Genome-wide profiling of Sus scrofa circular RNAs across nine organs and three developmental stages

Abstract

The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs. S. scrofa circRNAs show modest sequence conservation with human and mouse circRNAs, are flanked by long introns, exhibit low abundance, and are expressed dynamically in a spatio-temporally specific manner. S. scrofa circRNAs show the greatest abundance and complexity in the testis. Notably, 31% of circRNAs harbour well-conserved canonical miRNA seed matches, suggesting that some circRNAs act as miRNAs sponges. We identified 149 circRNAs potentially associated with muscle growth and found that their host genes were significantly involved in muscle development, contraction, chromatin modification, cation homeostasis, and ATP hydrolysis-coupled proton transport; moreover, this set of genes was markedly enriched in genes involved in tight junctions and the calcium signalling pathway. Finally, we constructed the first public S. scrofa circRNA database, allowing researchers to query comprehensive annotation, expression, and regulatory networks of circRNAs.

Circular RNAs in hepatocellular carcinoma: Functions and implications

“…CircRNAs harbor well‐conserved canonical miRNA response elements (MREs), suggesting that some circRNAs act as miRNA sequesters or sponges . A portion of circRNAs are thought to negatively regulate the levels of miRNAs and increase or decrease the expression levels of their corresponding targeted genes (Figure B).…”

“…Circular RNAs are generated from lariat-driven circulation or back-splicing events between the splice donor site of a downstream exon and the splice acceptor site of an upstream exon act as miRNA sequesters or sponges. [17][18][19][20] A portion of cir-cRNAs are thought to negatively regulate the levels of miR-NAs and increase or decrease the expression levels of their corresponding targeted genes ( Figure 2B). As a representative circRNA, cerebellar degeneration-related protein 1 antisense (CDR1as) is the sponge of miR-7 in the embryonic zebrafish and has been reported to be related to brain dysfunction and many cancers, such as HCC and gastric cancer.…”

Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages

“…, testes (Liang et al 2017b), peripheral whole blood 62 (Memczak et al 2015), peripheral blood mononucleotide cells (Qian et al 2018), platelets 63 (Alhasan et al 2016), and exosomes (Li et al 2015a). CircRNAs have also been related to the 64 development of the fetal human brain (Szabo et al 2015), mouse brain (You et al 2015), fetal 65 porcine brain (Veno et al 2015), and Drosophila neural systems (Westholm et al 2014).…”

BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages

“…CircRNAs are conservatively expressed from orthologous genomic regions between humans and mice (Guo et al, 2014;Jeck et al, 2013) and among Drosophila species (Westholm et al, 2014). Detailed analyses of circRNA expression in humans (Guo et al, 2014;Liu et al, 2016b;Xia et al, 2016), mice (Xia et al, 2016), pigs (Liang et al, 2017b), and flies (Westholm et al, 2014) have revealed substantial tissue-specific patterns of circRNA expression. Notably, circRNAs are enriched and abundantly expressed in some specific tissue types and blood components, such as the brain (Rybak-Wolf et al, 2015;Szabo et al, 2015;Veno et al, 2015;Westholm et al, 2014), testes (Liang et al, 2017b), peripheral whole blood (Memczak et al, 2015), peripheral blood mononucleotide cells (Qian et al, 2017), platelets (Alhasan et al, 2016), and exosomes (Li et al, 2015a).…”

“…Detailed analyses of circRNA expression in humans (Guo et al, 2014;Liu et al, 2016b;Xia et al, 2016), mice (Xia et al, 2016), pigs (Liang et al, 2017b), and flies (Westholm et al, 2014) have revealed substantial tissue-specific patterns of circRNA expression. Notably, circRNAs are enriched and abundantly expressed in some specific tissue types and blood components, such as the brain (Rybak-Wolf et al, 2015;Szabo et al, 2015;Veno et al, 2015;Westholm et al, 2014), testes (Liang et al, 2017b), peripheral whole blood (Memczak et al, 2015), peripheral blood mononucleotide cells (Qian et al, 2017), platelets (Alhasan et al, 2016), and exosomes (Li et al, 2015a). CircRNAs have also been related to the development of the fetal human brain (Szabo et al, 2015), mouse brain (You et al, 2015), fetal porcine brain (Veno et al, 2015), and Drosophila neural systems (Westholm et al, 2014).…”