Identification of the X-linked germ cell specific miRNAs (XmiRs) and their functions

X-Chromosome-Linked miRNAs Regulate Sex Differences in Cardiac Physiology

BACKGROUND

Males and females exhibit distinct anatomic and functional characteristics of the heart, predisposing them to specific disease states.

METHODS

We identified microRNAs (miRNAs/miR) with sex-differential expression in mouse hearts.

RESULTS

Four conserved miRNAs are present in a single locus on the X-chromosome and are expressed at higher levels in females than males. We show miRNA, miR-871, is responsible for decreased expression of the protein SRL (sarcalumenin) in females. SRL is involved in calcium signaling, and we show it contributes to differences in electrophysiology between males and females. miR-871 overexpression mimics the effects of the cardiac physiology of conditional cardiomyocyte-specific Srl-null mice. Inhibiting miR-871 with an antagomir in females shortened ventricular repolarization. The human orthologue of miR-871, miR-888, coevolved with the SRL 3' untranslated region and regulates human SRL.

CONCLUSIONS

These data highlight the importance of sex-differential miRNA mechanisms in mediating sex-specific functions and their potential relevance to human cardiac diseases.

Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression

Sperm small RNAs have emerged as important non-genetic contributors to embryogenesis and offspring health. A subset of sperm small RNAs is thought to be acquired during epididymal transit. However, the identity of the specific small RNAs transferred remains unclear. Here, we employ Cre/Lox genetics to generate germline- and epididymal-specific Dgcr8 knockout (KO) mice to investigate the dynamics of sperm microRNAs (miRNAs) and their functions post-fertilization. Testicular sperm from germline Dgcr8 KO mice has reduced levels of 116 miRNAs. Enthrallingly, following epididymal transit, the abundance of 72% of these miRNAs is restored. Conversely, sperm from epididymal Dgcr8 KO mice displayed reduced levels of 27 miRNAs. This loss of epididymal miRNAs in sperm was accompanied by transcriptomic changes in embryos fertilized by this sperm, which was rescued by microinjection of epididymal miRNAs. These findings ultimately demonstrate the acquisition of miRNAs from the soma by sperm during epididymal transit and their subsequent regulation of embryonic gene expression.

MicroRNAs in spermatogenesis dysfunction and male infertility: clinical phenotypes, mechanisms and potential diagnostic biomarkers

Infertility affects approximately 10-15% of couples worldwide who are attempting to conceive, with male infertility accounting for 50% of infertility cases. Male infertility is related to various factors such as hormone imbalance, urogenital diseases, environmental factors, and genetic factors. Owing to its relationship with genetic factors, male infertility cannot be diagnosed through routine examination in most cases, and is clinically called 'idiopathic male infertility.' Recent studies have provided evidence that microRNAs (miRNAs) are expressed in a cell-or stage-specific manner during spermatogenesis. This review focuses on the role of miRNAs in male infertility and spermatogenesis. Data were collected from published studies that investigated the effects of miRNAs on spermatogenesis, sperm quality and quantity, fertilization, embryo development, and assisted reproductive technology (ART) outcomes. Based on the findings of these studies, we summarize the targets of miRNAs and the resulting functional effects that occur due to changes in miRNA expression at various stages of spermatogenesis, including undifferentiated and differentiating spermatogonia, spermatocytes, spermatids, and Sertoli cells (SCs). In addition, we discuss potential markers for diagnosing male infertility and predicting the varicocele grade, surgical outcomes, ART outcomes, and sperm retrieval rates in patients with non-obstructive azoospermia (NOA).

Small RNAs, spermatogenesis, and male infertility: a decade of retrospect

Small non-coding RNAs (sncRNAs), being the top regulators of gene expression, have been thoroughly studied in various biological systems, including the testis. Research over the last decade has generated significant evidence in support of the crucial roles of sncRNAs in male reproduction, particularly in the maintenance of primordial germ cells, meiosis, spermiogenesis, sperm fertility, and early post-fertilization development. The most commonly studied small RNAs in spermatogenesis are microRNAs (miRNAs), PIWI-interacting RNA (piRNA), small interfering RNA (siRNA), and transfer RNA-derived small RNAs (ts-RNAs). Small non-coding RNAs are crucial in regulating the dynamic, spatial, and temporal gene expression profiles in developing germ cells. A number of small RNAs, particularly miRNAs and tsRNAs, are loaded on spermatozoa during their epididymal maturation. With regard to their roles in fertility, miRNAs have been studied most often, followed by piRNAs and tsRNAs. Dysregulation of more than 100 miRNAs has been shown to correlate with infertility. piRNA and tsRNA dysregulations in infertility have been studied in only 3-5 studies. Sperm-borne small RNAs hold great potential to act as biomarkers of sperm quality and fertility. In this article, we review the role of small RNAs in spermatogenesis, their association with infertility, and their potential as biomarkers of sperm quality and fertility.

