Comprehensive Analysis of Differentially Expressed CircRNAs in the Ovaries of Low- and High-Fertility Sheep

Abstract

CircRNAs are essential in regulating follicle growth and development and the female reproductive system at multiple levels. However, the molecular mechanism by which circRNAs regulate reproduction in sheep is unclear and requires further exploration. In this study, RNA sequencing was performed to reveal the circRNA expression profiles in the ovaries of Cele black sheep and Hetian sheep during estrus. Analysis of the number of circRNAs in their host genes revealed that 5031 genes could produce 20,835 circRNAs. Among the differentially expressed circRNAs (DEcircRNA), 75 were upregulated, and 105 were downregulated. Functional enrichment analysis showed that the host genes of DEcircRNA were involved in several pathways, including the MAPK and Hippo signaling pathway. In addition, we constructed a subnetwork of competitive endogenous RNA (ceRNA) containing 4 mRNAs, 4 microRNAs (miRNAs), and 10 circRNAs, potentially related to follicle development. Functional circRNAs (e.g., novel_circ_0003851, novel_circ_0015526, novel_circ_0008117) were found to act as ceRNAs for follicle growth and development-related mRNAs (CUEDC1, KPNB1, ZFPM2) by sponging functional miRNAs (miR-29a, miR-29b, miR-17-5p). Finally, through an RNA pull-down assay, oar-miR-125b was selected and confirmed as the target miRNA of novel-circ-0041512. We analyzed the overall expression of circRNAs in sheep ovaries. Further, we explored the potential mechanisms underlying the circRNA functions, providing a theoretical basis for the genetic progress of reproductive traits in sheep.

Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development

“…We use the intersection of circRNA predicted by find_circ and CIRC software can improve the accuracy of circRNA. This method has been used in mice [52], cattle [53], sheep [54], chicken [55] and other species [56]. We identified a total of 16,990 expressed circRNAs, which is much higher than the number reported in one recent study.…”

Cellular mechanism of gain-of-function mutation I173M in sheep MC4R gene identified in year-round and seasonal estrus breeds through whole-genome resequencing

“…2E). Previous studies have demonstrated the crucial importance of the third and fourth transmembrane domains of MC4R for its binding 20 . Hence, it is inferred that this mutation may potentially impact the functionality of receptor.…”

RNA sequencing and gene co-expression network of in vitro matured oocytes and blastocysts of buffalo

“…RNA-seq estimates gene expression by quantifying the number of reads derived from each gene ( Mortazavi et al, 2008 )⁠⁠⁠. This method has been used to study oocyte competence ( Feuerstein et al, 2012 ; Bunel et al, 2015 ; Luo et al, 2016 ; Du et al, 2018 ; Wang et al, 2023b )⁠⁠⁠⁠⁠ and embryo competence ( Bauer et al, 2010 ; Redel et al, 2012 ; Cao et al, 2014 ; Kropp and Khatib, 2015a , 2015b ; Milazzotto et al, 2016 ; Boroviak et al, 2018 ; Sood et al; 2019 ; Li et al, 2020 ; Goel et al, 2022 )⁠⁠ across various species. Moreover, to investigate in vitro maturation ( Reyes et al, 2015 ; Gilchrist et al, 2016 ; Angel-Velez et al, 2023 )⁠⁠⁠ and in vitro embryo development⁠⁠ in mammalian ( Østrup et al, 2013 ; Xue et al, 2013 ; Graf et al, 2014 ; Jiang et al, 2015 ; Song et al, 2022 ; Rabaglino et al, 2023 )⁠.…”