Systematic identification and comparison of expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in mouse germline stem cells

Abstract

Accumulating evidence indicates that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) involve in germ cell development. However, little is known about the functions and mechanisms of lncRNAs and circRNAs in self-renewal and differentiation of germline stem cells. Therefore, we explored the expression profiles of mRNAs, lncRNAs, and circRNAs in male and female mouse germline stem cells by high-throughput sequencing. We identified 18573 novel lncRNAs and 18822 circRNAs in the germline stem cells and further confirmed the existence of these lncRNAs and circRNAs by RT-PCR. The results showed that male and female germline stem cells had similar GDNF signaling mechanism. Subsequently, 8115 mRNAs, 3996 lncRNAs, and 921 circRNAs exhibited sex-biased expression that may be associated with germline stem cell acquisition of the sex-specific properties required for differentiation into gametes. Gene Ontology (GO) and KEGG pathway enrichment analyses revealed different functions for these sex-biased lncRNAs and circRNAs. We further constructed correlated expression networks including coding–noncoding co-expression and competing endogenous RNAs with bioinformatics. Co-expression analysis showed hundreds of lncRNAs were correlated with sex differences in mouse germline stem cells, including lncRNA Gm11851, lncRNA Gm12840, lncRNA 4930405O22Rik, and lncRNA Atp10d. CeRNA network inferred that lncRNA Meg3 and cirRNA Igf1r could bind competitively with miRNA-15a-5p increasing target gene Inha, Acsl3, Kif21b, and Igfbp2 expressions. These findings provide novel perspectives on lncRNAs and circRNAs and lay a foundation for future research into the regulating mechanisms of lncRNAs and circRNAs in germline stem cells.

Enrichment of Female Germline Stem Cells from Mouse Ovaries Using the Differential Adhesion Method

“…It is well-known that the AKT pathway is involved in self-renewal of SSCs, but little is known regarding the effects of the AKT pathway on self-renewal of FGSCs. FGSCs and spermatogonial stem cells are similar in their proliferation and differentiation patterns [28, 46], which raises the possibility that the self-renewal mechanism may be similar between these two systems. It has been reported that the PI3K-AKT pathway is highly expressed in FGSCs, demonstrating that the PI3K-AKT pathway may participate in the self-renewal of FGSCs [46].…”

“…Next, we investigated the molecular mechanisms that control the proliferation of FGSCs and found that the AKT pathway mediates self-renewal of FGSCs. Previous studies have shown that the PI3K-AKT pathway was strongly observed in the mRNAs and lncRNAs of FGSCs [28]. It is known that the AKT pathway is involved in self-renewal of spermatogonial stem cells, but little is known regarding the effects of the AKT pathway on self-renewal of FGSCs.…”

Noncoding RNAs: Potential players in the self‐renewal of mammalian spermatogonial stem cells

“…In recent years, it has become clear that serval types of ncRNAs, involving miRNA, lncRNA, piRNA, small nucleolar RNA, and circRNAs, play important roles in stem cell self‐renewal by forming complicated epigenetic regulatory networks together with other epigenetic factors related to DNA methylation, histone methylation, and acetylation (Dupuis‐Sandoval, Poirier, & Scott, ; S. Hu & Shan, ; Rojas‐Rios, Chartier, Pierson, & Simonelig, ; C. Y. Yu et al, ; Z. Yu, Li, Fan, Liu, & Pestell, ). As for SSCs, although a large number of ncRNAs have been screened as potential regulatory molecules for SSC self‐renewal using high‐throughput RNA sequencing and bioinformatics approaches, only a small portion of them have been validated and functionally characterized using biological experiment to uncover roles in SSCs self‐renewal, particularly lncRNAs, piRNA, and circRNAs (K. Hu et al, ; Li et al, ; X. Li, Ao, et al, ), thus there is an urgent need to reveal more ncRNAs associated with SSC self‐renewal to elucidate the molecular mechanisms underlying SSC self‐renewal. Encouragingly, great improvements of technologies have been recently made on isolation, characterization, in vitro culture, and in vivo transplantation of SSCs will provide us a robust research platform to explore the function of ncRNAs in SSC self‐renewal (X. Li, Ao, et al, ; Mulder et al, ; Takashima & Shinohara, ; Zhang, Sun, & Zou, ).…”

“…And they further found these circRNA hosting genes were expressed in cell‐specific pattern and GO analysis indicated their functions were mainly involved in GSCs self‐renewal and differentiation, such as stem cell maintenance, cell differentiation, germ cell development, and stem cell division. Additionally, X. Li, Ao, and Wu () also demonstrated 921 circRNAs exhibited a sex‐biased expression between the SSCs and FGSCs and of 245 circRNAs displayed a male‐biased expression (X. Li, Ao, & Wu, ). Despite the expression pattern of circRNA in mouse SSC was represented recently and suggest that circRNAs are likely to play potential roles in SSC self‐renewal, yet their biological functions in SSC self‐renewal remains largely unknown.…”

“…In the study performed by Lin et al (), 5,573 circRNAs were identified to be expressed in SSC and the average level of circRNAs exhibited dynamic changes during male germ cell development, indicating these circRNAs probably involved in SSC self‐renewal and differentiation. A recent study, to probe the functions of circRNAs in GSCs including SSCs and female GSCs (FGSCs), X. Li, Ao, and Wu () explored the expression profiles of circRNAs in mouse SSCs and FGSCs by high‐throughput sequencing and a total of 18,822 circRNAs derived from 5,334 hosting genes were identified in the mouse GSCs. And they further found these circRNA hosting genes were expressed in cell‐specific pattern and GO analysis indicated their functions were mainly involved in GSCs self‐renewal and differentiation, such as stem cell maintenance, cell differentiation, germ cell development, and stem cell division.…”