A cluster of X-linked miRNAs are de-repressed with age in mouse liver and target growth hormone signaling

Growth hormone (GH) signaling influences lifespan in a wide variety of mammalian species. We previously reported that a cluster of miRNAs located on the X-chromosome are de-repressed with age in male mouse liver, and a subset, the mir-465 family, can directly attenuate expression of the growth hormone receptor (GHR) in vitro leading to a reduction in GH signaling. Here we show that this cluster of miRNAs is also upregulated in the liver with age in females, and that calorie restriction and the Ames dwarf genotype, both known to delay aging, attenuate the upregulation of the miRNA cluster. Upregulation of mir-465 in vivo leads to a reduction in GHR mRNA in the liver and an attenuation of GH signaling, indicated by a reduction in GHR, IGF-1, IGFBP3, and ALS mRNA expression. There is a corresponding reduction in IGF-1 protein levels in the liver and plasma. These results suggest that the age-associated upregulation of the X-chromosomal cluster of miRNAs could influence lifespan.

Odontoblasts release exosomes to regulate the odontoblastic differentiation of dental pulp stem cells

BACKGROUND

Dental pulp stem cells (DPSCs) play a crucial role in dentin-pulp complex regeneration. Further understanding of the mechanism by which DPSCs remain in a quiescent state could contribute to improvements in the dentin-pulp complex and dentinogenesis.

METHODS

TSC1 conditional knockout (DMP1-Cre+; TSC1f/f, hereafter CKO) mice were generated to increase the activity of mechanistic target of rapamycin complex 1 (mTORC1). H&E staining, immunofluorescence and micro-CT analysis were performed with these CKO mice and littermate controls. In vitro, exosomes were collected from the supernatants of MDPC23 cells with different levels of mTORC1 activity and then characterized by transmission electron microscopy and nanoparticle tracking analysis. DPSCs were cocultured with MDPC23 cells and MDPC23 cell-derived exosomes. Alizarin Red S staining, ALP staining, qRT‒PCR, western blotting analysis and micro-RNA sequencing were performed.

RESULTS

Our study showed that mTORC1 activation in odontoblasts resulted in thicker dentin and higher dentin volume/tooth volume of molars, and it increased the expression levels of the exosome markers CD63 and Alix. In vitro, when DPSCs were cocultured with MDPC23 cells, odontoblastic differentiation was inhibited. However, the inhibition of odontoblastic differentiation was reversed when DPSCs were cocultured with MDPC23 cells with mTORC1 overactivation. To further study the effects of mTORC1 on exosome release from odontoblasts, MDPC23 cells were treated with rapamycin or shRNA-TSC1 to inactivate or activate mTORC1, respectively. The results revealed that exosome release from odontoblasts was negatively correlated with mTORC1 activity. Moreover, exosomes derived from MDPC23 cells with active or inactive mTORC1 inhibited the odontoblastic differentiation of DPSCs at the same concentration. miRNA sequencing analysis of exosomes that were derived from shTSC1-transfected MDPC23 cells, rapamycin-treated MDPC23 cells or nontreated MDPC23 cells revealed that the majority of the miRNAs were similar among these groups. In addition, exosomes derived from odontoblasts inhibited the odontoblastic differentiation of DPSCs, and the inhibitory effect was positively correlated with exosome concentration.

CONCLUSION

mTORC1 regulates exosome release from odontoblasts to inhibit the odontoblastic differentiation of DPSCs, but it does not alter exosomal contents. These findings might provide a new understanding of dental pulp complex regeneration.

