Identification and Functional Analysis of circRNAs in Chicken (Gallus gallus) Small Yellow Follicle
SHEN Man-Man1, 2, LI Ting-Ting1, CHEN Lan1, WU Peng-Fei1, CHEN Fu-Xiang1, ZHANG Gen-Xi1, WANG Jin-Yu1, *
1 College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
2 Jiangsu Institute of Poultry Science, Yangzhou 225216, China
Abstract：The function of follicular theca cells and granulosa cells of chicken (Gallus gallus) is different from that of mammals.The most important process in chicken follicular development is the development of small yellow follicle (SYF).In order to study the expression level of circular RNA (circRNA) in chicken follicle and enrich follicular development theory in chickens, the present study used SYF granulosa cells (SYFG) and SYF theca cells (SYFT) from Jinghai Yellow chicken as samples.RNA-seq libraries with linear RNA removed were prepared and sequenced with Hi-Seq 4000 platform instrument, and differentially expressed circRNAs were preliminarily screened by bioinformatics analysis.Then Gene ontoloty (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for differentially expressed circRNAs were performed to find the putative functional annotation and enrichment of the host genes.Lastly, a total of 9 904 circRNAs in SYFG and SYFT were identified with 4 199 pervasively distributed in the two kinds of cells.The number of circRNAs in SYFT was greater than that in SYFG.When coming to the feature of circRNAs, it was found that the most length of circRNAs spanned from 100 to 400 nt with an average length of 296 nt, and they distributed on all chromosome 1~28 and sex chromosome with more distribution in longer chromosome.After differentially expressed analysis, 625 dysregulated circRNAs were found with 271 up-regulated in SYFG and 354 up-regulated in SYFT.The up-regulated circRNAs in SYFG might involve in cell proliferation, cell recognition, fatty acid biosynthesis, and metabolic process, and the candidate genes such as TOX high mobility group box family member 2 (TOX2), insulin like growth factor 1 receptor (IGF1R),and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit β (PIK3CB) potentially affect granulosa development as circRNAs isoform.The up-regulated circRNAs in SYFT might participate in nucleotide binding, focal adhesion, and several pathways such as gonadotropin releasing hormone (GnRH) signaling pathway, apoptosis, oocyte meiosis associated with reproduction, and candidate genes as monoamine oxidase A (MAOA), fibroblast growth factor receptor 2 (FGFR2) and mitogen-activated protein kinase 1 (MAPK1) were selected.In conclusion, the circRNAs screened in present study might play their roles mainly by competing with linear transcripts or as competitive endogenous RNA (ceRNA).The results of present study enrich the basic genetic theory of chicken follicular development in the perspective of circRNA.
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