Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken

Abstract

BackgroundCircular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovarian development. However, the function of circRNA in chicken follicles is unclear. To better understand the molecular mechanism underlying follicular development and granulosa cell function, we performed a strategy of second-generation sequencing and linear RNA depletion for granulosa cells from small yellow follicles (SYF, 5–8 mm), the smallest hierarchal follicles (F6, 9–12 mm), and the largest hierarchal follicles (F1, ~ 40 mm).ResultsWe predicted a total of 11,642 circRNAs that distributed on almost all chromosomes. The majority of the splice lengths of circRNAs were 200–500 nt and mainly produced from intron and CDS regions. During follicle growth, differentially expressed (DE) circRNAs showed dynamic changes which were tissue- and stage-specific. The host genes of DE circRNAs were functionally enriched in GTPase activity and several pathways involved in reproduction. Moreover, bioinformatic prediction analysis for circRalGPS2 demonstrated that circRNAs from the same genes may share common miRNA to act as a sponge. The predicted target genes were enriched in various biological processes including cognition, cell communication, and regulation of signaling, and several pathways related to reproduction such as tight junction, oocyte meiosis, progesterone-mediated oocyte maturation, and GnRH signaling.ConclusionsThis study provides a starting point for further experimental investigations into chicken circRNAs and casts a light on the understanding of follicle development.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5462-2) contains supplementary material, which is available to authorized users.

The circular RNA aplacirc_13267 upregulates duck granulosa cell apoptosis by the apla‐miR‐1‐13/THBS1 signaling pathway

“…In this study, we studied the expression of circRNAs by RNA‐seq during duck follicle development and explored their expression profiles and functions in duck follicles. We predicted a total of 4,204 circRNAs in two types of follicles, which was less than those detected in the muscles of embryonic chickens (13,377) (Ouyang et al, 2018) and in the follicle GCs of chickens (11,642) (Shen et al, 2019) and more than those detected in the livers of ALVJ‐resistant and susceptible chickens (1,800) (X. Zhang et al, 2017). All these results suggested that the expression of circRNAs was tissue‐specific and contributed to the hypothesis that in different tissues, circularization was a tightly regulated event (Rybak‐Wolf et al, 2015).…”

“…The reproductive performance of avian species mainly depends on the developmental status of their follicles. Follicle development is affected mainly by their physiology and the environment (Shen et al, 2019). Although the follicles of birds and mammals are different, the characteristics of ovarian follicles in maturing ducks are similar to those of mammals.…”

“…However, the main mechanism of circRNAs may be their ability to act as miRNA sponges to modulate posttranscriptional regulation (Memczak et al, 2013). Recently, with the rapid development of bioinformatics techniques and deep sequencing, more functional circRNAs have been discovered in animal follicle development (Shen et al, 2019). Previous studies have shown that the circRNAs of follicles and GCs in goats, chicken, and humans were detected (J. Cheng et al, 2017; Shen et al, 2019; Tao et al, 2017).…”

“…Recently, with the rapid development of bioinformatics techniques and deep sequencing, more functional circRNAs have been discovered in animal follicle development (Shen et al, 2019). Previous studies have shown that the circRNAs of follicles and GCs in goats, chicken, and humans were detected (J. Cheng et al, 2017; Shen et al, 2019; Tao et al, 2017). However, data associated with the function of circRNAs in ducks are still less reported, especially regarding follicle development.…”

Circular RNA profiling in the oocyte and cumulus cells reveals thatcircARMC4is essential for porcine oocyte maturation

“…CircRNA, formed by back-splicing of pre-mRNA transcripts, is a novel class of non-polyadenylated, single-stranded, covalently closed and long noncoding RNAs. Previous studies indicated that circRNA is mainly derived from exons, introns, intergenic regions (Lasda and Parker, 2014), and is widely distributed on the chromosomes in animal cells (Fan et al, 2015; Liang et al, 2017; Shen et al, 2019). CircRNA is discovered to frequently exert different molecular functions, such as transcriptional regulation, microRNA and RNA binding protein sponge, and mRNA trap (Bose and Ain, 2018).…”