In vivo functions of miRNAs in mammalian spermatogenesis

MicroRNAs (miRNAs) are believed to play important roles in mammalian spermatogenesis mainly because spermatogenesis is more or less disrupted when genes encoding key enzymes for miRNA biogenesis are mutated. However, it is challenging to study the functions of individual miRNAs due to their family-wise high sequence similarities and the clustered genomic distributions of their genes, both of which expose difficulties in using genetic methods. Accumulating evidence shows that a number of miRNAs indeed play important roles in mammalian spermatogenesis and the underlying mechanisms start to be understood. In this mini review, we focus on highlighting the roles of miRNAs in mammalian spermatogenesis elucidated mainly by using in vivo genetic methods and on discussing the underlying mechanisms. We propose that studies on the roles of miRNAs in spermatogenesis should and can be conducted in a more fruitful way given the progress in traditional methods and the birth of new technologies.

Identification of spermatogenesis-associated changes in DNA methylation induced by maternal exposure to chemicals in male germ cells

It is now recognized that maternal environmental factors, including chemical exposure and nutritional conditions, alter DNA methylation patterns in fetal germ cells, subsequently affecting germ cell development as well as offspring phenotypes. Here, we describe steps for detecting DNA methylation changes in mouse germ cells isolated from both embryonic and spermatogenic stages after maternal exposure to a chemical compound. For complete details on the use and execution of this protocol, please refer to Tando et al. (2021).¹.

Integrative Analysis of RNA Expression and Regulatory Networks in Mice Liver Infected by Echinococcus multilocularis

The larvae of Echinococcus multilocularis causes alveolar echinococcosis, which poses a great threat to the public health. However, the molecular mechanisms underlying the host and parasite interactions are still unclear. Exploring the transcriptomic maps of mRNA, miRNA and lncRNA expressed in the liver in response to E. multilocularis infection will help us to understand its pathogenesis. Using liver perfusion, different cell populations including the hepatic cells, hepatic stellate cells and Kupffer cells were isolated from mice interperitoneally inoculated with protoscoleces. Their transcriptional profiles including lncRNAs, miRNAs and mRNAs were done by RNA-seq. Among these cell populations, the most differentially-expressed (DE) mRNA, lncRNAs and miRNAs were annotated and may involve in the pathological processes, mainly including metabolic disorders, immune responses and liver fibrosis. Following the integrative analysis of 38 differentially-expressed DEmiRNAs and 8 DElncRNAs, the lncRNA-mRNA-miRNA networks were constructed, including F63-miR-223-3p-Fbxw7/ZFP36/map1b, F63-miR-27-5p-Tdrd6/Dip2c/Wdfy4 and IFNgAS1-IFN-γ. These results unveil the presence of several potential lncRNA-mRNA-miRNA axes during E. multilocularis infection, and further exploring of these axes may contribute to better understanding of the pathogenic mechanisms.

Roles of Noncoding RNA in Reproduction

The World Health Organization predicts that infertility will be the third major health threat after cancer and cardiovascular disease, and will become a hot topic in medical research. Studies have shown that epigenetic changes are an important component of gametogenesis and related reproductive diseases. Epigenetic regulation of noncoding RNA (ncRNA) is appropriate and is a research hotspot in the biomedical field; these include long noncoding RNA (lncRNA), microRNA (miRNA), and PIWI-interacting RNA (piRNA). As vital members of the intracellular gene regulatory network, they affect various life activities of cells. LncRNA functions as a molecular bait, molecular signal and molecular scaffold in the body through molecular guidance. miRNAs are critical regulators of gene expression; they mainly control the stability or translation of their target mRNA after transcription. piRNA functions mainly through silencing genomic transposable elements and the post-transcriptional regulation of mRNAs in animal germ cells. Current studies have shown that these ncRNAs also play significant roles in the reproductive system and are involved in the regulation of essential cellular events in spermatogenesis and follicular development. The abnormal expression of ncRNA is closely linked to testicular germ cell tumors, poly cystic ovary syndrome and other diseases. This paper briefly presents the research on the reproductive process and reproductive diseases involving ncRNAs.

