A Subpathway and Target Gene Cluster-Based Approach Uncovers lncRNAs Associated with Human Primordial Follicle Activation

Abstract

Long non-coding RNAs (lncRNAs) are emerging as a critical regulator in controlling the expression level of genes involved in cell differentiation and development. Primordial follicle activation (PFA) is the first step for follicle maturation, and excessive PFA results in premature ovarian insufficiency (POI). However, the correlation between lncRNA and cell differentiation was largely unknown, especially during PFA. In this study, we observed the expression level of lncRNA was more specific than protein-coding genes in both follicles and granulosa cells, suggesting lncRNA might play a crucial role in follicle development. Hence, a systematical framework was needed to infer the functions of lncRNAs during PFA. Additionally, an increasing number of studies indicate that the subpathway is more precise in reflecting biological processes than the entire pathway. Given the complex expression patterns of lncRNA target genes, target genes were further clustered based on their expression similarity and classification performance to reveal the activated/inhibited gene modules, which intuitively illustrated the diversity of lncRNA regulation. Moreover, the knockdown of SBF2-AS1 in the A549 cell line and ZFAS1 in the SK-Hep1 cell line further validated the function of SBF2-AS1 in regulating the Hippo signaling subpathway and ZFAS1 in the cell cycle subpathway. Overall, our findings demonstrated the importance of subpathway analysis in uncovering the functions of lncRNAs during PFA, and paved new avenues for future lncRNA-associated research.

Influence of Long Non-Coding RNAs on Human Oocyte Development

“… 34 In follicles, 91 lncRNAs were found to be involved in 210 dynamic sub-pathways, whereas in GCs, 17 lncRNAs were found to be involved in 234 dynamic sub-pathways. 32 These findings suggest that lncrnas may play a role in oocyte development.…”

“… 31 The number of lncRNAs expressed in follicles gradually increases from the primitive stage to the preovulation stage, and lncRNA demonstrates stronger cell type selectivity than protein-coding genes during follicle development. 32 These indicated that lncRNAsare involved in the regulation of human follicular development and are essential for the growth of oocytes. Four lncRNAs were found to be differentially expressed in mature and immature follicles of healthy women.…”