Regulation of crucial lncRNAs in differentiation of chicken embryonic stem cells to spermatogonia stem cells

Abstract

Regulation of crucial lncRNAs involved in differentiation of chicken embryonic stem cells (ESCs) to spermatogonia stem cells (SSCs) was explored by sequencing the transcriptome of ESCs, primordial germ cells (PGCs) and SSCs with RNA-Seq; analytical bioinformatic methods were used to excavate candidate lncRNAs. We detected expression of candidate lncRNAs in ESCs, PGCs and SSCs and forecasted related target genes. Utilizing wego, david and string, function and protein-protein interactions of target genes were analyzed. Finally, based on string analysis, interaction diagrams and relevant signaling pathways were established. Our results indicate a total of 9657 lncRNAs in ESCs, PGCs and SSCs, with 3549 defined as significantly different. We screened 20 candidate lncRNAs, each demonstrating a greater than eight-fold difference in |logFC| value between groups (ESCs vs. PGCs, ESCs vs. SSCs and PGCs vs. SSCs) or specifically expressed in an individual cell type. qRT-PCR results indicated that expression tendencies of candidate lncRNAs were consistent with RNA-Seq. Fifteen cis and four trans target genes were forecasted. Based on wego and string analyses, we found lnc-SSC1, lnc-SSC5, lnc-SSC2 and lnc-ESC2 negatively regulated target genes SUFU, EPHA3, KLF3, ARL3 and TRIM8, whereas SHH, NOTCH, TGF-β, cAMP/cGMP and JAK/STAT signaling pathways were promoted, causing differentiation of ESCs into SSCs. Our findings represent a preliminary unveiling of lncRNA-associated regulatory mechanisms during differentiation of chicken ESCs into SSCs, filling a research void in male germ cell differentiation related to lncRNA. Our results also provide basic information for improving in vitro induction systems for differentiation of chicken ESCs into SSCs.

RETRACTED ARTICLE: Production of viable chicken by allogeneic transplantation of primordial germ cells induced from somatic cells

“…Moreover, we found that epigenetic regulation by addition of VC or VPA, as well as glycolytic inhibition with VK3, could significantly enhance PGC formation (from 12.2% to 16.41%). In addition, studies have shown that lncRNAs 42 , ubiquitination 43 , phosphorylation 44 , and histone methylation 45 promote iPGC formation, which should also be considered to optimize the iPGC induction system.…”

Long noncoding RNA CASC2 predicts the prognosis of glioma patients and functions as a suppressor for gliomas by suppressing Wnt/β-catenin signaling pathway

“…They are involved in the regulation of gene expression at different levels, affecting multiple cellular processes including cell differentiation, stem cell maintenance, and epithelial–mesenchymal transition 3–5. Accumulating evidence has strongly suggested that many lncRNAs function as oncogenes and/or tumor suppressors in tumor initiation and development 6.…”

Systematic screening of long intergenic noncoding RNAs expressed during chicken embryogenesis

“…A microRNA catalog of the developing post-oviposited chicken embryo provided an important foundation for further investigations on miRNA gene regulation in the chicken embryo ( Glazov, et al., 2008 ). Genome-wide identification of lncRNAs in embryonic skeletal muscle ( Li, et al., 2012 ; Zhenhui, et al., 2017 ), liver ( Ning, et al., 2020 ), and brain ( Xu, et al., 2018 ), and embryonic stem cells has also been performed ( Li, et al, 2017 ), suggesting lncRNA regulatory and functional roles in chicken embryonic development. These analyses show that noncoding RNAs constitute a substantial portion of the transcriptome and suggest that these play critical roles in animal embryogenesis.…”