Identification of wnt2 in the pearl mussel Hyriopsis cumingii and its role in innate immunity and gonadal development

Wnt2 is a significant factor in the Wnt signaling pathway, which is associated with a variety of physiological activities, including inflammatory response, cell apoptosis, reproductive system development, and cell differentiation. Hyriopsis cumingii is the main pearl breeding mussel in China. However, the role of wnt2 in this species remains unclear. In this study, wnt2 from H. cumingii was cloned and identified. The full-length cDNA of wnt2 is 1524 bp, containing a 963 bp open reading frame (ORF), encoding 320 amino acid residues. The tissue distribution of H. cumingii indicated that wnt2 was predominantly highly expressed in the ovary and gill. And the expression profile after Aeromonas hydrophila or LPS injection indicated that wnt2 was up-regulated in gill, suggesting its role in the innate immune response. The expression of wnt2 was high at 4-month-old of early gonadal development and throughout ovarian development. In situ hybridization (ISH) showed significant hybridization signals on the gills and mature eggs of female gonads. In addition, miR-1988b-5p was found to negatively regulate wnt2 to affect the expression of key genes (frizzled-5, ctnnb1, and tcf7l) in the Wnt signaling pathway. Thus, these findings suggest a key role for wnt2 in immune regulation and gonadal development in H. cumingii.

Epi-mutations for spermatogenic defects by maternal exposure to di(2-ethylhexyl) phthalate

Exposure to environmental factors during fetal development may lead to epigenomic modifications in fetal germ cells, altering gene expression and promoting diseases in successive generations. In mouse, maternal exposure to di(2-ethylhexyl) phthalate (DEHP) is known to induce defects in spermatogenesis in successive generations, but the mechanism(s) of impaired spermatogenesis are unclear. Here, we showed that maternal DEHP exposure results in DNA hypermethylation of promoters of spermatogenesis-related genes in fetal testicular germ cells in F1 mice, and hypermethylation of Hist1h2ba, Sycp1, and Taf7l, which are crucial for spermatogenesis, persisted from fetal testicular cells to adult spermatogonia, resulting in the downregulation of expression of these genes. Forced methylation of these gene promoters silenced expression of these loci in a reporter assay. These results suggested that maternal DEHP exposure-induced hypermethylation of Hist1h2ba, Sycp1, and Taf7l results in downregulation of these genes in spermatogonia and subsequent defects in spermatogenesis, at least in the F1 generation.

Identification of new semen trait-related candidate genes in Duroc boars through genome-wide association and weighted gene co-expression network analyses

Semen traits are crucial in commercial pig production since semen from boars is widely used in artificial insemination for both purebred and crossbred pig production. Revealing the genetic architecture of semen traits potentially promotes the efficiencies of improving semen traits through artificial selection. This study is aimed to identify candidate genes related to the semen traits in Duroc boars. First, we identified the genes that were significantly associated with three semen traits, including sperm motility (MO), sperm concentration (CON), and semen volume (VOL) in a Duroc boar population through a genome-wide association study (GWAS). Second, we performed a weighted gene co-expression network analysis (WGCNA). A total of 2, 3, and 20 single-nucleotide polymorphisms were found to be significantly associated with MO, CON, and VOL, respectively. Based on the haplotype block analysis, we identified one genetic region associated with MO, which explained 6.15% of the genetic trait variance. ENSSSCG00000018823 located within this region was considered as the candidate gene for regulating MO. Another genetic region explaining 1.95% of CON genetic variance was identified, and, in this region, B9D2, PAFAH1B3, TMEM145, and CIC were detected as the CON-related candidate genes. Two genetic regions that accounted for 2.23% and 2.48% of VOL genetic variance were identified, and, in these two regions, WWC2, CDKN2AIP, ING2, TRAPPC11, STOX2, and PELO were identified as VOL-related candidate genes. WGCNA analysis showed that, among these candidate genes, B9D2, TMEM145, WWC2, CDKN2AIP, TRAPPC11, and PELO were located within the most significant module eigengenes, confirming these candidate genes' role in regulating semen traits in Duroc boars. The identification of these candidate genes can help to better understand the genetic architecture of semen traits in boars. Our findings can be applied for semen traits improvement in Duroc boars.

miR-302d Competitively Binding with the lncRNA-341 Targets TLE4 in the Process of SSC Generation

MicroRNAs (miRNAs) are essential factors in the reproductive process of poultry. Here, we found miR-302d is a potential differentiation and negative factor of chicken embryonic stem cells (ESCs) into spermatogonia stem cells (SSCs). The competition mechanism was carried out for the preliminary exploration to determine the relationship among miR-302d, lncRNA-341(interacting with miR-302d), and target gene TLE4. The results showed that lncRNA-341 can competitively bind to miR-302d to decrease the targeted binding of miR-302d and TLE4 which promotes the differentiation of chicken SSCs. Moreover, it is suggested that miR-302d may participate in the Wnt signaling pathway through TLE4.

