant testing, whereas 51 genes showed significant association in the gene-burden analysis for genes that are expressed in preimplantation embryos. Interestingly, we found that many genes with disrupted 3ʼUTR miRNA binding sites follow gene expression patterns resembling MZT. In addition, some of these variants showed dramatic allele frequency difference between the patient and the normal group, offering potential utility as biomarkers for screening patients prior to IVF procedures.

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Fig. 1: Analysis workflow to identify candidate non-coding variants implicated in fertility.
Fig. 2: Variants stratified by miRNA gene regions.
Fig. 3: Genes enriched for 3'UTR variants within miRNA binding sites follow expression resembling maternal transcript clearance pattern.

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Acknowledgements

We thank the patients who participated in and contributed to this study. This work is supported by a grant from the NIH/NICHD to KS, JX, and XT: R01-HD091331. We gratefully acknowledge access to the HPC facilities and support of the computational STEM and bioinformatics scientists from the Office of Advanced Research Computing at Rutgers University.

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Correspondence to Jinchuan Xing.

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Tyc, K.M., Wong, A., Scott, R.T. et al. Analysis of DNA variants in miRNAs and miRNA 3ʼUTR binding sites in female infertility patients. Lab Invest (2020). https://doi.org/10.1038/s41374-020-00498-x

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