title: 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.
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: D
authors.initials: D
authors.lastname: Li
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Ji
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: F
authors.initials: F
authors.lastname: Wang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: M
authors.initials: M
authors.lastname: Wang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: C
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: W
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Z
authors.initials: Z
authors.lastname: Lu
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: C
authors.initials: C
authors.lastname: Sun
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: M F
authors.initials: MF
authors.lastname: Ahmed
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: N
authors.initials: N
authors.lastname: He
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: K
authors.initials: K
authors.lastname: Jin
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: S
authors.initials: S
authors.lastname: Cheng
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: He
authors.affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
authors.forename: J
authors.initials: J
authors.lastname: Song
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Jiangsu Province Key Laboratory of Animal Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
authors.forename: B
authors.initials: B
authors.lastname: Li
mesh_terms: D000072956:Adult Germline Stem Cells / Q000166:cytology*; D000818:Animals; D002454:Cell Differentiation; D002642:Chick Embryo / Q000166:cytology* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000032:analysis* / Q000378:metabolism*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D015398:Signal Transduction
chemical_list: D062085:RNA, Long Noncoding
keywords: embryonic stem cells; long non-coding RNA; primordial germ cells; signaling pathway; spermatogonia stem cells; target gene