Reverse genetics reveals single gene of every candidate on Hybrid sterility, X Chromosome QTL 2 (Hstx2) are dispensable for spermatogenesis

F1 hybrid progenies between related subspecies often show hybrid sterility (HS) or inviability. HS is caused by failure of meiotic chromosome synapsis and sex body formation in house mouse. Previous studies identified two HS critical genomic regions named Hstx2 on Chr X and Hst1 on Chr 17 by murine forward genetic approaches. HS gene on Hst1 was reported to be Prdm9. Intersubspecific polymorphisms of Prdm9 induce HS in hybrids, and Prdm9 null mutation leads to sterility in the inbred strain. However, HS gene on Hstx2 remains unknown. Here, using knock-out studies, we showed that HS candidate genes on Hstx2 are not individually essential for spermatogenesis in B6 strain. We examined 12 genes on Hstx2: Ctag2, 4930447F04Rik, Mir743, Mir465d, Mir465c-2, Mir465b-1, Mir465c-1, Mir465, Gm1140, Gm14692, 4933436I01Rik, and Gm6812. These genes were expressed in adult testes, and showed intersubspecific polymorphisms on expressed regions. This first reverse genetic approach to identify HS gene on Hstx2 suggested that the loss of function of any one HS candidate gene does not cause complete sterility, unlike Prdm9. Thus, the mechanism(s) of HS by the HS gene on Hstx2 might be different from that of Prdm9.

Genomic Structure of Hstx2 Modifier of Prdm9-Dependent Hybrid Male Sterility in Mice

F1 hybrids between mouse inbred strains PWD and C57BL/6 represent the most thoroughly genetically defined model of hybrid sterility in vertebrates. Hybrid male sterility can be fully reconstituted from three components of this model, the Prdm9 gene, intersubspecific homeology of Mus musculus musculus and Mus musculus domesticus autosomes, and the X-linked Hstx2 locus. Hstx2 modulates the extent of Prdm9-dependent meiotic arrest and harbors two additional factors responsible for intersubspecific introgression-induced oligospermia (Hstx1) and meiotic recombination rate (Meir1). To facilitate positional cloning and to overcome the recombination suppression within the 4.3 Mb encompassing the Hstx2 locus, we designed Hstx2-CRISPR and SPO11/Cas9 transgenes aimed to induce DNA double-strand breaks specifically within the Hstx2 locus. The resulting recombinant reduced the Hstx2 locus to 2.70 Mb (chromosome X: 66.51-69.21 Mb). The newly defined Hstx2 locus still operates as the major X-linked factor of the F1 hybrid sterility, and controls meiotic chromosome synapsis and meiotic recombination rate. Despite extensive further crosses, the 2.70 Mb Hstx2 interval behaved as a recombination cold spot with reduced PRDM9-mediated H3K4me3 hotspots and absence of DMC1-defined DNA double-strand-break hotspots. To search for structural anomalies as a possible cause of recombination suppression, we used optical mapping and observed high incidence of subspecies-specific structural variants along the X chromosome, with a striking copy number polymorphism of the microRNA Mir465 cluster. This observation together with the absence of a strong sterility phenotype in Fmr1 neighbor (Fmr1nb) null mutants support the role of microRNA as a likely candidate for Hstx2.

A New MicroRNA Cluster Involved in the Reprogramming to a Pluripotent State

Reprogramming of somatic cells to a pluripotent state is a complex, multistage process that is regulated by many factors. Among these factors, non-coding RNAs and microRNAs (miRNAs) have been intensively studied in recent years. MiRNAs play an important role in many processes, particularly in cell reprogramming. In this study, we investigated the reprogramming of rat fibroblasts with a deleted locus encoding a cluster comprising 14 miRNAs (from miR-743a to miR-465). The deletion of this locus was demonstrated to decrease significantly the efficiency of the cell reprogramming. In addition, the cells produced by the reprogramming differed from rat embryonic and induced pluripotent stem cells, which was an indication that reprogramming in these cells had not been completed. We suggest that this miRNA cluster or some of its members are involved in regulating the reprogramming of rat cells to a pluripotent state.