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Regulation of crucial lnc RNA s in differentiation of chicken embryonic stem cells to spermatogonia stem cells
Author(s) -
Li D.,
Ji Y.,
Wang F.,
Wang Y.,
Wang M.,
Zhang C.,
Zhang W.,
Lu Z.,
Sun C.,
Ahmed M. F.,
He N.,
Jin K.,
Cheng S.,
Wang Y.,
He Y.,
Song J.,
Zhang Y.,
Li B.
Publication year - 2017
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12510
Subject(s) - biology , transcriptome , embryonic stem cell , rna , stem cell , microbiology and biotechnology , gene , gene expression , cellular differentiation , microrna , gene expression profiling , genetics
Summary Regulation of crucial lnc RNA s involved in differentiation of chicken embryonic stem cells ( ESC s) to spermatogonia stem cells ( SSC s) was explored by sequencing the transcriptome of ESC s, primordial germ cells ( PGC s) and SSC s with RNA ‐Seq; analytical bioinformatic methods were used to excavate candidate lnc RNA s. We detected expression of candidate lnc RNA s in ESC s, PGC s and SSC s 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 lnc RNA s in ESC s, PGC s and SSC s, with 3549 defined as significantly different. We screened 20 candidate lnc RNA s, each demonstrating a greater than eight‐fold difference in |log FC | value between groups ( ESC s vs. PGC s, ESC s vs. SSC s and PGC s vs. SSC s) or specifically expressed in an individual cell type. qRT ‐ PCR results indicated that expression tendencies of candidate lnc RNA s 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‐ ESC 2 negatively regulated target genes SUFU , EPHA 3 , KLF 3 , ARL 3 and TRIM 8 , whereas SHH , NOTCH , TGF ‐ β , cAMP / cGMP and JAK / STAT signaling pathways were promoted, causing differentiation of ESC s into SSC s. Our findings represent a preliminary unveiling of lnc RNA ‐associated regulatory mechanisms during differentiation of chicken ESC s into SSC s, filling a research void in male germ cell differentiation related to lnc RNA . Our results also provide basic information for improving in vitro induction systems for differentiation of chicken ESC s into SSCs.